ATRX c.4231G>T, p.(Glu1411Ter)

Reasoning

PVS1 is met at full strength under the generic ClinGen SVI PVS1 framework (PMC6185798). NM_000489.5 is the RefSeq-selected transcript for ATRX, and NM_000489.5:c.4231G>T is a nonsense variant producing NP_000480.3:p.(Glu1411Ter). VariantValidator places it in exon 14, well upstream of the transcript's terminal coding region, so the premature termination codon is predicted to trigger nonsense-mediated decay rather than escape it. The predicted protein is shortened from 2493 amino acids to 1411 amino acids, removing the C-terminal portion of ATRX. The gene-level evidence supports ATRX loss of function as a germline disease mechanism, and no applicable VCEP/CSPEC specification or named downgrade rule is available. Therefore no NMD-escape, non-critical-exon, distal-truncation, or other specific SVI downgrade applies, and the correct strength is very strong.

Rule

Generic ClinGen SVI PVS1 framework (PMC6185798): premature termination in a relevant transcript and upstream coding exon with predicted NMD and substantial protein truncation supports full-strength PVS1.

Evidence considered

• The governing generic ClinGen SVI PVS1 framework is PMC6185798; its NMD rule predicts decay when a premature termination codon is not in the 3-prime-most exon or the 3-prime-most 50 bases of the penultimate exon.
• VariantValidator identifies NM_000489.5 as the RefSeq-selected ATRX transcript, places NM_000489.5:c.4231G>T in exon 14, and predicts NP_000480.3:p.(Glu1411Ter).
• The normalized protein annotation gives a full length of 2493 amino acids and a predicted truncated length of 1411 amino acids; the variant therefore removes the downstream C-terminal sequence.
• The gene-level assessment supports ATRX loss of function as a germline disease mechanism and marks the generic PVS1 gate eligible; no official CSPEC/VCEP framework is available for this case.
• No specific named SVI or VCEP downgrade rule is triggered: the variant is not documented as an NMD-escaping terminal-exon change or a non-critical distal truncation.

Sources

Reasoning

No applicable ATRX-specific VCEP or gene-specific population specification was available, so the supplied generic PM2 rule was used. The variant is absent from gnomAD v2.1 and gnomAD v4.1, corresponding to an observed allele frequency of 0 in both queried datasets and meeting the generic PM2 supporting threshold of <=0.0001. The available records do not indicate a population-specific threshold artifact or a cancer-cohort-only observation; the all-comers datasets are therefore the applicable defaults.

Rule

Generic ClinGen SVI PM2: apply supporting evidence when the variant allele frequency is <=0.0001 in an appropriate population database. No applicable ATRX-specific framework was available.

Evidence considered

• gnomAD v2.1 reports the variant as absent, corresponding to observed allele frequency 0 in that dataset.
• gnomAD v4.1 reports the variant as absent, corresponding to observed allele frequency 0 in that dataset.
• The supplied generic PM2 threshold is allele frequency <=0.0001 at supporting strength; both queried datasets meet this criterion.
• No ATRX-specific VCEP or gene-specific population rule was available, so the all-comers gnomAD v2.1 and v4.1 defaults were used.

Sources

Reasoning

ClinVar has no exact-variant record for NM_000489.5:c.4231G>T: no variation ID, exact match, classification, or review status was found. Consequently, there is no exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion to support PP5. Ordinary submissions, aggregate labels, and non-expert assertions were not used.

Rule

PP5 is applied only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• ClinVar exact-variant searches returned no result for NM_000489.5:c.4231G>T and no expert-panel classification was present.

Sources

Reasoning

No applicable ATRX-specific VCEP or gene-specific framework was available, so the generic ACMG/AMP BA1 threshold was used. The variant is absent from gnomAD v2.1 and gnomAD v4.1; therefore no population allele frequency reaches the stand-alone benign threshold of >=0.05. The available population evidence does not support BA1.

Rule

Generic ACMG/AMP BA1: apply stand-alone benign evidence at allele frequency >=0.05. No applicable ATRX-specific framework was available.

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• The generic ACMG/AMP BA1 threshold is allele frequency >=0.05; no observed frequency approaches this threshold.

Sources

Reasoning

No applicable ATRX-specific VCEP or gene-specific frequency threshold was available, so the supplied generic BS1 threshold was used. The variant is absent from gnomAD v2.1 and gnomAD v4.1, providing no allele frequency >=0.01 that would support BS1. The absence of a variant is not evidence that it exceeds a benign frequency threshold.

Rule

Generic ACMG/AMP BS1: apply strong benign evidence at an allele frequency >=0.01 when the frequency is greater than expected for the disorder. No applicable ATRX-specific framework was available.

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• The supplied generic BS1 threshold is allele frequency >=0.01; no observed frequency reaches it.

Sources

Reasoning

No applicable ATRX-specific VCEP or gene-specific framework was available. The available gnomAD records report the variant as absent and provide no observed healthy homozygotes or, for this X-linked locus, healthy hemizygous males carrying the variant. Consequently, the available evidence does not satisfy BS2.

Rule

Generic ACMG/AMP BS2: apply benign evidence when the variant is observed in healthy adults at an appropriate age, including homozygous observations where relevant; no qualifying observation is available.

Evidence considered

• gnomAD v2.1 reports the variant as absent and contains no reported healthy homozygote or hemizygote observation.
• gnomAD v4.1 reports the variant as absent and contains no reported healthy homozygote or hemizygote observation.
• Because ATRX is X-linked, an equivalent healthy hemizygous male observation would be relevant, but none is reported.

Sources

Reasoning

ClinVar has no exact-variant record for NM_000489.5:c.4231G>T: no variation ID, exact match, classification, or review status was found. Consequently, there is no exact-variant ClinVar expert-panel Benign or Likely benign assertion to support BP6. Ordinary submissions, aggregate labels, and non-expert assertions were not used.

Rule

BP6 is applied only for an exact-variant ClinVar expert-panel Benign or Likely benign classification; ordinary laboratory submissions, aggregate labels, and non-expert assertions do not qualify.

Evidence considered

• ClinVar exact-variant searches returned no result for NM_000489.5:c.4231G>T and no expert-panel classification was present.

Sources

Reasoning

No case-level evidence documents that NM_000489.5:c.4231G>T arose de novo in an affected proband. The available records contain no proband description, parental genotypes or testing methods, confirmation of maternity and paternity, or evidence excluding parental mosaicism. Therefore, the generic ACMG/AMP PS2 criterion cannot be assessed.

Rule

Generic ACMG/AMP PS2: de novo occurrence in a patient with the disease and no family history, with appropriate parental and relationship confirmation; apply only when the required case-level evidence is documented.

Evidence considered

• The case records identify NM_000489.5:c.4231G>T in ATRX but provide no proband, parental-testing, or de novo occurrence data.
• No applicable ATRX-specific VCEP specification was available; generic ACMG/AMP PS2 was therefore considered, but its required de novo evidence is absent.

Still missing

• Affected proband identity and phenotype consistent with an ATRX-related disorder
• Maternal and paternal genotypes for NM_000489.5:c.4231G>T
• Parental testing methodology and confirmation of maternity and paternity
• Assessment for parental mosaicism

Reasoning

No applicable ATRX-specific VCEP/CSPEC specification was available, so generic ACMG/AMP functional-evidence guidance was used. The reviewed functional literature did not report or experimentally test NM_000489.5:c.4231G>T (NP_000480.3:p.(Glu1411Ter)); therefore, no validated variant-specific assay demonstrating a damaging effect, with appropriate controls and biologic relevance, is available to support PS3 at any strength. Gene-level observations involving other ATRX variants or ATRX-mutant tumors cannot be used as direct PS3 evidence for this variant.

Evidence considered

• The extracted findings for PMID:14592816, PMID:15591283, PMID:17609377, PMID:18409179, and PMID:21719641 all state that NM_000489.5:c.4231G>T or NP_000480.3:p.(Glu1411Ter) was not specifically mentioned or tested.
• PMID:15591283 experimentally studied a different ATRX premature-stop variant, R37X, using patient-derived lymphoblastoid cells, western blotting, RT-PCR, and reporter assays; these results are not transferable as direct PS3 evidence for p.Glu1411Ter.
• PMID:21719641 assessed ATRX/DAXX-mutant tumors for ALT and ATRX expression, but did not test this variant and therefore does not provide variant-specific PS3 evidence.
• Generic ACMG/AMP PS3 application requires well-established functional studies of the variant; no such study was identified in the reviewed sources.

Still missing

• A validated functional assay directly testing ATRX c.4231G>T (p.Glu1411Ter), with appropriate controls and biologically relevant readout, is needed.
• Variant-specific assay results are needed to calibrate PS3 strength.
• No ATRX-specific VCEP/CSPEC functional-assay calibration was available.

Sources

Reasoning

No case-control study, affected-case series, control comparison, odds ratio, relative risk, likelihood ratio, or other statistically supported enrichment estimate was identified for NM_000489.5:c.4231G>T. Therefore the required disease prevalence/enrichment evidence for PS4 is unavailable, and no numeric comparison can be performed.

Rule

Generic ACMG/AMP PS4 requires statistically significant increased prevalence of the variant in affected individuals compared with controls; no applicable ATRX VCEP specification was retrieved.

Evidence considered

• The reviewed evidence contains no exact-variant case-control or prevalence-enrichment analysis for NM_000489.5:c.4231G>T (NP_000480.3:p.(E1411*)).

Still missing

• Exact-variant case series or case-control data with affected and control counts and an enrichment statistic are unavailable.

Reasoning

No affected-proband, genotype, phase, or second pathogenic-variant observations are documented for NM_000489.5:c.4231G>T. ATRX-related disease is X-linked, so the generic recessive PM3 trans-configuration rule is not directly applicable without case-specific evidence demonstrating a relevant allelic configuration or inheritance context.

Rule

Generic ACMG/AMP PM3: pathogenic or likely pathogenic variant detected in trans with a pathogenic variant for a recessive disorder; no applicable ATRX-specific specification was available.

Evidence considered

• The case records contain no documented affected-proband observations, second pathogenic ATRX variant, phase result, or segregation data relevant to PM3.
• ATRX-related disease is described as X-linked; therefore, the generic recessive PM3 trans rule cannot be applied from the available evidence alone.

Still missing

• Affected-proband genotype and phenotype data are unavailable.
• No second pathogenic or likely pathogenic ATRX variant is documented.
• No phasing or inheritance information is available.

Reasoning

No case-level evidence documents a presumed de novo occurrence of NM_000489.5:c.4231G>T without confirmed parental testing. The available records contain no affected proband phenotype, parental genotypes, maternity or paternity confirmation, or information about the number and quality of independent de novo observations. Therefore, the generic ACMG/AMP PM6 criterion cannot be assessed.

Rule

Generic ACMG/AMP PM6: assumed de novo, without confirmation of parental identity or testing, in an affected individual with a phenotype consistent with the disease; apply only when such case evidence is documented.

Evidence considered

• The case records identify NM_000489.5:c.4231G>T in ATRX but provide no presumed-de-novo case observations or parental information.
• No applicable ATRX-specific VCEP specification was available; generic ACMG/AMP PM6 was therefore considered, but its required case-level evidence is absent.

Still missing

• Affected proband identity and phenotype consistent with an ATRX-related disorder
• Evidence that the variant was presumed de novo
• Parental genotypes or documented absence of parental testing
• Confirmation of maternity and paternity
• Number and independence of qualifying observations

Reasoning

No family-level segregation data are available for NM_000489.5:c.4231G>T. The records do not identify affected or unaffected relatives, informative meioses, genotypes, phenotype status, or the number of independent families. Consequently, concordant segregation cannot be evaluated and PP1 cannot be assigned.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease; strength requires documented informative segregation data and must not be inferred from variant classification.

Evidence considered

• The case records contain no pedigree, familial genotype, phenotype-segregation, meiosis, or independent-family observations for NM_000489.5:c.4231G>T.
• No applicable ATRX-specific VCEP specification was available; generic ACMG/AMP PP1 was therefore considered, but no co-segregation evidence is documented.

Still missing

• Family pedigrees and affected-relative status
• Genotypes of informative relatives
• Phenotype assessment in relatives
• Number of informative meioses and independent families

Reasoning

The case materials do not provide a patient phenotype, clinical presentation, or phenotype-to-disease specificity assessment for the variant. Gene-level descriptions of ATR-X syndrome in background literature do not establish that this patient's phenotype is highly specific for an ATRX-related disorder, so PP4 cannot be assessed.

Rule

Generic ACMG/AMP PP4 may support pathogenicity when the patient's phenotype or family history is highly specific for a disease with a single genetic etiology; no applicable ATRX VCEP specification was retrieved.

Evidence considered

• The case materials provide variant normalization and molecular database results but no clinical phenotype or phenotype-specificity evidence for the patient.

Still missing

• A documented patient phenotype and an assessment of its specificity for ATRX-related disease are unavailable.

Reasoning

No applicable ATRX-specific VCEP/CSPEC specification was available, so generic ACMG/AMP functional-evidence guidance was used. None of the reviewed studies experimentally tested NM_000489.5:c.4231G>T (NP_000480.3:p.(Glu1411Ter)) and demonstrated a normal or benign functional result in a validated assay with appropriate controls and biologic relevance. Findings for other ATRX variants or ATRX-mutant tumors cannot establish BS3 for this variant.

Evidence considered

• The extracted findings for PMID:14592816, PMID:15591283, PMID:17609377, PMID:18409179, and PMID:21719641 all indicate that NM_000489.5:c.4231G>T or NP_000480.3:p.(Glu1411Ter) was not specifically mentioned or tested.
• PMID:15591283 reports residual ATRX protein for the different R37X variant, not a benign result for p.Glu1411Ter; it cannot support BS3 for this case.
• PMID:17609377 examined structural and protein consequences of different ATRX ADD-domain mutations, not this distal truncating variant, and does not provide a normal functional result for it.
• Generic ACMG/AMP BS3 application requires a well-established functional study showing no damaging effect for the tested variant; no such study was identified in the reviewed sources.

Still missing

• A validated functional assay directly testing ATRX c.4231G>T (p.Glu1411Ter), with appropriate controls and a normal/benign readout, is needed.
• Variant-specific assay results are needed to calibrate BS3 strength.
• No ATRX-specific VCEP/CSPEC functional-assay calibration was available.

Sources

Reasoning

No family-level evidence is available showing that NM_000489.5:c.4231G>T fails to segregate with disease. The records do not document unaffected relatives who carry the variant, affected relatives who lack it, informative genotypes, phenotype evaluations, or the number of tested relatives. Therefore, non-segregation cannot be assessed and BS4 cannot be assigned.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family, or presence of the variant in unaffected relatives when disease status is informative; apply only with documented familial genotype-phenotype discordance.

Evidence considered

• The case records contain no discordant familial genotype-phenotype observations for NM_000489.5:c.4231G>T.
• No applicable ATRX-specific VCEP specification was available; generic ACMG/AMP BS4 was therefore considered, but no non-segregation evidence is documented.

Still missing

• Genotypes of relatives with documented phenotype status
• Evidence of variant carriage in unaffected relatives or absence in affected relatives
• Pedigree structure and informative meioses
• Number and independence of discordant observations

Reasoning

No affected-proband, genotype, phase, or family-inheritance observations are documented for NM_000489.5:c.4231G>T. There is no evidence that this variant is in trans with a pathogenic variant or in cis with a pathogenic variant in a relevant dominant context; ATRX-related disease is X-linked.

Rule

Generic ACMG/AMP BP2: variant observed in trans with a pathogenic variant for a fully penetrant recessive disorder or in cis with a pathogenic variant for a dominant disorder; no applicable ATRX-specific specification was available.

Evidence considered

• The case records contain no documented affected-proband observations, second pathogenic ATRX variant, phase result, or family-inheritance data relevant to BP2.
• ATRX-related disease is described as X-linked, and the available evidence does not establish a cis or trans configuration that satisfies generic BP2.

Still missing

• Affected-proband genotype and phenotype data are unavailable.
• No second pathogenic or likely pathogenic ATRX variant is documented.
• No phasing, family testing, or inheritance information is available.

Reasoning

No case-level evidence was identified showing that the patient has an established alternative molecular basis for the phenotype that would explain the presentation independently of NM_000489.5:c.4231G>T. The available molecular database and literature results do not provide the required alternate-cause evidence, so BP5 is not assessable.

Rule

Generic ACMG/AMP BP5 requires a pathogenic variant in an alternative gene that explains the patient's phenotype; no applicable ATRX VCEP specification was retrieved.

Evidence considered

• The case materials contain no patient-level alternate pathogenic variant or other molecular diagnosis that independently explains a reported phenotype.

Still missing

• A documented alternative molecular basis for the patient's phenotype is unavailable.