Is DMD p.Thr279= (c.837G>T) pathogenic?

DMD p.Thr279= (c.837G>T) is classified Likely benign in DMD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-20). Ultra-rare (popmax 0.0129%, sas); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Thr279= (c.837G>T)?

DMD p.Thr279= (c.837G>T) is associated with Cardiovascular phenotype, Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Thr279= (c.837G>T) in the general population?

DMD p.Thr279= (c.837G>T) is ultra-rare (popmax 0.0129%, sas) (gnomAD).

DMD p.Thr279=

c.837G>T · rs1800265 · VCV1152827

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0129%, sas)

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 -0.93	GERP -4, phastCons 0.002
Overall
CADD	0.868	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0129% South Asian · 7/54,289 alleles

Filtering AF 0.00604% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00423%

Overall 0.000757% 9/1,189,035 alleles · ultra-rare exomes 8/1,080,504 · genomes 1/108,531 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0129%	7,756
European (non-Finnish)	0.000226%	442,601

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.Thr279=
Coding: c.837G>T
MANE Select: NM_004006
dbSNP: rs1800265
Type: single nucleotide variant
Location: chrX:32697993 (GRCh38)
Residue 279: a UniProt-annotated variant site (in cmd3b)

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.Thr279Met Uncertain significance ★★ ⚠ same residue
DMD p.Thr279Ala Uncertain significance ★ 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-thr279 (accessed [today's date]).

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