Is DMD p.Ser800Arg (c.2400C>A) pathogenic?

DMD p.Ser800Arg (c.2400C>A) is classified Uncertain significance in DMD (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-27). AlphaMissense: likely pathogenic (0.5854); Ultra-rare (popmax 0.0231%, mid); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Ser800Arg (c.2400C>A)?

DMD p.Ser800Arg (c.2400C>A) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Ser800Arg (c.2400C>A) in the general population?

DMD p.Ser800Arg (c.2400C>A) is ultra-rare (popmax 0.0231%, mid) (gnomAD).

What do computational predictors say about DMD p.Ser800Arg (c.2400C>A)?

AlphaMissense predicts likely pathogenic (score 0.5854) — an in-silico prediction, not a clinical call.

DMD p.Ser800Arg

c.2400C>A · rs142115986 · VCV1001786

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely pathogenic

0.5854 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0231%, mid)

Missense predictors

1/2 damaging

AlphaMissense, REVEL

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.5854	likely pathogenic
REVEL	0.026	moderately benign-leaning
⇒ AlphaMissense calls this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP -1.4, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	17.65	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 0.0231% Middle Eastern · 1/4,336 alleles

Overall 0.000331% 4/1,208,133 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0231%	4,336
Remaining individualsnot grpmax-eligible	0.0021%	47,524
South Asian	0.00177%	56,651
African / African-American	0.00175%	57,151

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.Ser800Arg
Coding: c.2400C>A
MANE Select: NM_004006
dbSNP: rs142115986
Type: single nucleotide variant
Location: chrX:32491499 (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.Ser800Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Ser800Gly Uncertain significance ★ ⚠ same residue
DMD p.Ser800= Likely benign ★ 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

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-ser800arg (accessed [today's date]).

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