Is DMD p.Arg1957Trp (c.5869C>T) pathogenic?

DMD p.Arg1957Trp (c.5869C>T) is classified Conflicting classifications of pathogenicity in DMD (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-01-13). AlphaMissense: likely benign (0.1353); Very rare (popmax 0.00439%, amr); Associated with Duchenne muscular dystrophy.

What condition is associated with DMD p.Arg1957Trp (c.5869C>T)?

DMD p.Arg1957Trp (c.5869C>T) is associated with Duchenne muscular dystrophy, Becker muscular dystrophy, dilated cardiomyopathy 3B (ClinVar).

How common is DMD p.Arg1957Trp (c.5869C>T) in the general population?

DMD p.Arg1957Trp (c.5869C>T) is very rare (popmax 0.00439%, amr) (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.Arg1957Trp (c.5869C>T)?

AlphaMissense predicts likely benign (score 0.1353) — an in-silico prediction, not a clinical call.

DMD p.Arg1957Trp

c.5869C>T · rs755477994 · VCV201753

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.1353 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00439%, amr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Conditions

Duchenne muscular dystrophy

Computational evidence

Protein change
AlphaMissense	0.1353	likely benign
REVEL	0.212	benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.3	GERP 0.41, 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 0.00439% Admixed American · 2/45,567 alleles

Filtering AF 0.000728% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000272%

Overall 0.00119% 13/1,096,139 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00439%	22,784
South Asian	0.00353%	28,338
African / African-American	0.00351%	28,510
East Asian	0.00297%	33,678
European (non-Finnish)	0.000671%	148,943

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.Arg1957Trp
Coding: c.5869C>T
MANE Select: NM_004006
dbSNP: rs755477994
Type: single nucleotide variant
Location: chrX:32342153 (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.Arg1957= Likely benign ★★ same residue
DMD p.Arg1957Gln 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
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-arg1957trp (accessed [today's date]).

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