Is DMD p.Gln2046= (c.6138A>G) pathogenic?

DMD p.Gln2046= (c.6138A>G) is classified Likely benign in DMD (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-10-26). Very rare (popmax 0.00661%, amr); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Gln2046= (c.6138A>G)?

DMD p.Gln2046= (c.6138A>G) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Gln2046= (c.6138A>G) in the general population?

DMD p.Gln2046= (c.6138A>G) is very rare (popmax 0.00661%, amr) (gnomAD).

DMD p.Gln2046=

c.6138A>G · rs780018882 · VCV706796

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00661%, amr)

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	GERP -1.1, phastCons 0.005
Overall
CADD	1.045	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00661% Admixed American · 3/45,394 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000886%

Overall 0.000333% 4/1,201,910 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00661%	15,131
Remaining individualsnot grpmax-eligible	0.00211%	47,300

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.Gln2046=
Coding: c.6138A>G
MANE Select: NM_004006
dbSNP: rs780018882
Type: single nucleotide variant
Location: chrX:32287681 (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 p.Gln2046Ter Pathogenic/Likely 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
DMD c.10224-2A>G 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-gln2046 (accessed [today's date]).

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