Is DMD p.Ile99= (c.297C>T) pathogenic?

DMD p.Ile99= (c.297C>T) is classified Likely benign in DMD (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-03-06). Very rare (popmax 0.00303%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Ile99= (c.297C>T)?

DMD p.Ile99= (c.297C>T) is associated with Cardiovascular phenotype, cardiomyopathy, Becker muscular dystrophy (ClinVar).

How common is DMD p.Ile99= (c.297C>T) in the general population?

DMD p.Ile99= (c.297C>T) is very rare (popmax 0.00303%, nfe) (gnomAD).

DMD p.Ile99=

c.297C>T · rs1004456825 · VCV415857

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00303%, nfe)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2	GERP -2.9, phastCons 1
Overall
CADD	8.634	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00303% European (non-Finnish) · 27/892,250 alleles

Filtering AF 0.00207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00182%

Overall 0.0024% 29/1,206,091 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00303%	33,046
East Asian	0.00297%	33,650
African / African-American	0.00176%	56,972

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.Ile99=
Coding: c.297C>T
MANE Select: NM_004006
dbSNP: rs1004456825
Type: single nucleotide variant
Location: chrX:32823355 (GRCh38)
Residue 99: the calponin-homology (ch) 1 domain; an α-helix; the 'actin-binding' 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.Ile99Thr Uncertain significance ★★ ⚠ same residue
DMD p.Ile99Val Conflicting classifications of pathogenicity ★ ⚠ 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-ile99 (accessed [today's date]).

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