Is DMD p.Cys3319Phe (c.9956G>T) pathogenic?

DMD p.Cys3319Phe (c.9956G>T) is classified Uncertain significance in DMD (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-26). AlphaMissense: ambiguous (0.4456); Absent from gnomAD v4.1; Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Cys3319Phe (c.9956G>T)?

DMD p.Cys3319Phe (c.9956G>T) is associated with Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Cys3319Phe (c.9956G>T) in the general population?

DMD p.Cys3319Phe (c.9956G>T) is absent from gnomAD v4.1 (gnomAD).

How is Duchenne muscular dystrophy inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about DMD p.Cys3319Phe (c.9956G>T)?

AlphaMissense predicts ambiguous (score 0.4456) — an in-silico prediction, not a clinical call.

DMD p.Cys3319Phe

c.9956G>T · rs2041296375 · VCV1381253

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4456 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,206,178)

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
AlphaMissense	0.4456	ambiguous
REVEL	0.794	moderately pathogenic-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 3.4, phastCons 1
Regional constraint	o/e 0.66	unconstrained · MANE · 170 kb · p 2.6e-08 · regional, not allelic
Overall
CADD	24.6	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

No allele count reported in gnomAD v4.1 (AN 1,206,178). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DMD
Protein: p.Cys3319Phe
Coding: c.9956G>T
MANE Select: NM_004006
dbSNP: rs2041296375
Type: single nucleotide variant
Location: chrX:31182756 (GRCh38)
Residue 3319: the 'interaction with synm' region

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

Disease context

Duchenne muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Duchenne muscular dystrophy (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

DMD p.Cys3319Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Cys3319Ter Likely pathogenic ★ 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-cys3319phe (accessed [today's date]).

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