Is DMD p.Ser1104Arg (c.3310A>C) pathogenic?

DMD p.Ser1104Arg (c.3310A>C) is classified Uncertain significance in DMD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-13). AlphaMissense: likely pathogenic (0.7835); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Ser1104Arg (c.3310A>C)?

DMD p.Ser1104Arg (c.3310A>C) is associated with Cardiovascular phenotype (ClinVar).

How common is DMD p.Ser1104Arg (c.3310A>C) in the general population?

DMD p.Ser1104Arg (c.3310A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DMD p.Ser1104Arg (c.3310A>C)?

AlphaMissense predicts likely pathogenic (score 0.7835) — an in-silico prediction, not a clinical call.

DMD p.Ser1104Arg

c.3310A>C · VCV3272381

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7835 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.7835	likely pathogenic
REVEL	0.305	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.9, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	25.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DMD
Protein: p.Ser1104Arg
Coding: c.3310A>C
MANE Select: NM_004006
Type: single nucleotide variant
Location: chrX:32463561 (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

Similar variants

DMD p.Ser1104= Likely benign ★ same residue
DMD p.Ser1104Asn Uncertain significance ★ ⚠ same residue
DMD p.Ser1104Ile Uncertain significance ★ same residue
DMD p.Ser1104Thr Uncertain significance ★ ⚠ same residue
DMD c.2804-2A>C Pathogenic/Likely pathogenic ★★ same condition
DMD c.31+1G>C Pathogenic ★★ same condition
DMD c.3432+2036A>G Pathogenic/Likely pathogenic ★★ same condition
DMD c.3433-1G>A 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-ser1104arg (accessed [today's date]).

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