Is DMD p.Pro2962= (c.8886C>T) pathogenic?

DMD p.Pro2962= (c.8886C>T) is classified Conflicting classifications of pathogenicity in DMD (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2025-04-11). Very rare (popmax 0.00905%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Pro2962= (c.8886C>T)?

DMD p.Pro2962= (c.8886C>T) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Pro2962= (c.8886C>T) in the general population?

DMD p.Pro2962= (c.8886C>T) is very rare (popmax 0.00905%, nfe) (gnomAD).

DMD p.Pro2962=

c.8886C>T · rs371648038 · VCV389901

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00905%, nfe)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.026	moderately benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -8.9	GERP -3.4
Overall
CADD	0.022	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00905% European (non-Finnish) · 81/894,751 alleles

Filtering AF 0.00742% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00679%

Overall 0.00695% 84/1,208,582 alleles · very rare exomes 79/1,097,314 · genomes 5/111,268 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00905%	11,046
Admixed American	0.00219%	45,580
South Asian	0.00177%	56,499
African / African-American	0.00176%	56,950

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.Pro2962=
Coding: c.8886C>T
MANE Select: NM_004006
dbSNP: rs371648038
Type: single nucleotide variant
Location: chrX:31478157 (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.Pro2962Thr Uncertain significance ★★ same residue
DMD p.Pro2962Leu Conflicting classifications of pathogenicity ★ 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

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-pro2962 (accessed [today's date]).

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