Is DMD p.Arg488Ser (c.1462C>A) pathogenic?

DMD p.Arg488Ser (c.1462C>A) is classified Uncertain significance in DMD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-11-03). AlphaMissense: likely benign (0.1949); Absent from gnomAD v4.1.

How common is DMD p.Arg488Ser (c.1462C>A) in the general population?

DMD p.Arg488Ser (c.1462C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DMD p.Arg488Ser (c.1462C>A)?

AlphaMissense predicts likely benign (score 0.1949) — an in-silico prediction, not a clinical call.

DMD p.Arg488Ser

c.1462C>A · rs758932385 · VCV871127

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1949 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.1949	likely benign
REVEL	0.062	moderately 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 2.1	GERP -1, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	18.96	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DMD
Protein: p.Arg488Ser
Coding: c.1462C>A
MANE Select: NM_004006
dbSNP: rs758932385
Type: single nucleotide variant
Location: chrX:32614323 (GRCh38)

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

Similar variants

DMD p.Arg488Cys Benign/Likely benign ★★ same residue
DMD p.Arg488His Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Arg488Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Arg488= Likely benign ★ same residue
DMD c.10086+1G>A Pathogenic ★★ same type
DMD c.10086+1G>T Pathogenic ★★ same type
DMD c.10086+2T>C Pathogenic ★★ same type
DMD c.10087-2A>G Pathogenic/Likely pathogenic ★★ same type

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-arg488ser (accessed [today's date]).

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