Is DMD p.Arg1955Cys (c.5863C>T) pathogenic?

DMD p.Arg1955Cys (c.5863C>T) is classified Conflicting classifications of pathogenicity in DMD (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2025-06-22). AlphaMissense: likely pathogenic (0.7387); Very rare (popmax 0.00351%, afr); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Arg1955Cys (c.5863C>T)?

DMD p.Arg1955Cys (c.5863C>T) is associated with Duchenne muscular dystrophy, Becker muscular dystrophy, dilated cardiomyopathy 3B (ClinVar).

How common is DMD p.Arg1955Cys (c.5863C>T) in the general population?

DMD p.Arg1955Cys (c.5863C>T) is very rare (popmax 0.00351%, afr) (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.Arg1955Cys (c.5863C>T)?

AlphaMissense predicts likely pathogenic (score 0.7387) — an in-silico prediction, not a clinical call.

DMD p.Arg1955Cys

c.5863C>T · rs377039314 · VCV1176295

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely pathogenic

0.7387 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00351%, afr)

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
AlphaMissense	0.7387	likely pathogenic
REVEL	0.335	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.8, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	29.9	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 0.00351% African / African-American · 2/57,056 alleles

Filtering AF 0.000811% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000625%

Overall 0.00132% 16/1,207,947 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00351%	28,528
South Asian	0.00176%	56,738
European (non-Finnish)	0.00145%	68,755

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.Arg1955Cys
Coding: c.5863C>T
MANE Select: NM_004006
dbSNP: rs377039314
Type: single nucleotide variant
Location: chrX:32342159 (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: Becker muscular dystrophy dilated cardiomyopathy 3B

For Duchenne muscular dystrophy (Orphanet):

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

Similar variants

DMD p.Arg1955His Uncertain significance ★★ ⚠ same residue
DMD p.Arg1955fs 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-arg1955cys (accessed [today's date]).

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