Is DMD p.Tyr301= (c.903C>T) pathogenic?

DMD p.Tyr301= (c.903C>T) is classified Likely benign in DMD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-11-15). Very rare (popmax 0.000224%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Tyr301= (c.903C>T)?

DMD p.Tyr301= (c.903C>T) is associated with Cardiovascular phenotype, Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Tyr301= (c.903C>T) in the general population?

DMD p.Tyr301= (c.903C>T) is very rare (popmax 0.000224%, nfe) (gnomAD).

DMD p.Tyr301=

c.903C>T · rs2147581521 · VCV1541844

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000224%, nfe)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.9	GERP -1.3, phastCons 1
Overall
CADD	5.985	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000224% European (non-Finnish) · 2/894,188 alleles

Filtering AF 3.7e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.4e-05%

Overall 0.000165% 2/1,209,010 alleles · very rare exomes 2/1,096,033 · genomes 0/112,977 · joint denominator

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.Tyr301=
Coding: c.903C>T
MANE Select: NM_004006
dbSNP: rs2147581521
Type: single nucleotide variant
Location: chrX:32697927 (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: Duchenne muscular dystrophy

Similar variants

DMD p.Tyr301Cys Uncertain significance ★★ ⚠ same residue
DMD p.Tyr301Ter Pathogenic ★ same residue
DMD p.Tyr301His Uncertain significance ★ same residue
DMD p.Tyr301Ser Uncertain significance ★ same residue
DMD p.Tyr301fs 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

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-tyr301 (accessed [today's date]).

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