Is DMD p.Ser2102Phe (c.6305C>T) pathogenic?

DMD p.Ser2102Phe (c.6305C>T) is classified Uncertain significance in DMD (ClinVar, Single submitter, 2 submitters; last evaluated 2022-01-19). AlphaMissense: ambiguous (0.468); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Ser2102Phe (c.6305C>T)?

DMD p.Ser2102Phe (c.6305C>T) is associated with Cardiovascular phenotype (ClinVar).

How common is DMD p.Ser2102Phe (c.6305C>T) in the general population?

DMD p.Ser2102Phe (c.6305C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DMD p.Ser2102Phe (c.6305C>T)?

AlphaMissense predicts ambiguous (score 0.468) — an in-silico prediction, not a clinical call.

DMD p.Ser2102Phe

c.6305C>T · rs2097114904 · VCV1752750

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.468 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.468	ambiguous
REVEL	0.087	moderately benign-leaning
SaProt	—	not scored · why
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 8.4	GERP 1.6, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	23.5	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.Ser2102Phe
Coding: c.6305C>T
MANE Select: NM_004006
dbSNP: rs2097114904
Type: single nucleotide variant
Location: chrX:32217049 (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.Ser2102Cys 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
DMD c.357+1G>T Pathogenic ★★ same condition
DMD c.9974+1G>A Pathogenic/Likely pathogenic ★★ same condition
DMD p.Arg3034Ter 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-ser2102phe (accessed [today's date]).

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