NM_003925.3:c.1015G>A

MBD4 · NP_003916.1:p.(Ala339Thr) · NM_003925.3

GRCh37: chr3:129155472 C>T · GRCh38: chr3:129436629 C>T

Gene: MBD4 Transcript: NM_003925.3

Final call

VUS

PM2 supporting BP1 supporting benign

Variant details

Gene

MBD4

Transcript

NM_003925.3

Protein

NP_003916.1:p.(Ala339Thr)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_003925.3:c.1015G>A (p.Ala339Thr) is absent from all gnomAD population databases (v2.1, v4.1, Canada), meeting PM2 at supporting strength.

MBD4 germline disease is mediated by loss-of-function via truncating variants; this missense variant qualifies for BP1 (supporting benign) as missense variation is not the established pathogenic mechanism.

Computational predictors are discordant: REVEL 0.302 (weakly pathogenic-leaning), BayesDel -0.489624 (benign-leaning), SpliceAI max delta 0.27 (intermediate). Neither PP3 nor BP4 is met.

No functional studies, no case-control data, no segregation data, no de novo observations, and no ClinVar entries exist for this variant. All other criteria are not met or not applicable.

With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP1), the net evidence score is zero, consistent with a variant of uncertain significance (VUS) per ACMG/AMP 2015 generic classification rules.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_003925.3:c.1015G>A (p.Ala339Thr) is a missense variant, not a null variant (nonsense, frameshift, or canonical ±1,2 splice consensus). SpliceAI max delta score of 0.27 is below the threshold to invoke a splicing null effect per ClinGen SVI PVS1 recommendations (PMC6185798). PVS1 is not applicable.	pvs1_generic_framework spliceai
PS1	Not met	No established pathogenic variant with the same amino acid change (Ala339Thr) has been reported in ClinVar or the literature. PS1 cannot be applied.	clinvar
PS2	Not met	No de novo occurrence of NM_003925.3:c.1015G>A with confirmed maternity and paternity has been reported in the literature, ClinVar, or de novo databases.
PS3	Not met	No well-established functional studies demonstrating a damaging effect of p.Ala339Thr on MBD4 glycosylase activity or protein function have been identified. In silico predictions (REVEL, BayesDel) are not a substitute for functional evidence.	oncokb
PS4	Not met	The variant is absent from ClinVar and gnomAD, and no case-control study demonstrating statistically significant enrichment of this variant in affected individuals has been identified.	gnomad_v2 gnomad_v4 clinvar
PS5	Not met	NM_003925.3:c.1015G>A has not been reported as pathogenic by a reputable source. It is absent from ClinVar and has no published clinical assertions.	clinvar
PM1	Not met	Residue Ala339 is located in the MBD4 uracil-DNA glycosylase domain, a critical functional region. However, PM1 requires evidence that the domain has a low rate of benign missense variation, which has not been established through gnomAD constraint metrics or domain-specific benign variation analysis.
PM2	Met	NM_003925.3:c.1015G>A is absent from gnomAD v2.1 (0 alleles), gnomAD v4.1 (0 alleles), and gnomAD-Canada v1.0 (0 alleles), with allele frequency of 0% in all populations, well below the PM2 threshold of 0.1%.	gnomad_v2 gnomad_v4
PM5	Not met	No established pathogenic missense variant at the same residue (Ala339) with a different amino acid change has been identified. The automatic PM5 candidate harvest returned zero candidates.	pm5_candidates
PM6	Not met	No de novo observation of NM_003925.3:c.1015G>A, with or without confirmation of maternity and paternity, has been reported.
PP1	Not met	No segregation data are available for NM_003925.3:c.1015G>A. No family studies demonstrating co-segregation of this variant with disease have been identified.
PP2	Not met	MBD4 disease mechanism is loss-of-function via truncating variants, not missense. Known pathogenic MBD4 variants are primarily nonsense/frameshift (e.g., c.217C>T/p.Gln73*). HCI prior score is unavailable for MBD4. PP2 is not applicable to a gene where missense is not the established disease mechanism.
PP3	Not met	In silico predictions are discordant: REVEL score is 0.302 (below the typical pathogenic threshold of 0.5), BayesDel score is -0.489624 (benign-leaning), and SpliceAI max delta is 0.27 (intermediate). Multiple lines of computational evidence do not consistently support a deleterious effect.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or family history data are available for NM_003925.3:c.1015G>A. The variant has not been observed in any clinically characterized individual.
PP5	Not met	NM_003925.3:c.1015G>A has not been reported as pathogenic by a reputable clinical source. It is absent from ClinVar and has no published clinical assertions of pathogenicity.	clinvar
BA1	Not met	NM_003925.3:c.1015G>A is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with an allele frequency of 0%, which is well below the BA1 threshold of 1%.	gnomad_v2 gnomad_v4
BS1	Not met	NM_003925.3:c.1015G>A is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with an allele frequency of 0%, which is well below the BS1 threshold of 0.3%.	gnomad_v2 gnomad_v4
BS2	Not met	No observation of NM_003925.3:c.1015G>A in healthy adults has been reported. BS2 requires documented observation in healthy individuals for a fully penetrant disorder, which is not available.
BS3	Not met	No well-established functional studies demonstrating a benign effect of p.Ala339Thr on MBD4 function have been identified. Computational predictions alone do not constitute BS3-level evidence.
BS4	Not met	No evidence of lack of segregation in affected families has been reported for NM_003925.3:c.1015G>A.
BP1	Met	NM_003925.3:c.1015G>A is a missense variant in MBD4, a gene for which the established disease mechanism is loss-of-function via truncating variants. The known germline pathogenic variants in MBD4 are primarily nonsense and frameshift alterations (e.g., c.217C>T/p.Gln73* reported in PMID:31322271; multi-tumor syndrome described in PMID:35460607). A missense variant in a primarily truncating-disease gene warrants BP1.
BP2	Not met	No observation of NM_003925.3:c.1015G>A in trans with a pathogenic variant in a fully penetrant dominant gene has been reported. BP2 is not applicable in the absence of such data.
BP4	Not met	Multiple lines of computational evidence do not consistently support a benign effect. BayesDel score is -0.489624 (benign-leaning), but REVEL score is 0.302 (weakly pathogenic-leaning) and SpliceAI max delta is 0.27 (intermediate). Discordant predictions do not meet the 'multiple lines' requirement for BP4.	revel bayesdel spliceai
BP5	Not met	No case has been reported in which NM_003925.3:c.1015G>A was observed in an individual with an alternate molecular basis for disease.
BP6	Not met	NM_003925.3:c.1015G>A is absent from ClinVar and has not been reported as benign by a reputable clinical source.	clinvar
BP7	N/A	NM_003925.3:c.1015G>A is a missense variant (p.Ala339Thr), not a synonymous variant. BP7 applies only to synonymous variants with no predicted splice impact.
BP3	N/A	NM_003925.3:c.1015G>A is a single-nucleotide substitution, not an in-frame insertion or deletion. BP3 applies to in-frame indels in repeat regions.
PM3	N/A	No second pathogenic MBD4 variant has been identified in trans with NM_003925.3:c.1015G>A; no biallelic observation available for assessment.
PM4	N/A	NM_003925.3:c.1015G>A is a single-nucleotide substitution, not a non-frameshift indel or stop-loss variant. PM4 applies to protein-length-altering variants.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.