Is DMD p.Val1545Ile (c.4633G>A) pathogenic?

DMD p.Val1545Ile (c.4633G>A) is classified Uncertain significance in DMD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-05-27). AlphaMissense: likely benign (0.112); Very rare (popmax 0.000112%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Val1545Ile (c.4633G>A)?

DMD p.Val1545Ile (c.4633G>A) is associated with Cardiovascular phenotype (ClinVar).

How common is DMD p.Val1545Ile (c.4633G>A) in the general population?

DMD p.Val1545Ile (c.4633G>A) is very rare (popmax 0.000112%, nfe) (gnomAD).

What do computational predictors say about DMD p.Val1545Ile (c.4633G>A)?

AlphaMissense predicts likely benign (score 0.112) — an in-silico prediction, not a clinical call.

DMD p.Val1545Ile

c.4633G>A · rs2523041067 · VCV1742055

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.112 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000112%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.112	likely benign
REVEL	0.028	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.085	GERP -4, phastCons 0.65
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	13.3	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 is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000112% European (non-Finnish) · 1/893,967 alleles

Overall 9.12e-05% 1/1,096,727 alleles · very rare

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.Val1545Ile
Coding: c.4633G>A
MANE Select: NM_004006
dbSNP: rs2523041067
Type: single nucleotide variant
Location: chrX:32386351 (GRCh38)
Residue 1545: the 'interaction with synm' region

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

Similar variants

DMD p.Val1545Ala Uncertain significance ★★ ⚠ same residue
DMD p.Val1545= Likely benign ★ same residue
DMD c.2804-2A>C Pathogenic/Likely pathogenic ★★ same condition
DMD c.31+1G>C Pathogenic ★★ same condition
DMD c.3432+2036A>G Pathogenic/Likely pathogenic ★★ same condition
DMD c.3433-1G>A Pathogenic ★★ same condition
DMD c.357+1G>T Pathogenic ★★ same condition
DMD c.9974+1G>A 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-val1545ile (accessed [today's date]).

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