Is DMD p.Leu1900= (c.5700A>G) pathogenic?

DMD p.Leu1900= (c.5700A>G) is classified Likely benign in DMD (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-02). Ultra-rare (popmax 0.0193%, afr); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Leu1900= (c.5700A>G)?

DMD p.Leu1900= (c.5700A>G) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Leu1900= (c.5700A>G) in the general population?

DMD p.Leu1900= (c.5700A>G) is ultra-rare (popmax 0.0193%, afr) (gnomAD).

DMD p.Leu1900=

c.5700A>G · rs374387166 · VCV696548

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0193%, afr)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 6.1	GERP 2.9, phastCons 1
Overall
CADD	9.153	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0193% African / African-American · 11/57,086 alleles

Filtering AF 0.0108% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00832%

Overall 0.00091% 11/1,209,170 alleles · ultra-rare exomes 3/1,097,608 · genomes 8/111,562 · joint denominator

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.Leu1900=
Coding: c.5700A>G
MANE Select: NM_004006
dbSNP: rs374387166
Type: single nucleotide variant
Location: chrX:32343173 (GRCh38)
Residue 1900: 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

Also linked: cardiomyopathy Becker muscular dystrophy Duchenne muscular dystrophy

Similar variants

DMD p.Leu1900Ter Pathogenic ★ same residue
DMD p.Leu1900fs Pathogenic ★★ 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-leu1900 (accessed [today's date]).

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