Is DMD p.His3076= (c.9228C>T) pathogenic?

DMD p.His3076= (c.9228C>T) is classified Likely benign in DMD (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-03-25). Ultra-rare (popmax 0.0148%, eas); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.His3076= (c.9228C>T)?

DMD p.His3076= (c.9228C>T) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.His3076= (c.9228C>T) in the general population?

DMD p.His3076= (c.9228C>T) is ultra-rare (popmax 0.0148%, eas) (gnomAD).

DMD p.His3076=

c.9228C>T · rs761925260 · VCV1117445

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0148%, eas)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.26 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.35	GERP -3.4, phastCons 0.005
Overall
CADD	1.468	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0148% East Asian · 5/33,761 alleles

Filtering AF 0.00581% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00373%

Overall 0.000662% 8/1,207,609 alleles · ultra-rare exomes 6/1,096,149 · genomes 2/111,460 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0148%	6,752
African / African-American	0.00351%	28,498
European (non-Finnish)	0.000112%	893,599

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.His3076=
Coding: c.9228C>T
MANE Select: NM_004006
dbSNP: rs761925260
Type: single nucleotide variant
Location: chrX:31261013 (GRCh38)
Residue 3076: a turn; the ww domain; the 'interaction with synm' region

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 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
DMD c.10224-2A>G Likely pathogenic ★★ same condition
DMD c.10554-2A>G Pathogenic/Likely 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-his3076 (accessed [today's date]).

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