Is DMD p.Ser1007= (c.3021G>A) pathogenic?

DMD p.Ser1007= (c.3021G>A) is classified Benign/Likely benign in DMD (ClinVar, Multiple submitters, 16 submitters; last evaluated 2026-02-04). Low-frequency (popmax 2.12%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Ser1007= (c.3021G>A)?

DMD p.Ser1007= (c.3021G>A) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Ser1007= (c.3021G>A) in the general population?

DMD p.Ser1007= (c.3021G>A) is low-frequency (popmax 2.12%, nfe) (gnomAD).

DMD p.Ser1007=

c.3021G>A · rs1800268 · VCV94548

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 16 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.12%, nfe)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.1	GERP -4.3, phastCons 0.002
Overall
CADD	0.626	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.12% European (non-Finnish) · 19,008/894,886 alleles

Filtering AF 2.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.09%

Overall 1.76% 21,316/1,209,308 alleles · low-frequency exomes 19,962/1,097,794 · genomes 1,354/111,514 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	2.12%	47
Remaining individualsnot grpmax-eligible	1.53%	65
Middle Eastern	1.38%	72
Admixed American	1.14%	87
South Asian	1.08%	92
Finnishnot grpmax-eligible	0.35%	285
African / African-American	0.302%	331
Ashkenazi Jewishnot grpmax-eligible	0.209%	479
East Asian	0.00593%	16,862

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.Ser1007=
Coding: c.3021G>A
MANE Select: NM_004006
dbSNP: rs1800268
Type: single nucleotide variant
Location: chrX:32468639 (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 dilated cardiomyopathy 3B Duchenne muscular dystrophy

Similar variants

DMD p.Ser1007Leu Benign/Likely benign ★★ same residue
DMD p.Ser1007Ter 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
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-ser1007 (accessed [today's date]).

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