Is DMD p.Leu962Val (c.2884C>G) pathogenic?

DMD p.Leu962Val (c.2884C>G) is classified Benign/Likely benign in DMD (ClinVar, Multiple submitters, 8 submitters; last evaluated 2025-12-17). AlphaMissense: likely benign (0.0977); Ultra-rare (popmax 0.0468%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Leu962Val (c.2884C>G)?

DMD p.Leu962Val (c.2884C>G) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Leu962Val (c.2884C>G) in the general population?

DMD p.Leu962Val (c.2884C>G) is ultra-rare (popmax 0.0468%, nfe) (gnomAD).

What do computational predictors say about DMD p.Leu962Val (c.2884C>G)?

AlphaMissense predicts likely benign (score 0.0977) — an in-silico prediction, not a clinical call.

DMD p.Leu962Val

c.2884C>G · rs150959827 · VCV264229

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

AlphaMissense

likely benign

0.0977 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0468%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.0977	likely benign
REVEL	0.054	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.4	GERP 2.2, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	16.97	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0468% European (non-Finnish) · 419/894,560 alleles

Filtering AF 0.0431% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0416%

Overall 0.0369% 446/1,209,030 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0468%	2,135
Remaining individualsnot grpmax-eligible	0.0442%	2,264
African / African-American	0.00701%	14,258
Finnishnot grpmax-eligible	0.00429%	23,297

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DMD
Protein: p.Leu962Val
Coding: c.2884C>G
MANE Select: NM_004006
dbSNP: rs150959827
Type: single nucleotide variant
Location: chrX:32472229 (GRCh38)

Full DMD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cardiomyopathy Becker muscular dystrophy Duchenne muscular dystrophy

Similar variants

DMD p.Leu962= Likely benign ★ same residue
DMD c.10086+1G>A Pathogenic ★★ same condition
DMD c.10086+1G>T Pathogenic ★★ same condition
DMD c.10086+2T>C Pathogenic ★★ same condition
DMD c.10087-2A>G Pathogenic/Likely pathogenic ★★ same condition
DMD c.10223+1G>A Pathogenic ★★ same condition
DMD c.10223+1G>C Pathogenic ★★ same condition
DMD c.10224-2A>G Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dmd-p-leu962val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown