Is DMD p.Leu3038Val (c.9112C>G) pathogenic?

DMD p.Leu3038Val (c.9112C>G) is classified Uncertain significance in DMD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-12). AlphaMissense: ambiguous (0.5243); Absent from gnomAD v4.1.

How common is DMD p.Leu3038Val (c.9112C>G) in the general population?

DMD p.Leu3038Val (c.9112C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DMD p.Leu3038Val (c.9112C>G)?

AlphaMissense predicts ambiguous (score 0.5243) — an in-silico prediction, not a clinical call.

DMD p.Leu3038Val

c.9112C>G · VCV4536808

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5243 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.5243	ambiguous
REVEL	0.72	pathogenic-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.7	GERP 1.7, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	24.8	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

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.Leu3038Val
Coding: c.9112C>G
MANE Select: NM_004006
Type: single nucleotide variant
Location: chrX:31348607 (GRCh38)

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

Similar variants

DMD p.Leu3038Gln Uncertain significance ★ ⚠ same residue
DMD p.Leu3038= 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
DMD c.10223+1G>A Pathogenic ★★ same type
DMD c.10223+1G>C 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-leu3038val (accessed [today's date]).

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