NM_003925.3:c.682G>C

MBD4 · NP_003916.1:p.(Val228Leu) · NM_003925.3

GRCh37: chr3:129155805 C>G · GRCh38: chr3:129436962 C>G

Gene: MBD4 Transcript: NM_003925.3

Final call

VUS

PM2 supporting BP4 supporting

Variant details

Gene

MBD4

Transcript

NM_003925.3

Protein

NP_003916.1:p.(Val228Leu)

gnomAD AF

7.868464063423538e-05 (v4.1)

ClinVar

Likely benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_003925.3:c.682G>C (p.Val228Leu) is a missense variant in MBD4 exon 3, observed at extremely low frequency in population databases (gnomAD v2.1 AF = 0.011%, 31/282,140 alleles; gnomAD v4.1 AF = 0.0079%, 127/1,614,038 alleles; no homozygotes).

Multiple in silico tools unanimously predict a benign effect: REVEL score 0.199, BayesDel score −0.381, SpliceAI max delta 0.00, and CADD 7.985. Repo et al. (2020) also reported in silico predictions as polymorphism, benign, tolerated, and no splicing impact.

This variant has been reported in ClinVar as Likely benign by Ambry Genetics (SCV005618014) and as Uncertain significance by Invitae (SCV003476936). No expert panel review has been performed (ClinVar Variation ID: 2163156).

The variant was identified in 1 of 440 Finnish patients with uveal melanoma (Repo et al. 2020). The authors considered it likely benign based on in silico predictions and noted no enrichment in cases compared to the Finnish population frequency (0.032%).

No functional studies, segregation data, de novo observations, or case-control association data are available for this variant. MBD4 is not an established gene where missense variants are a common disease mechanism; the primary pathogenic mechanism is loss of function via truncating variants.

Based on generic ACMG/AMP 2015 criteria, the evidence profile consists of PM2_supporting (low population frequency) and BP4_supporting (multiple benign in silico predictions). These opposing criteria result in an overall classification of Uncertain significance.

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.682G>C is a missense variant (p.Val228Leu) and does not fall into the null-variant categories of nonsense, frameshift, or canonical ±1,2 splice consensus variants required for PVS1 application.	pvs1_variant_assessment pvs1_generic_framework
PS1	N/A	No previously classified pathogenic variant at the same amino acid residue (Val228) was identified. PM5 candidate harvesting found no same-residue comparator variants with established pathogenicity.	pm5_candidates
PS2	Not met	No de novo observation of NM_003925.3:c.682G>C has been reported in any reviewed publication or database.	clinvar PMID:32421892
PS3	Not met	No variant-specific functional assay for NM_003925.3:c.682G>C (p.Val228Leu) was identified. The one paper that examined this variant (Repo et al. 2020, PMID:32421892) relied solely on in silico predictions and did not perform any functional characterization.	PMID:32421892 oncokb
PS4	Not met	The variant was observed in 1 of 440 Finnish uveal melanoma patients (Repo et al. 2020), yielding a prevalence of 0.23% in cases, which is comparable to the Finnish population allele frequency of 0.032% (gnomAD v2.1). No case-control enrichment or statistical evidence supporting pathogenicity exists.	PMID:32421892 gnomad_v2
PS5	Not met	No reputable source has classified NM_003925.3:c.682G>C as pathogenic. ClinVar submissions are Likely benign (Ambry Genetics) and Uncertain significance (Invitae), neither meeting the pathogenic threshold required for PS5.	clinvar
PM1	Not met	The variant resides in exon 3 of MBD4, within the methyl-CpG binding domain region, but residue Val228 is not located in a statistically significant mutational hotspot, and no functional domain-specific constraint evidence supports PM1.
PM2	Met	NM_003925.3:c.682G>C is present at extremely low frequency in population databases: gnomAD v2.1 overall allele frequency is 0.011% (31/282,140 alleles) and gnomAD v4.1 overall allele frequency is 0.0079% (127/1,614,038 alleles), both below the 0.1% PM2 threshold. No homozygotes are observed. The highest subpopulation frequency is in the Finnish population at 0.032% (v2.1), also well below 0.1%.	gnomad_v2 gnomad_v4
PM5	N/A	Unable to confirm classic same-residue PM5 semantics safely; no same-residue comparator variants with established pathogenicity were identified at Val228.	pm5_candidates
PM6	Not met	No de novo observation of NM_003925.3:c.682G>C has been reported; no maternity/paternity confirmation data exist for this variant.	clinvar
PP1	Not met	No family segregation data are available for NM_003925.3:c.682G>C in any reviewed publication or database.
PP2	Not met	MBD4 is not a gene in which missense variants are a recognized common mechanism of disease. The established disease mechanism for MBD4 is loss of function (truncating variants). The gene has a low pLI of 0 and is tolerant to missense variation.	pvs1_gene_context PMID:32421892
PP3	Not met	Multiple in silico tools unanimously predict a benign effect: REVEL score 0.199 (below the 0.29 benign threshold), BayesDel score −0.381 (negative scores favor benign), SpliceAI max delta 0.00 (no splicing impact), and CADD 7.985 (below common pathogenicity thresholds). These results do not support PP3.	revel bayesdel spliceai PMID:32421892
PP4	Not met	No specific patient phenotype data for NM_003925.3:c.682G>C carriers are available that would allow evaluation of phenotype specificity. The single carrier in Repo et al. 2020 was a Finnish uveal melanoma patient, but the variant was considered likely benign by the authors.	PMID:32421892
PP5	Not met	No reputable source has independently classified NM_003925.3:c.682G>C as pathogenic. The ClinVar submissions are Likely benign (Ambry Genetics) and Uncertain significance (Invitae). PP5 requires a pathogenic classification from a reputable source, which is not met here.	clinvar
BA1	Not met	The overall allele frequency in gnomAD v2.1 is 0.011%, well below the BA1 threshold of >1%. The variant is rare, not common, in population databases.	gnomad_v2 gnomad_v4
BS1	Not met	The overall allele frequency in gnomAD v2.1 is 0.011%, well below the BS1 threshold of >0.3%. The highest subpopulation frequency is Finnish at 0.032%, also below the threshold.	gnomad_v2 gnomad_v4
BS2	Not met	No evidence of observation in healthy adult controls specifically documented for this variant. While the variant is present in gnomAD (presumed healthy population), the total allele count is low (31 in v2.1, 127 in v4.1), and no dedicated control cohort study has confirmed benign observation in a sufficient number of healthy individuals.	gnomad_v2
BS3	Not met	No functional studies demonstrating a benign effect of NM_003925.3:c.682G>C (p.Val228Leu) have been performed. The assessment of likely benign in Repo et al. 2020 was based solely on in silico predictions, not functional assays.	PMID:32421892
BS4	Not met	No segregation data are available for NM_003925.3:c.682G>C. BS4 requires lack of cosegregation with disease in affected family members, which cannot be assessed.
BP1	Not met	Although MBD4 disease mechanism is primarily loss of function via truncating variants, the missense variant NM_003925.3:c.682G>C cannot automatically be considered benign under BP1. The gene is not established with a clear rule that missense variants are exclusively benign; some MBD4 missense variants (e.g., Asp568His) have shown functional impact.	pvs1_gene_context PMID:32421892
BP2	Not met	No observation of NM_003925.3:c.682G>C in trans with a known pathogenic MBD4 variant has been reported. Without such data, BP2 cannot be applied.
BP4	Met	Multiple lines of computational evidence unanimously predict a benign effect: REVEL score 0.199, BayesDel score −0.381, SpliceAI max delta 0.00, and CADD 7.985. Repo et al. 2020 also reported in silico predictions as polymorphism (MutationTaster), benign (PolyPhen), tolerated (SIFT), and no splicing impact (HSF), supporting BP4 at supporting strength.	revel bayesdel spliceai PMID:32421892
BP5	Not met	No alternate molecular basis for disease has been identified in individuals carrying NM_003925.3:c.682G>C. BP5 requires observation of the variant in a case with an alternate confirmed genetic cause, which has not been reported.
BP6	Not met	No reputable source has independently classified NM_003925.3:c.682G>C as benign. While Ambry Genetics submitted a Likely benign classification, this is a single submitter without expert panel review. BP6 requires a reputable source classification as benign, which is not met here.	clinvar
BP7	N/A	NM_003925.3:c.682G>C is a missense variant (p.Val228Leu), not a synonymous variant. BP7 applies only to synonymous variants without predicted splice impact.
BP3	N/A	NM_003925.3:c.682G>C is a substitution, not an in-frame deletion/insertion. BP3 applies only to in-frame indels in repetitive regions.
PM3	N/A	PM3 applies to recessive disorders. MBD4-associated conditions are not established as autosomal recessive; the disease mechanism is autosomal dominant with loss of function.	pvs1_gene_context
PM4	N/A	NM_003925.3:c.682G>C is a missense substitution and does not alter protein length. PM4 applies to non-frameshift and stop-loss variants that change protein length.

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