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.1 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.2 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.3 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.4
MBD4
Final classification
VUS
MBD4 c.1015G>A · p.Ala339Thr
MBD4
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.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP1 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2
BP1
VUS
MBD4 c.1015G>A
PM2 + BP1
→
VUS
2
revelbayesdelspliceai ↗
4
generic_acmg_combination_rules
Gene diagram
· NM_003925.3 · variants mapped to exon structure
MBD4
NM_003925.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
✓
PM2
supporting
Pathogenic
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%.
Absent from gnomAD v2.1 (0/0 allelesAF=0%)absent from gnomAD v4.1 (0/0 alleles
✓
BP1
supporting
Benign
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.
MBD4 germline disease mechanism is LoF via truncating variants (PMID:31322271 reports p.Gln73*PMID:35460607 establishes biallelic LoF as multi-tumor predisposition syndrome). Missense variants are not the established mechanism.
Assessed · not applied
Pathogenic
PS1
No established pathogenic variant with the same amino acid change (Ala339Thr) has been reported in ClinVar or the literature.
PS2
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
No well-established functional studies demonstrating a damaging effect of p.Ala339Thr on MBD4 glycosylase activity or protein function have been identified.
PS4
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.
PM1
Residue Ala339 is located in the MBD4 uracil-DNA glycosylase domain, a critical functional region.
PM5
No established pathogenic missense variant at the same residue (Ala339) with a different amino acid change has been identified.
PM6
No de novo observation of NM_003925.3:c.1015G>A, with or without confirmation of maternity and paternity, has been reported.
PP1
No segregation data are available for NM_003925.3:c.1015G>A.
PP2
MBD4 disease mechanism is loss-of-function via truncating variants, not missense.
PP3
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).
PP4
No patient phenotype or family history data are available for NM_003925.3:c.1015G>A.
PP5
NM_003925.3:c.1015G>A has not been reported as pathogenic by a reputable clinical source.
Benign
BA1
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%.
BS1
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%.
BS2
No observation of NM_003925.3:c.1015G>A in healthy adults has been reported.
BS3
No well-established functional studies demonstrating a benign effect of p.Ala339Thr on MBD4 function have been identified.
BS4
No evidence of lack of segregation in affected families has been reported for NM_003925.3:c.1015G>A.
BP2
No observation of NM_003925.3:c.1015G>A in trans with a pathogenic variant in a fully penetrant dominant gene has been reported.
BP4
Multiple lines of computational evidence do not consistently support a benign effect.
BP5
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
NM_003925.3:c.1015G>A is absent from ClinVar and has not been reported as benign by a reputable clinical source.
N/A · 5
PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
In silico
SpliceAI predicts possible splice impact for this variant (max delta score = 0.27). REVEL score = 0.302. BayesDel score = -0.489624.
Functional
Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MBD4, a DNA glycosylase, is infrequently altered in cancer.
COSMIC
Cancer hotspots
Somatic evidence
Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
2papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
PMID 31322271
Found
MBD4 germline disease mechanism is LoF via truncating variants (PMID:31322271 reports p.Gln73* PMID:35460607 establishes biallelic LoF as multi-tumor predisposition syndrome).
Applied to
→BP1 supports · met
PMID 35460607
Found
MBD4 germline disease mechanism is LoF via truncating variants (PMID:31322271 reports p.Gln73* PMID:35460607 establishes biallelic LoF as multi-tumor predisposition syndrome).
Applied to
→BP1 supports · met
Sources & reference links