Is DMD p.Thr2532= (c.7596C>T) pathogenic?

DMD p.Thr2532= (c.7596C>T) is classified Benign/Likely benign in DMD (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-12-08). Ultra-rare (popmax 0.0207%, eas); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Thr2532= (c.7596C>T)?

DMD p.Thr2532= (c.7596C>T) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Thr2532= (c.7596C>T) in the general population?

DMD p.Thr2532= (c.7596C>T) is ultra-rare (popmax 0.0207%, eas) (gnomAD).

DMD p.Thr2532=

c.7596C>T · rs778412539 · VCV227310

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0207%, eas)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.139	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP 0.33, phastCons 1
Overall
CADD	7.044	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0207% East Asian · 7/33,743 alleles

Filtering AF 0.00968% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00713%

Overall 0.0086% 104/1,209,578 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0207%	4,820
Remaining individualsnot grpmax-eligible	0.0147%	6,798
European (non-Finnish)	0.00938%	10,656
Finnishnot grpmax-eligible	0.0086%	11,632
African / African-American	0.00351%	28,505

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.Thr2532=
Coding: c.7596C>T
MANE Select: NM_004006
dbSNP: rs778412539
Type: single nucleotide variant
Location: chrX:31729695 (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: 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-thr2532 (accessed [today's date]).

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