No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.MBD4 encodes a DNA glycosylase that detects and repairs deaminated methyl-cytosines in DNA, using a methyl-CpG binding domain to anchor to methylated DNA and a glycosylase domain to carry out mismatch repair in CpG-rich regions. The protein also helps repress transcription from methylated gene promoters. MBD4 acts as a tumor suppressor, and its loss has been linked to colorectal cancer, acute myeloid leukemia, and uveal melanoma.
The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met (supporting): gnomAD allele frequency 0.00124-0.00159% is far below the 0.1% threshold, with zero homozygotes.
No benign criterion marked as applied in the recorded assessment.
No ClinGen or custom gene-specific framework exists for MBD4, so generic ACMG/AMP 2015 rules applied; with only PM2 (supporting) met, no combination threshold is reached and the variant is classified as VUS.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 20 / 1,613,874 alleles. Recorded AF 1.23925e-05. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 1.59093e-05; MAF= 0.00159%, 4/251426 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 4.62193e-05; MAF= 0.00462%, 1/21636 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
Absent from gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.060. Refer to the recorded PP3/BP4 rationale for interpretation.
3 Pathogenic. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
28 criteria with recorded statuses: 1 met · 12 not met · 7 not assessed · 8 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
No applicable VCEP/CSPEC exists for MBD4 (cspec.found=false; vcep_materials.json empty; final_classification_framework source=generic_acmg_fallback, precedence_rank=3), so generic ACMG/AMP 2015 (Richards et al. 2015, PMID:25741868) governs this group.
All four criteria in the segregation_de_novo group (PS2, PM6, PP1, BS4) are returned as not_assessed: the case bundle contains no proband record, no parental/trio testing, no family pedigree, and no segregation or non-segregation data.
Both germline MBD4 publications retrieved (PMID:35460607, PMID:30049810) were reviewed in full text; neither mentions the exact variant NM_003925.3:c.1231_1234del (p.Arg411GlyfsTer79), so under strict citation-grounding rules neither can provide variant-specific de novo or segregation evidence.
PMID:35460607 documents autosomal-recessive-compatible segregation for other MBD4 LoF alleles (c.612_615del, c.939dup, c.1688T>A) in four families; this is gene-level evidence for the AR mode of inheritance of MBD4-associated neoplasia syndrome (MANS) but is not variant-specific and does not support PP1 for this variant.
Zygosity of the proband for c.1231_1234del is unknown; MANS is autosomal recessive (biallelic LoF) with additional risk phenotypes reported in heterozygous carriers, so PS2/PM6 applicability cannot be evaluated without proband and parental data.
The gap for this group is data, not adjudication: obtaining proband phenotype/zygosity, parental testing (for PS2/PM6), and affected-family-member genotyping (for PP1/BS4) would be required before any of these criteria can be scored.
No ClinGen CSPEC/VCEP specification exists for MBD4 (vcep_materials.json: no cspec; final_classification_framework.json: generic_acmg_fallback), so generic ACMG/AMP 2015 (Richards et al., PMID:25741868) governs PS3/BS3 calibration.
PS3 not assessed: the exact variant c.1231_1234del / p.Arg411GlyfsTer79 is absent from every available functional full text; no validated assay has tested this variant. Gene-level and variant-class functional data (PMID:17285135, PMID:30049810, PMID:10545939, PMID:35460607) establish MBD4 truncation as a LoF mechanism but do not constitute variant-specific PS3 evidence; flagged for human review for the optional PS3_supporting class-level argument.
BS3 not met: no functional evidence of a benign/no-damaging effect exists for this variant; all available data (frameshift removing the catalytic domain, OncoKB Likely LoF, extreme population rarity with zero homozygotes, LoF assay data on related truncations) contradict BS3.
PS3 is intentionally not credited so that the LoF prediction (PVS1, consequence_lof group) is not double-counted with functional evidence; if class-level functional data are later credited at supporting strength, the combined PVS1+PS3 weighting should be reviewed for consistency.
SpliceAI (max delta 0.06) shows no splice impact; the variant's effect is at the protein level (frameshift), so no BS3 splice-function consideration applies beyond the protein-level analysis above.
No ClinGen CSPEC/VCEP or gene-specific framework exists for MBD4 (cspec.found=false; vcep_materials.json final_classification_framework found=false, source=generic_acmg_fallback, precedence_rank=3); generic ACMG/AMP 2015 rules (PMID:25741868) govern this group.
PS4 not met: no case-control or variant-level prevalence enrichment exists for c.1231_1234del, and the exact variant is absent from the published germline MBD4-deficiency cohorts (PMID:30049810, PMID:35460607), which report other MBD4 LOF variants (H567del; exon 3 fs + exon 7 splice acceptor; c.939dup p.Glu314Argfs*13; c.612_615del; c.1688T>A p.Leu563*; c.1562-1G>T; c.1699_1701del). Gene-level disease association must not be converted into variant-level PS4 enrichment evidence.
PP4 not assessed: the case bundle contains no proband phenotype or family-history data; PP4 phenotype-specificity cannot be judged from ClinVar condition labels alone ('Inborn genetic diseases', 'Tumor predisposition syndrome 2', 'not provided').
PP5 not met: the rule restricts PP5 to an exact-variant ClinVar EXPERT-PANEL Pathogenic/LP classification. ClinVar 1976297 has 0 expert-panel submissions; the aggregate Pathogenic from 3 ordinary clinical laboratories (Labcorp/Invitae, Ambry, Myriad; 2-star 'criteria provided, multiple submitters, no conflicts') is ordinary-laboratory/aggregate evidence, which must never trigger PP5.
BP5 not met: no alternative molecular basis of disease is documented for the proband in the case bundle; nothing supports applying the alternative-cause benign-supporting criterion.
BP6 not met: the rule restricts BP6 to an exact-variant ClinVar EXPERT-PANEL Benign/LB classification; no such classification exists (the variant is Pathogenic in 3 clinical labs), so BP6 cannot be applied.
This group yields no pathogenic or benign supporting criteria; the phenotype/prevalence evidence does not contribute to the variant's classification beyond the gene-disease context used elsewhere.
PM3 (moderate, ACMG/AMP 2015): MBD4 deficiency is autosomal recessive (bi-allelic LOF germline MBD4 variants cause MANS, PMID:35460607), making PM3 applicable in principle; however, NM_003925.3:c.1231_1234del has no documented trans observation - no homozygous or compound-heterozygous proband carrying this variant is reported in ClinVar (no zygosity/phase data in any of the 3 submissions), gnomAD v2.1/v4.1 report 0 homozygotes, and neither PMID:35460607 nor PMID:30049810 (the papers cited for this variant by the Labcorp submission) mentions c.1231_1234del. PM3: not met.
BP2 (supporting benign, ACMG/AMP 2015): the fully-dominant in-trans arm does not apply because MBD4 deficiency is recessive, and no cis observation of this variant with a pathogenic variant exists in any source. BP2: not met.
No ClinGen CSPEC/VCEP or gene-specific framework exists for MBD4 (cspec.found=false; vcep_materials.json: files_found=[], gene_vcep_dir=null, final_classification_framework found=false, source=generic_acmg_fallback, precedence_rank=3); generic ACMG/AMP 2015 rules (PMID:25741868) govern. No VCEP PP3/BP4 lookup spreadsheet pre-assigned codes.
PP3 not met: SpliceAI max delta 0.06 (<0.2 threshold) predicts no splice impact; REVEL/BayesDel/aGVGD are not applicable to this non-SNV frameshift (pipeline skipped: 'not snv or no coords'); the frameshift loss-of-function effect is already captured by PVS1, and stacking PP3 would double-count the same prediction (pvs1_variant_assessment downgrade consideration).
BP4 not met: the low SpliceAI score reflects only the absence of additional splice disruption and is a single computational line; it cannot establish a no-impact prediction because the variant is a coding frameshift (p.(Arg411GlyfsTer79)) with a definite protein consequence.
No double-counting: the SpliceAI low-delta result was evaluated only within the splice-impact path and was not credited to both PP3 and BP4 (or BP7, which is inapplicable to this non-synonymous variant).
In-silico computational evidence makes no net contribution to the pathogenic or benign side for this variant; the computational group yields no criteria (PP3 not_met, BP4 not_met).
Framework: no MBD4 VCEP/CSPEC exists (cspec found=false; final_classification_framework.json: generic_acmg_fallback, scoring_model 'ACMG/AMP 2015'); generic ACMG/AMP 2015 population criteria applied with user-specified non-VCEP gnomAD thresholds (BA1 > 1%, BS1 > 0.3%, PM2 < 0.1%).
BA1 not met: maximum AF across all datasets/subpopulations is 0.0174% (gnomAD v2.1 NFE_SEU 2/11502), vs 1% threshold; total AFs 0.00159% (v2.1) and 0.00124% (v4.1); grpmax FAF 7.01e-06 / 9.53e-06 confirm no inflation artifact.
BS1 not met: maximum AF 0.0174% is 17-fold below the 0.3% threshold and far below AF expected for a benign allele given the ultra-rare prevalence of MANS (PMID:35460607).
BS2 not met: zero homozygotes in gnomAD v2.1 (125,713 individuals) and v4.1 (806,937 individuals); PMID:35460607 confirms no homozygous germline LoF MBD4 carriers in gnomAD, 100KGP, or UK Biobank; biallelic disease appears fully penetrant.
PM2 met (supporting): AF 0.00124-0.00159% (highest subpopulation 0.0174%) is well below the 0.1% threshold; FAF values far below threshold; absent from gnomAD-Canada; 0 homozygotes; consistent with ultra-rare autosomal recessive disorder.
Population evidence as a whole supports pathogenicity direction: the variant is very rare, never homozygous in large control datasets, and present only as a rare heterozygous allele, consistent with a recessive disease-causing allele.
No criteria match.
PM2 (extremely low/absent population frequency) is met at supporting strength (ClinGen SVI PM2_Supporting convention, consistent with the generic ACMG/AMP 2015 fallback and user-specified non-VCEP threshold PM2 < 0.1%). gnomAD v2.1 AF is 0.00159% (4/251426, 0 homozygotes) and gnomAD v4.1 AF is 0.00124% (20/1613874, 0 homozygotes); the highest subpopulation AF anywhere is 0.0174% (NFE_SEU v2.1) — all well below 0.1%. Filtering allele frequencies (grpmax FAF 7.01e-06 v2.1; 9.53e-06 v4.1) are likewise far below threshold, and the variant is absent from gnomAD-Canada v1.0. The ultra-rare disorder context supports this: MANS is an autosomal recessive condition with only ~8 biallelic individuals reported worldwide (PMID:35460607), and no homozygous germline LoF MBD4 carriers exist in gnomAD, 100KGP, or UK Biobank. The observed allele count is consistent with a very rare disease allele, not a common polymorphism. PM2_Supporting is met.
PM2_Supporting (ClinGen SVI; Richards 2015 PM2): allele frequency < 0.1% in gnomAD / absent from control cohorts
PS4 (Richards et al. 2015, PMID:25741868) requires the prevalence of the variant in affected individuals to be significantly increased relative to controls (case-control or equivalent enrichment), or a very strong variant-level case series. For NM_003925.3:c.1231_1234del (MBD4, p.(Arg411GlyfsTer79)): (1) no case-control or variant-level prevalence/enrichment study exists for this exact variant in any reviewed source; (2) the exact variant is not reported in the two key germline MBD4-deficiency publications - PMID:30049810 (Sanders 2018, 3 early-onset AML cases with germline MBD4 LOF; reported variants were H567del homozygous and an exon 3 frameshift + exon 7 splice-acceptor compound heterozygote) and PMID:35460607 (Palles 2022, 5 individuals from 4 families plus a 309-individual polyposis/CRC cohort; reported variants c.939dup p.Glu314Argfs*13, c.612_615del, c.1688T>A p.Leu563*, c.1562-1G>T, c.1699_1701del - none is c.1231_1234del); (3) the gene-level observation that germline MBD4 loss-of-function causes a tumor predisposition syndrome establishes the gene-disease association but cannot be credited to PS4 for this specific variant, since PS4 is variant-level enrichment evidence and must not be inferred from gene-level disease association or from other variants in the same gene; (4) the variant is extremely rare in population databases (gnomAD v4.1 AF 1.24e-05, 20/1,613,874 alleles, 0 homozygotes), providing no population prevalence signal either way. PS4 therefore not met with the available evidence.
generic_acmg_2015:PS4 - prevalence of variant in affected individuals significantly increased vs controls (case-control/prevalence enrichment); not met - no variant-level enrichment data exists and the exact variant is absent from the published germline MBD4-deficiency cohorts
Under generic ACMG/AMP 2015 (Richards et al., PMID:25741868; no MBD4 VCEP/CSPEC exists, framework_mode=generic_acmg), PM3 applies to recessive disorders when the variant is detected in trans with a pathogenic variant. MBD4 deficiency (MBD4-associated neoplasia syndrome, MANS) is an autosomal recessive disorder caused by bi-allelic loss-of-function germline MBD4 variants (PMID:35460607), so PM3 is applicable in principle to this frameshift LOF variant (NP_003916.1:p.(Arg411GlyfsTer79)). However, no available source documents NM_003925.3:c.1231_1234del in trans with a pathogenic variant: (1) all three ClinVar submissions (SCV003013098 Labcorp, SCV006273336 Ambry, SCV007517521 Myriad) classify the variant Pathogenic but report no zygosity or phase information; (2) the two papers cited by the Labcorp submission, PMID:35460607 and PMID:30049810, describe homozygous and compound-heterozygous MBD4 LOF cases carrying other variants (c.612_615del p.Ser205Thrfs*9, c.939dup p.Glu314Argfs*13, c.1688T>A p.Leu563*, homozygous H567del, exon 3 frameshift + exon 7 splice acceptor disruption) and do not mention c.1231_1234del at all; (3) gnomAD v2.1 and v4.1 report zero homozygotes for this variant. Without any documented trans (or homozygous) observation, the criterion is not met on current evidence.
acmg2015_pm3_requires_documented_trans_observation
PP3 (Richards et al. 2015, PMID:25741868) requires multiple lines of computational evidence supporting a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). For NM_003925.3:c.1231_1234del in MBD4 (frameshift, NP_003916.1:p.(Arg411GlyfsTer79), exon 4 of 8): (1) splice-impact path - SpliceAI reports max delta score 0.06 (DS_AG 0.06, DS_AL 0.04, DS_DG 0.02, DS_DL 0.01), well below the 0.2 threshold used to call predicted splice disruption, so no splice-impact evidence supports PP3; (2) missense path - REVEL and BayesDel were skipped by the pipeline ('not snv or no coords') and aGVGD/HCI-prior are unavailable (hci_prior gene_not_supported), so no missense computational scores exist for this non-SNV variant; (3) the variant's frameshift consequence is itself the loss-of-function mechanism and is captured by PVS1; applying PP3 here would double-count the same variant-class prediction (consistent with the pvs1_variant_assessment caution against stacking PP3 on the same effect prediction). No computational line meeting threshold therefore supports a deleterious effect attributable to PP3. Framework: generic ACMG/AMP 2015 fallback (no MBD4 CSPEC/VCEP; vcep_materials final_classification_framework found=false).
generic_acmg_2015:PP3 - multiple lines of computational evidence support deleterious effect; not met (no qualifying computational line; no stacking on variant-class LOF)
PP5 (reputable source recently reports variant as pathogenic without accessible evidence) is applied ONLY for an exact-variant ClinVar expert-panel classification of Pathogenic/Likely pathogenic. ClinVar variation 1976297 (exact variant match for NM_003925.3:c.1231_1234del, also listed as NM_001276270.2:c.1213_1216del p.Arg405fs; audit matched_by=transcript_hgvs, exact_match=true) has 3 submissions - Labcorp Genetics (SCV003013098), Ambry Genetics (SCV006273336), Myriad Genetics (SCV007517521) - all clinical-testing single-submitter 'Pathogenic' with review status 'criteria provided, single submitter' (2 stars, 'criteria provided, multiple submitters, no conflicts' per API). expert_panel_submissions = 0; no ClinGen/VCEP expert-panel classification exists for this variant. Per the governing rule, ordinary laboratory submissions and aggregate ClinVar labels must NEVER trigger PP5. PP5 not met.
PP5 - reputable source reports variant pathogenic without accessible evidence; restricted to exact-variant ClinVar expert-panel classification (Pathogenic/LP); not met - no expert-panel submission exists (3 ordinary clinical-lab submissions only)
No governing VCEP/CSPEC exists for MBD4 (cspec found=false; vcep_materials: 'no cspec url available'), so generic ACMG/AMP 2015 (Richards et al., PMID:25741868) applies with user-specified non-VCEP gnomAD thresholds (BA1 > 1%). The highest allele frequency observed for NM_003925.3:c.1231_1234del anywhere is 0.0174% (gnomAD v2.1 NFE_SEU, 2/11502 alleles), with gnomAD v2.1 total AF 0.00159% (4/251426) and gnomAD v4.1 total AF 0.00124% (20/1613874). All frequencies are more than two orders of magnitude below the 1% BA1 threshold (and far below the alternative 5% threshold). Filtering allele frequencies are even lower (grpmax FAF 7.01e-06 v2.1; 9.53e-06 v4.1), confirming the raw AFs are not inflated by sequencing artifacts. BA1 is not met.
BA1 (Richards 2015): population allele frequency > 1% in gnomAD (non-VCEP threshold; 5% alternative also evaluated)
BS1 (AF greater than expected for the disorder) is not met. Applying the user-specified non-VCEP BS1 threshold of > 0.3%, the maximum observed AF is 0.0174% (gnomAD v2.1 NFE_SEU, 2/11502) — 17-fold below the threshold; gnomAD v2.1 total AF is 0.00159% and gnomAD v4.1 total AF 0.00124%. This is also consistent with disease prevalence: MBD4-associated neoplasia syndrome (MANS) is an ultra-rare autosomal recessive condition with only ~8 biallelic individuals reported worldwide (PMID:35460607), and heterozygous MBD4 LoF carrier frequency is low (48/64,600 in gnomAD per PMID:35460607); the observed AF of this specific variant is far below what would be expected for a benign polymorphism. BS1 is not met.
BS1 (Richards 2015): allele frequency greater than expected for the disorder (non-VCEP threshold > 0.3% in gnomAD)
BS2 requires observation of the variant in a healthy adult — for a recessive disorder such as MANS, in the homozygous state at full penetrance. Zero homozygotes are observed for c.1231_1234del in gnomAD v2.1 (0/251426 alleles; 125,713 individuals) and gnomAD v4.1 (0/1613874 alleles; 806,937 individuals), and no population subpopulation has any homozygote. Corroborating cohort-level evidence: PMID:35460607 reports no individuals with homozygous germline LoF MBD4 variants in gnomAD, the UK 100,000 Genomes Project, or UK Biobank WGS, and biallelic MBD4 LoF appears highly penetrant (all biallelic individuals with colonoscopy had multiple colorectal polyps), which is consistent with the absence of healthy homozygotes. BS2 is not met.
BS2 (Richards 2015): observed in a healthy adult individual for a recessive (homozygous) disorder at full penetrance
BS3 (Richards et al. 2015, PMID:25741868) requires well-established functional studies showing NO damaging effect on protein function or splicing. No source in the case bundle provides any functional evidence of preserved MBD4 function for c.1231_1234del. To the contrary, all available data point to loss of function: (1) the variant is a frameshift whose product p.Arg411GlyfsTer79 loses the entire C-terminal DNA-glycosylase catalytic domain (codons 455-580 per PMID:10545939) and acquires 79 novel residues before the premature stop; (2) OncoKB curated this exact variant as biological-effect 'Likely Loss-of-function' / 'Likely Oncogenic' (variant-specific, not_reviewed=false); (3) the variant is extremely rare (gnomAD v2.1 total AF 0.00159%, 0 homozygotes; gnomAD v4.1 total AF 0.00124%, 0 homozygotes; absent from gnomAD-Canada), with no benign functional or population evidence; (4) well-established functional assays on other MBD4 truncations/catalytic mutants show loss of glycosylase activity (PMID:17285135, PMID:30049810). No functional study shows a benign effect, and no evidence suggests BS3 applicability; the criterion is not met.
BS3 - Well-established functional studies show no damaging effect on protein function or splicing (Richards et al. 2015, PMID:25741868; generic ACMG/AMP fallback, no MBD4 CSPEC)
Under generic ACMG/AMP 2015 (PMID:25741868), BP2 requires either (a) observation in trans with a pathogenic variant for a fully dominant disease/disorder, or (b) observation in cis with a pathogenic variant in any inheritance pattern. Arm (a) does not apply: MBD4 deficiency (MANS) is an autosomal recessive disorder (PMID:35460607; bi-allelic LOF germline variants cause disease), not a fully dominant disorder, so an in-trans observation would constitute pathogenic (PM3-type) rather than benign evidence and BP2's dominant arm is inapplicable. Arm (b) is unsupported: no source reports this variant in cis with a pathogenic variant - ClinVar submissions contain no phase/zygosity information and the cited literature (PMID:30049810, PMID:35460607) does not contain this variant. BP2 is therefore not met.
acmg2015_bp2_trans_dominant_or_cis_observation
BP4 (Richards et al. 2015, PMID:25741868) requires multiple lines of computational evidence suggesting no impact on the gene or gene product. The only computational line available for this variant is the splice path: SpliceAI max delta score 0.06 indicates no predicted splice disruption. That result is not BP4 evidence here because (1) it is a single tool, not multiple lines, and (2) absence of additional splice disruption does not imply a benign/no-impact effect for a coding frameshift: NM_003925.3:c.1231_1234del unambiguously alters the reading frame and protein product (NP_003916.1:p.(Arg411GlyfsTer79), NMD-eligible truncation), so the variant has a definite impact on the gene product by variant class regardless of splice prediction. Missense in-silico tools (REVEL/BayesDel/aGVGD) do not apply to this non-SNV. BP4 therefore not met; the low SpliceAI score was considered only in the splice path and was not double-counted as benign evidence.
generic_acmg_2015:BP4 - multiple lines of computational evidence suggest no impact; not met (single low-splice line cannot outweigh definite frameshift protein consequence)
BP5 (Richards et al. 2015, PMID:25741868) applies when the variant is found in a case with an alternative molecular basis for disease (e.g., a different pathogenic variant in another gene fully explaining the phenotype). The case evidence bundle contains no information indicating an alternative molecular diagnosis in the proband: no second pathogenic variant, no alternate-gene finding, and no competing molecular explanation is documented in case_summary.json, prefetch.json, or evidence.json. The variant's own profile (frameshift p.(Arg411GlyfsTer79), extremely rare in gnomAD, consistent ClinVar Pathogenic across 3 labs) provides no suggestion of an alternate cause. BP5 therefore not met; nothing in the available evidence supports an alternative molecular basis.
generic_acmg_2015:BP5 - variant found in a case with an alternative molecular basis of disease; not met - no evidence of an alternative molecular diagnosis in the bundle
BP6 (reputable source recently reports variant as benign without accessible evidence) is applied ONLY for an exact-variant ClinVar expert-panel classification of Benign/Likely benign. ClinVar variation 1976297 carries no expert-panel submissions (expert_panel_submissions=0) and no benign or likely-benign classification at all - the aggregate classification is Pathogenic from 3 ordinary clinical laboratories with 2-star review status. Per the governing rule, ordinary laboratory submissions and aggregate ClinVar labels must NEVER trigger BP6, and there is no expert-panel benign assertion to consider. BP6 not met.
BP6 - reputable source reports variant benign without accessible evidence; restricted to exact-variant ClinVar expert-panel classification (Benign/LB); not met - no expert-panel benign classification exists (variant is Pathogenic in 3 clinical labs)
PVS1 could not be assessed because its agent did not produce valid output.
PS2 (Richards et al. 2015, PMID:25741868) requires a documented de novo occurrence in a proband with the disease and no family history, with paternity and maternity confirmed. The case bundle contains no proband phenotype, no family-history data, no parental testing, and no trio/genotype data of any kind (case_summary.json, evidence.json, prefetch.json, literature_pass.json all lack proband/pedigree sections). No retrieved publication mentions the exact variant NM_003925.3:c.1231_1234del (p.Arg411GlyfsTer79); PMID:35460607 and PMID:30049810 report other MBD4 loss-of-function alleles only (c.612_615del, c.939dup, c.1688T>A, c.1562-1G>T, c.1699_1701del, exon-3 frameshift) and contain no de novo observation relevant to this variant. Evidence is insufficient; the criterion cannot be applied.
De novo (paternity and maternity confirmed) in a patient with the disease and no family history (Richards et al. 2015, PMID:25741868)
PS3 (Richards et al. 2015, PMID:25741868) requires well-established functional studies showing a deleterious effect of the variant. No ClinGen CSPEC/VCEP exists for MBD4 (vcep_materials.json: 'no cspec url available'; final_classification_framework: generic_acmg_fallback), so generic ACMG/AMP 2015 applies. The exact variant NM_003925.3:c.1231_1234del (p.Arg411GlyfsTer79; alternative-transcript notation c.1213_1216del/p.Arg405fs) is NOT mentioned in any of the five functional-relevant full texts reviewed (PMID:10545939, PMID:10637515, PMID:17285135, PMID:35460607, PMID:30049810) - full-text searches for 'c.1231_1234del', 'p.Arg411GlyfsTer79', 'p.R411Gfs*79', 'c.1213_1216del', 'Arg405' returned zero hits. The available functional evidence concerns other MBD4 alterations: (1) PMID:17285135 (Millar 2007) - well-established cell-free T.G glycosylase inhibition assays, UDG competitive-inhibition assays, and Big Blue cell-based mutation-frequency assays on the MSI A10-tract truncation (MBD4tru, a more N-terminal truncation), showing the truncated protein is glycosylase-defective and dominant-negative; (2) PMID:30049810 (Sanders 2018) - in vitro glycosylase assay with catalytic controls (H567del, D560A) showing loss of activity; (3) PMID:10545939 (Riccio 1999) - structural prediction that truncations lacking the C-terminal catalytic domain (codons 455-580) are non-functional; (4) PMID:35460607 (Palles 2022) - germline biallelic LoF frameshift variants (c.612_615del, c.939dup) cause an autosomal recessive MBD4-deficiency syndrome, establishing LoF as the disease mechanism. These data establish the gene-level LoF mechanism and are biologically relevant (p.R411Gfs*79 removes the entire C-terminal glycosylase catalytic domain), but no validated assay was performed on this exact variant, so variant-specific PS3 evidence is insufficient. Per adjudication rules, insufficient evidence returns not_assessed with the gap identified. NOTE FOR HUMAN REVIEW: a defensible PS3_supporting argument exists via the variant-class/truncation extrapolation (PMID:17285135 assays + catalytic-domain deletion), but applying it risks double-counting the LoF prediction already captured by PVS1 (consequence_lof group); the pipeline should decide explicitly whether to credit class-level functional data at supporting strength or rely on PVS1 alone.
PS3 - Well-established functional studies show a deleterious effect (Richards et al. 2015, PMID:25741868; generic ACMG/AMP fallback, no MBD4 CSPEC)
PM6 (Richards et al. 2015, PMID:25741868) requires an assumed de novo occurrence without confirmation of paternity and maternity. No de novo observation of c.1231_1234del exists in any case artifact or retrieved publication; there is no proband record at all against which an assumed-de novo event could be assessed. The two germline MBD4 publications retrieved (PMID:35460607, PMID:30049810) do not mention the exact variant and report no de novo determinations. Evidence is insufficient; the criterion cannot be applied.
Assumed de novo, but without confirmation of paternity and maternity (Richards et al. 2015, PMID:25741868)
PP1 (Richards et al. 2015, PMID:25741868) requires co-segregation of the variant with disease in multiple affected family members in a gene definitively known to cause the disease. The case bundle contains no family pedigree, no genotyping of affected relatives, and no segregation analysis for c.1231_1234del. PMID:35460607 demonstrates autosomal-recessive-compatible segregation for OTHER MBD4 loss-of-function alleles (c.612_615del homozygous in family D; c.939dup in families CRDFF-292 and CRDFF-336; compound-heterozygous c.939dup/c.1688T>A in DB1) but does not mention c.1231_1234del; per strict citation-grounding rules, gene-level segregation of different alleles cannot be used as variant-specific segregation evidence. Evidence is insufficient; the criterion cannot be applied.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease (Richards et al. 2015, PMID:25741868)
PP4 (Richards et al. 2015, PMID:25741868) requires the proband's phenotype or family history to be highly specific for a genetic disease with a single genetic etiology. The case evidence bundle contains no proband clinical phenotype data (no phenotype, indication, or family-history section in case_summary.json; condition labels in ClinVar submissions are empty or generic - 'Inborn genetic diseases', 'Tumor predisposition syndrome 2', 'not provided'). MBD4 bi-allelic loss-of-function is associated with a multi-tumor predisposition phenotype (adenomatous polyposis, AML, uveal melanoma; PMID:35460607), but PP4 requires phenotype specificity at the level of the individual being assessed, and that information is absent. PP4 cannot be evaluated from the available bundle.
generic_acmg_2015:PP4 - phenotype or family history highly specific for a genetic disease with single genetic etiology; not assessable - no proband phenotype data in the case bundle
BS4 (Richards et al. 2015, PMID:25741868) requires demonstrated non-segregation of the variant with disease in affected family members. There is no family testing data whatsoever in the case bundle, and no publication reporting c.1231_1234del in any affected or unaffected relative. Non-segregation evidence is therefore entirely absent; the criterion cannot be applied (nor can it be refuted).
Non-segregation with disease in affected family members (Richards et al. 2015, PMID:25741868)
PS1 (Richards et al. 2015, PMID:25741868) requires the same amino acid change as a previously established pathogenic variant, evaluated regardless of the underlying nucleotide change. NM_003925.3:c.1231_1234del in MBD4 is a frameshift variant predicted to produce NP_003916.1:p.(Arg411GlyfsTer79). As a result, no altered amino acid exists at this position to compare against any previously established pathogenic missense variant, so PS1's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false); the generic ACMG/AMP 2015 fallback applies.
deterministic_prefilter: requires_missense
PM1 (Richards et al. 2015, PMID:25741868) applies to a missense variant located in a mutational hot spot and/or a critical, well-established functional domain without benign variation. NM_003925.3:c.1231_1234del in MBD4 is a frameshift variant predicted to produce NP_003916.1:p.(Arg411GlyfsTer79). As a result, no altered residue exists to evaluate for mutational hot-spot or critical-domain membership, so PM1's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false); the generic ACMG/AMP 2015 fallback applies.
deterministic_prefilter: requires_missense
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_003925.3:c.1231_1234del in MBD4 is a frameshift variant predicted to produce NP_003916.1:p.(Arg411GlyfsTer79). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false); the generic ACMG/AMP 2015 fallback applies.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
PM5 (Richards et al. 2015, PMID:25741868) requires a novel missense change at an amino acid residue where a different missense change has previously been determined to be pathogenic. NM_003925.3:c.1231_1234del in MBD4 is a frameshift variant predicted to produce NP_003916.1:p.(Arg411GlyfsTer79). As a result, no missense change exists at this residue to compare against a different pathogenic missense change at the same position, so PM5's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false); the generic ACMG/AMP 2015 fallback applies.
deterministic_prefilter: requires_missense
PP2 (Richards et al. 2015, PMID:25741868) applies to a missense variant in a gene with a low rate of benign missense variation, where missense variants are a common mechanism of disease. NM_003925.3:c.1231_1234del in MBD4 is a frameshift variant predicted to produce NP_003916.1:p.(Arg411GlyfsTer79). As a result, the gene's missense-constraint properties are irrelevant because no missense change is present to evaluate, so PP2's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false); the generic ACMG/AMP 2015 fallback applies.
deterministic_prefilter: requires_missense
BP1 (Richards et al. 2015, PMID:25741868) applies to a missense variant in a gene for which primarily truncating variants are known to cause disease. NM_003925.3:c.1231_1234del in MBD4 is a frameshift variant predicted to produce NP_003916.1:p.(Arg411GlyfsTer79). As a result, the gene's truncating-variant mechanism is irrelevant because no missense change is present to evaluate, so BP1's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false); the generic ACMG/AMP 2015 fallback applies.
deterministic_prefilter: requires_missense
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_003925.3:c.1231_1234del in MBD4 is a frameshift variant predicted to produce NP_003916.1:p.(Arg411GlyfsTer79). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false); the generic ACMG/AMP 2015 fallback applies.
deterministic_prefilter: requires_repeat_region_indel
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_003925.3:c.1231_1234del in MBD4 is a frameshift variant predicted to produce NP_003916.1:p.(Arg411GlyfsTer79). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false); the generic ACMG/AMP 2015 fallback applies.
deterministic_prefilter: requires_synonymous
Every interpreted variant in MBD4, mapped onto the exon structure of NM_003925.3. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| European (Finnish)1 / 64,006 | 1.6e-05 |
| European (non-Finnish)18 / 1,179,940 | 1.5e-05 |
| South Asian1 / 91,086 | 1.1e-05 |
| European (Finnish)1 / 21,636 | 4.6e-05 |
| European (non-Finnish)3 / 113,730 | 2.6e-05 |
This variant is present in gnomAD v4.1 (AF= 1.23925e-05; MAF= 0.00124%, 20/1613874 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 1.56235e-05; MAF= 0.00156%, 1/64006 alleles, homozygotes = 0); grpmax FAF= 9.53e-06.
This variant is present in gnomAD v2.1 (AF= 1.59093e-05; MAF= 0.00159%, 4/251426 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 4.62193e-05; MAF= 0.00462%, 1/21636 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
Absent from gnomAD-Canada v1.0.
PP3 (Richards et al. 2015, PMID:25741868) requires multiple lines of computational evidence supporting a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). For NM_003925.3:c.1231_1234del in MBD4 (frameshift, NP_003916.1:p.(Arg411GlyfsTer79), exon 4 of 8): (1) splice-impact path - SpliceAI reports max delta score 0.06 (DS_AG 0.06, DS_AL 0.04, DS_DG 0.02, DS_DL 0.01), well below the 0.2 threshold used to call predicted splice disruption, so no splice-impact evidence supports PP3; (2) missense path - REVEL and BayesDel were skipped by the pipeline ('not snv or no coords') and aGVGD/HCI-prior are unavailable (hci_prior gene_not_supported), so no missense computational scores exist for this non-SNV variant; (3) the variant's frameshift consequence is itself the loss-of-function mechanism and is captured by PVS1; applying PP3 here would double-count the same variant-class prediction (consistent with the pvs1_variant_assessment caution against stacking PP3 on the same effect prediction). No computational line meeting threshold therefore supports a deleterious effect attributable to PP3. Framework: generic ACMG/AMP 2015 fallback (no MBD4 CSPEC/VCEP; vcep_materials final_classification_framework found=false).
generic_acmg_2015:PP3 - multiple lines of computational evidence support deleterious effect; not met (no qualifying computational line; no stacking on variant-class LOF)
BP4 (Richards et al. 2015, PMID:25741868) requires multiple lines of computational evidence suggesting no impact on the gene or gene product. The only computational line available for this variant is the splice path: SpliceAI max delta score 0.06 indicates no predicted splice disruption. That result is not BP4 evidence here because (1) it is a single tool, not multiple lines, and (2) absence of additional splice disruption does not imply a benign/no-impact effect for a coding frameshift: NM_003925.3:c.1231_1234del unambiguously alters the reading frame and protein product (NP_003916.1:p.(Arg411GlyfsTer79), NMD-eligible truncation), so the variant has a definite impact on the gene product by variant class regardless of splice prediction. Missense in-silico tools (REVEL/BayesDel/aGVGD) do not apply to this non-SNV. BP4 therefore not met; the low SpliceAI score was considered only in the splice path and was not double-counted as benign evidence.
generic_acmg_2015:BP4 - multiple lines of computational evidence suggest no impact; not met (single low-splice line cannot outweigh definite frameshift protein consequence)
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_003925.3:c.1231_1234del in MBD4 is a frameshift variant predicted to produce NP_003916.1:p.(Arg411GlyfsTer79). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication, because no structured VCEP criteria-combination framework governs this case (framework_complete=false); the generic ACMG/AMP 2015 fallback applies.
deterministic_prefilter: requires_synonymous
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06).
10 paper records listed. 1 cited in the classification. None of the listed paper records explicitly indicates that the variant is named.
After genotyping of available additional family members, all were compatible with an autosomal recessive trait. ... Simplex individual D:II-1 was homozygous for a 4-bp MBD4 deletion (GenBank: NM_003925.2 : c.612_615del [p.Ser205Thrfs ∗ 9]) and the other (CRDFF-292:II-3) was homozygous for an adenine duplication (GenBank: NM_003925.2 : c.939dup [p.Glu314Argfs ∗ 13]).
Location Main text, Results section (paragraphs describing WGS/WES discovery of bi-allelic MBD4 variants and family genotyping); Figure 1 pedigrees; Table 1 'Clinical phenotype of individuals with bi-allelic germline MBD4 loss-of-protein-function variants'
Context WGS/WES of constitutional DNA in 309 individuals from 198 families with multiple colorectal adenomas or familial CRC, plus targeted MBD4 sequencing in replication cohorts (1,611 individuals); family genotyping and pedigrees; NM_003925.2 transcript nomenclature
The resulting truncated proteins are predicted to be non-functional, as they lack the carboxy-terminal catalytic domain located at codons 455–580 (ref. 6).
Full text, passage describing MBD4 frameshift mutations in MSI carcinomas (truncated-protein prediction); also the dominant-negative deletion-construct transfection sentence (ref 6) nearby
This mutation would ensure truncation of the protein between the methyl-CpG binding and glycosylase domains, thus potentially generating a dominant negative eect.
Discussion, section on A10-tract frameshift mutations in RER+ colon cancers
Cell-free assays with the purified recombinant proteins showed that MBD4 tru could inhibit T·G glycosylase activity of full-length MBD4 (Figure 2A).
Results, 'Dominant negative inhibition in glycosylase assays' (Figures 2A-2C) and Big Blue cell mutation-frequency assays; also 'expression of MBD4 tru roughly doubles mutation frequency in cells even on the background of MMR defect'
Sequencing germline DNA from the three cases identified loss-of-function variants in the gene encoding the DNA glycosylase MBD4 ... Case EMC-AML-1 carried a homozygous deletion of Histidine 567 (H567) in the glycosylase domain of MBD4. ... The siblings (WEHI-AML-1, WEHI-AML-2) were compound heterozygotes with a frameshift in exon 3 and a variant that disrupts the splice acceptor of exon 7 of MBD4.
Main text, section 'Germline Loss of MBD4 Predisposes to AML with a Novel Mutational Signature' (Figure 1C; Supplemental Table 2)
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 1.23925e-05; MAF= 0.00124%, 20/1613874 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 1.56235e-05; MAF= 0.00156%, 1/64006 alleles, homozygotes = 0); grpmax FAF= 9.53e-06.
This variant is present in gnomAD v2.1 (AF= 1.59093e-05; MAF= 0.00159%, 4/251426 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 4.62193e-05; MAF= 0.00462%, 1/21636 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Pathogenic (3 clinical laboratories). (ClinVarID = 1976297)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06).
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.