No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.
Pathogenic.A pathogenic classification under the recorded framework.
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 at very strong: RNA evidence shows c.335+1G>A causes an 88-base splice deletion and premature p.Arg83Profs*5 truncation.
Met at supporting: RNA-seq showed c.335+1G>A activated a cryptic donor, deleted 88 bases, and produced a premature stop codon.
Met at supporting: gnomAD v4.1 overall AF is 2.36811e-05, below the generic PM2 threshold of 0.0001, with zero homozygotes.
Met: SpliceAI maximum delta 0.81 meets the >=0.5 PP3 moderate threshold.
No benign criterion marked as applied in the recorded assessment.
Pathogenic: PVS1 (very strong), PP3 (moderate), PS3 (supporting), and PM2 (supporting) support the generic ACMG/AMP fallback call.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 38 / 1,604,652 alleles. Recorded AF 2.36811e-05. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 1.06066e-05; MAF= 0.00106%, 3/282844 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.32274e-05; MAF= 0.00232%, 3/129158 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
Not available in gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.810. Refer to the recorded PP3/BP4 rationale for interpretation.
2 Likely pathogenic.
No standalone functional evidence summary is recorded in evidence_summary.functional.
This variant has not previously been reported in somatic cancers (COSMIC).
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
28 criteria with recorded statuses: 4 met · 7 not met · 9 not assessed · 8 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
No MBD4-specific ClinGen CSPEC/VCEP specification was available, so generic ACMG/AMP criteria logic was used.
The reviewed exact-variant publications provide germline case or cohort observations but do not provide parental testing, de novo documentation, familial segregation, informative meioses, or non-segregation evidence.
Accordingly, PS2, PM6, PP1, and BS4 are all not assessed rather than inferred from the variant's clinical classification or from recurrence in separate patients.
Generic ACMG/ClinGen SpliceAI calibration was used because no applicable MBD4-specific VCEP specification was available; the maximum delta score supports PP3 at moderate strength and does not support BP4.
No criteria match.
No MBD4-specific VCEP or CSPEC specification is available, so the generic ClinGen SVI PVS1 framework applies. MBD4 loss of function is an established germline disease mechanism in the case evidence. NM_001276270.2 is the MANE Select/refSeq transcript, and c.335+1G>A is a canonical splice-donor variant. Variant-specific RNA-sequencing evidence reports use of a cryptic splice donor, loss of 88 bases, and a premature stop codon, with the resulting protein consequence reported as p.Arg83Profs*5; this is an early truncating consequence in the 568-amino-acid MBD4 protein and is consistent with loss of the DNA glycosylase function. The exact variant was also observed as a germline protein-truncating MBD4 variant in a cohort of 1093 uveal-melanoma patients. No evidence indicates a rescued in-frame product, a distal non-critical truncation, or a repeat-region complication, and the observed early premature stop does not trigger an NMD-escape or non-critical-exon downgrade under the generic SVI framework. Therefore PVS1 is met at full strength, recorded as the literal tier "very strong".
Generic ClinGen SVI PVS1 framework (PMC6185798): canonical splice-site loss-of-function variant with established gene-level loss-of-function mechanism; no applicable downgrade rule identified.
PS3 is met at supporting strength under the generic ACMG/AMP framework. The exact variant, NM_001276270.2:c.335+1G>A, was evaluated in a TCGA glioblastoma case with tumor and germline sequencing plus RNA-seq. The study reported somatic loss of heterozygosity and use of a cryptic splice donor, resulting in loss of 88 bases and a premature stop codon, directly demonstrating a deleterious splice consequence for this variant. The assay is biologically relevant and variant-specific, but the available evidence describes a single tumor-based observation and does not provide a fully detailed independent validation/control series sufficient for moderate or strong functional weighting. The result is therefore calibrated to supporting strength. No additional splice-prediction criterion is used here; the SpliceAI result is not a functional assay and is outside this requested group.
No applicable MBD4-specific VCEP framework was available, so the supplied generic PM2 supporting threshold of allele frequency <=0.0001 applies. This canonical splice variant is rare in population data: gnomAD v2.1 non-cancer exomes show AF 8.44188e-06 (2/236,914 alleles; homozygotes 0), gnomAD v3.1 non-cancer genomes show AF 1.35155e-05 (2/147,978; homozygotes 0), and gnomAD v4.1 all-comers show AF 2.36811e-05 overall (38/1,604,652; homozygotes 0), with the highest reported subgroup AF 3.21875e-05. All observed frequencies are below 0.0001, supporting PM2 at supporting strength.
generic_acmg_pm2: allele_frequency <= 0.0001; supporting
The variant is an intronic canonical splice-region substitution, so the SpliceAI path is applicable. SpliceAI reports a maximum delta score of 0.81 (DS_DL), which meets the generic PP3 moderate threshold of >=0.5 from the Jaganathan et al. 2019 SpliceAI calibration (PMID:30661751). No MBD4-specific VCEP specification or lookup was available. This prediction should not be double-counted with other evidence assessing the same splice consequence.
Generic ACMG PP4 requires a patient's phenotype or family history to be highly specific for a disease with a single-gene etiology. The exact variant is reported in patients with uveal melanoma and glioblastoma, but these tumor phenotypes are not sufficiently specific to MBD4-related disease on their own, and the available reports do not establish a highly characteristic single-gene phenotype for this individual.
PP4: patient's phenotype or family history is highly specific for a disease with a single-gene etiology; no disease-specific VCEP specification was available.
PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. ClinVar variation 2910176 is an exact match for NM_001276270.2:c.335+1G>A and is labeled Likely pathogenic, but its review status is criteria provided, single submitter; the audit records 0 expert-panel submissions. The laboratory submissions cannot trigger PP5.
PP5 applies only when an exact-variant ClinVar expert-panel classification is Pathogenic or Likely pathogenic; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.
No applicable MBD4-specific VCEP framework was available, so the generic ACMG/AMP stand-alone BA1 threshold of allele frequency >=0.05 (Richards et al. 2015, PMID:25741868) applies. The highest observed frequency is 3.21875e-05 in gnomAD v4.1 Remaining individuals, while gnomAD v2.1 non-cancer exomes show 8.44188e-06 and gnomAD v3.1 non-cancer genomes show 1.35155e-05; all are far below 0.05. Therefore, BA1 is not met.
generic_acmg_ba1: allele_frequency >= 0.05
No applicable MBD4-specific VCEP framework was available, so the supplied generic BS1 threshold of allele frequency >=0.01 applies. The highest observed frequency is 3.21875e-05 in gnomAD v4.1 Remaining individuals; the non-cancer subset frequencies are 8.44188e-06 in gnomAD v2.1 exomes and 1.35155e-05 in gnomAD v3.1 genomes. These frequencies do not reach 0.01, and no disease-prevalence or penetrance-based MBD4-specific frequency threshold was available to support BS1. Therefore, BS1 is not met.
generic_acmg_bs1: allele_frequency >= 0.01
BS2 requires observation of the variant in healthy individuals in a homozygous state, or in a hemizygous state where relevant. gnomAD v2.1, gnomAD v2.1 non-cancer exomes, gnomAD v3.1 non-cancer genomes, and gnomAD v4.1 all report zero homozygotes for this variant. The available population data therefore provide no BS2 evidence, and BS2 is not met.
generic_acmg_bs2: requires affected-relevant homozygous or hemizygous observations in healthy individuals
The variant is an intronic canonical splice-region substitution, so the SpliceAI path is applicable. SpliceAI reports a maximum delta score of 0.81 (DS_DL), which does not meet the generic BP4 supporting threshold of <=0.1 from the Jaganathan et al. 2019 SpliceAI calibration (PMID:30661751). No MBD4-specific VCEP specification or lookup was available.
BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. ClinVar variation 2910176 is an exact match but is labeled Likely pathogenic with review status criteria provided, single submitter, and the audit records 0 expert-panel submissions. No qualifying expert-panel benign assertion exists, so BP6 is not met.
BP6 applies only when an exact-variant ClinVar expert-panel classification is Benign or Likely benign; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.
PS2 requires evidence that the variant arose de novo in an affected proband, ideally with confirmed maternity and paternity and documented phenotype consistency. The available evidence reports the variant as a germline finding in affected individuals but does not document parental genotypes, maternity/paternity confirmation, or a de novo determination. Therefore PS2 cannot be applied.
Generic ACMG/AMP PS2: de novo occurrence in an affected individual requires documented parental testing; no de novo claim is made without that evidence.
Generic ACMG PS4 requires a statistically significant increase in the prevalence of the disease in affected individuals compared with controls. PMID:32239153 reports the exact variant in 2 of 1093 consecutive uveal melanoma patients, and PMID:29760383 reports it in one glioblastoma patient, but the available evidence supplies no control-group frequency, odds ratio, p-value, likelihood ratio, or other case-control enrichment statistic. These reports therefore establish observations in affected individuals but do not permit a PS4 enrichment adjudication.
PS4: prevalence of the disease in affected individuals is significantly increased compared with controls; no disease-specific VCEP specification was available, so generic ACMG/AMP wording governs.
No gene-specific VCEP specification is available, so generic ACMG/AMP is used. PM3 requires an affected individual with the evaluated variant established in trans with a pathogenic or likely pathogenic variant for a recessive disorder, with phase and disease-model context documented. The evaluated MBD4 c.335+1G>A variant is reported as a germline splice-site variant in two uveal-melanoma patients and in one glioblastoma case with somatic loss of heterozygosity, but the available records do not document a second germline pathogenic allele, germline trans phase, or an affected proband with biallelic MBD4 variants. The compound-heterozygous observations in PMID:30049810 involve different MBD4 variants and cannot be transferred to this variant. Therefore PM3 cannot be scored from the available evidence.
Generic ACMG/AMP PM3: apply only when the evaluated variant is observed in trans with a pathogenic variant in an affected individual with a recessive disorder; phase and phenotype must be established.
PM6 is considered when a variant appears de novo but parental testing is incomplete or unavailable. The evidence establishes neither a documented de novo observation nor a credible clinical record describing an affected proband with an apparently de novo variant. Germline reporting alone is insufficient for PM6, so this criterion cannot be applied.
Generic ACMG/AMP PM6: an apparently de novo variant may support PM6 only when de novo occurrence is reported but parental testing is incomplete; germline status alone does not satisfy PM6.
PP1 requires co-segregation of the variant with disease in affected relatives, with strength dependent on the number and informativeness of meioses and the phenotype of relatives. The exact variant is reported in two unrelated or separately described patients, but the available evidence does not document affected relatives, family relationships, informative meioses, or segregation testing. Multiple affected individuals in a cohort are not segregation evidence.
Generic ACMG/AMP PP1: apply only for documented co-segregation with disease in affected relatives; increase strength only when the number and informativeness of meioses justify it.
No validated benign functional assay for NM_001276270.2:c.335+1G>A was identified. The available exact-variant RNA evidence demonstrates aberrant splicing and a premature stop codon, which is inconsistent with a benign functional result. A functional assay performed in PMID:30049810 concerned a different MBD4 alteration and cannot establish BS3 for this variant. Therefore BS3 is not assessed rather than applied as absent or benign evidence.
BS4 requires a demonstrated lack of segregation in affected family members, generally based on reliable phenotyping and variant testing in informative relatives. The available sources contain no documented affected relatives who lack the variant and no family-level non-segregation analysis. Absence of segregation data is not evidence of non-segregation, so BS4 cannot be applied.
Generic ACMG/AMP BS4: apply only when a variant fails to segregate with disease in informative affected relatives; missing family data does not satisfy BS4.
No gene-specific VCEP specification is available, so generic ACMG/AMP is used. BP2 requires observation of the evaluated variant in trans with a pathogenic variant for a dominant disorder, or in cis with a pathogenic variant, in a setting where that allelic relationship provides benign evidence. The available target-variant reports identify c.335+1G>A as a germline MBD4 splice-site variant and describe somatic loss of heterozygosity in one tumor, but they do not establish cis or trans phase with another germline pathogenic variant. The case evidence also contains no documented affected-proband haplotype, parental phasing, or paired pathogenic allele that would support BP2. Therefore BP2 cannot be scored.
Generic ACMG/AMP BP2: apply only when the evaluated variant is observed in cis or trans with a pathogenic variant in a context where that phase relationship supports a benign interpretation; phase must be established.
Generic ACMG BP5 concerns a variant found in a patient with a disease-causing variant in an alternative gene or another established molecular basis that explains the phenotype. The available case evidence documents the MBD4 variant and tumor observations but does not identify an alternative pathogenic variant or alternative molecular diagnosis explaining the relevant phenotype. BP5 therefore cannot be assessed from the available evidence.
BP5: variant found in a patient with an alternative molecular basis for disease; no disease-specific VCEP specification was available.
deterministic_prefilter: requires_missense
deterministic_prefilter: requires_missense
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
deterministic_prefilter: requires_missense
deterministic_prefilter: requires_missense
deterministic_prefilter: requires_missense
deterministic_prefilter: requires_repeat_region_indel
deterministic_prefilter: requires_synonymous
Every interpreted variant in MBD4, mapped onto the exon structure of NM_001276270.2. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Remaining individuals2 / 62,136 | 3.2e-05 |
| European (non-Finnish)35 / 1,171,476 | 3e-05 |
| European (Finnish)1 / 64,034 | 1.6e-05 |
| European (non-Finnish)3 / 129,158 | 2.3e-05 |
This variant is present in gnomAD v4.1 (AF= 2.36811e-05; MAF= 0.00237%, 38/1604652 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 3.21875e-05; MAF= 0.00322%, 2/62136 alleles, homozygotes = 0); grpmax FAF= 2.169e-05.
This variant is present in gnomAD v2.1 (AF= 1.06066e-05; MAF= 0.00106%, 3/282844 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.32274e-05; MAF= 0.00232%, 3/129158 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
Not available in gnomAD-Canada v1.0.
The variant is an intronic canonical splice-region substitution, so the SpliceAI path is applicable. SpliceAI reports a maximum delta score of 0.81 (DS_DL), which meets the generic PP3 moderate threshold of >=0.5 from the Jaganathan et al. 2019 SpliceAI calibration (PMID:30661751). No MBD4-specific VCEP specification or lookup was available. This prediction should not be double-counted with other evidence assessing the same splice consequence.
The variant is an intronic canonical splice-region substitution, so the SpliceAI path is applicable. SpliceAI reports a maximum delta score of 0.81 (DS_DL), which does not meet the generic BP4 supporting threshold of <=0.1 from the Jaganathan et al. 2019 SpliceAI calibration (PMID:30661751). No MBD4-specific VCEP specification or lookup was available.
deterministic_prefilter: requires_synonymous
SpliceAI predicts possible splice impact for this variant (max delta score = 0.81). BayesDel score = 0.393717.
9 paper records listed. 2 cited in the classification.
Of these 20 cases, patient GBM_4 presented a glioblastoma carrying 1149 SNVs (440 non-synonymous SNVs) and a germline c.335+1G>A:p.R83Pfs*5 MBD4 mutation with somatic loss of heterozygosity leading to the use of a cryptic splice donor site, loss of 88 bases, and a premature stop codon
Location Results, "MBD4 germline mutations in UM and glioblastoma," paragraph 2
Context TCGA pan-cancer tumor analysis including a glioblastoma case, with tumor and germline sequencing and RNA-seq analysis of splice effects.
Targeted next-generation sequencing in pooled patient DNA followed by Sanger sequencing revealed germline MBD4 PTVs in 7 patients (Table 1): 2 splice site variants (c.1562-1G>T [p.Asp521Profs*4] in 2 patients and a c.335 + 1G>A [p.Arg83Profs*5] variant), 2 frameshift deletion variants (c.1443delT [p.Leu482Trpfs*9] and c.1384delG [p.Ala462Leufs*29]), and 1 stop-gain near the end of the last exon of MBD4 (c.1706G>A [p.Trp569*] in 2 patients).
Location Results, "Identification of MBD4 Germline Variants in the In-House Consecutive UM Series"; Discussion, paragraph beginning "Interestingly, 5 recurrent MBD4 germline deleterious mutations were identified"
Context Targeted sequencing of germline DNA from 1093 consecutive uveal-melanoma patients followed by Sanger confirmation; recurrence was assessed against public databases and other reports.
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 (Figure 1C and Supplemental Figure 2A). Analysis of the MBD4 mRNA allowed for phasing of the variants to distinct alleles and confirmed aberrant splicing that excludes exon 7 and disrupts the glycosylase domain (Supplemental Figure 2B).
Results, “Germline Loss of MBD4 Predisposes to AML with a Novel Mutational Signature,” paragraph 2
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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= 2.36811e-05; MAF= 0.00237%, 38/1604652 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 3.21875e-05; MAF= 0.00322%, 2/62136 alleles, homozygotes = 0); grpmax FAF= 2.169e-05.
This variant is present in gnomAD v2.1 (AF= 1.06066e-05; MAF= 0.00106%, 3/282844 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.32274e-05; MAF= 0.00232%, 3/129158 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Likely pathogenic (2 clinical laboratories). (ClinVarID = 2910176)
SpliceAI predicts possible splice impact for this variant (max delta score = 0.81). BayesDel score = 0.393717.
This variant has not previously been reported in somatic cancers (COSMIC).