Is DMD p.Leu2626Ser (c.7877T>C) pathogenic?

DMD p.Leu2626Ser (c.7877T>C) is classified Benign/Likely benign in DMD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-08). AlphaMissense: ambiguous (0.5632); Ultra-rare (popmax 0.0299%, sas); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Leu2626Ser (c.7877T>C)?

DMD p.Leu2626Ser (c.7877T>C) is associated with Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Leu2626Ser (c.7877T>C) in the general population?

DMD p.Leu2626Ser (c.7877T>C) is ultra-rare (popmax 0.0299%, sas) (gnomAD).

How is Duchenne muscular dystrophy inherited?

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

What do computational predictors say about DMD p.Leu2626Ser (c.7877T>C)?

AlphaMissense predicts ambiguous (score 0.5632) — an in-silico prediction, not a clinical call.

DMD p.Leu2626Ser

c.7877T>C · rs775555418 · VCV2163352

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.5632 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0299%, sas)

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
AlphaMissense	0.5632	ambiguous
REVEL	0.399	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.2	GERP 2.5, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	25.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0299% South Asian · 17/56,831 alleles

Filtering AF 0.0191% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0156%

Overall 0.00149% 18/1,209,702 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0299%	3,343
Middle Eastern	0.0229%	4,374

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.Leu2626Ser
Coding: c.7877T>C
MANE Select: NM_004006
dbSNP: rs775555418
Type: single nucleotide variant
Location: chrX:31658140 (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

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-leu2626ser (accessed [today's date]).

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