Is DMD p.Lys2906= (c.8718G>A) pathogenic?

DMD p.Lys2906= (c.8718G>A) is classified Likely benign in DMD (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-08-02). Very rare (popmax 0.00804%, nfe); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Lys2906= (c.8718G>A)?

DMD p.Lys2906= (c.8718G>A) is associated with Duchenne muscular dystrophy, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Lys2906= (c.8718G>A) in the general population?

DMD p.Lys2906= (c.8718G>A) is very rare (popmax 0.00804%, nfe) (gnomAD).

How is Duchenne muscular dystrophy inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DMD p.Lys2906=

c.8718G>A · rs377178242 · VCV455940

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00804%, nfe)

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.265	benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.007	GERP -2, phastCons 0.76
Overall
CADD	4.299	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00804% European (non-Finnish) · 72/895,286 alleles

Filtering AF 0.00652% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00599%

Overall 0.0062% 75/1,209,702 alleles · very rare exomes 70/1,098,203 · genomes 5/111,499 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00804%	12,435
African / African-American	0.0035%	28,537
Finnishnot grpmax-eligible	0.00215%	46,456

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.Lys2906=
Coding: c.8718G>A
MANE Select: NM_004006
dbSNP: rs377178242
Type: single nucleotide variant
Location: chrX:31478325 (GRCh38)

Full DMD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Duchenne muscular dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cardiomyopathy Becker muscular dystrophy

For Duchenne muscular dystrophy (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood
Prevalence: 1-9 / 100 000 (Worldwide)

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-lys2906 (accessed [today's date]).

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