Is DMD p.Leu2467= (c.7399T>C) pathogenic?

DMD p.Leu2467= (c.7399T>C) is classified Likely benign in DMD (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-27). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Leu2467= (c.7399T>C)?

DMD p.Leu2467= (c.7399T>C) is associated with Cardiovascular phenotype (ClinVar).

How common is DMD p.Leu2467= (c.7399T>C) in the general population?

DMD p.Leu2467= (c.7399T>C) is absent from gnomAD v4.1 (gnomAD).

DMD p.Leu2467=

c.7399T>C · rs2530840575 · VCV1758689

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.382	indeterminate
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 3.9	GERP 0.16, phastCons 1
Overall
CADD	7.351	PHRED · no single calibrated threshold — expert panels disagree

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.Leu2467=
Coding: c.7399T>C
MANE Select: NM_004006
dbSNP: rs2530840575
Type: single nucleotide variant
Location: chrX:31774103 (GRCh38)

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.Leu2467Ter Pathogenic ★ same residue
DMD p.Leu2467Ser Uncertain significance ★ ⚠ 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-leu2467 (accessed [today's date]).

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