Is DMD p.Ile245Thr (c.734T>C) pathogenic?

DMD p.Ile245Thr (c.734T>C) is classified Conflicting classifications of pathogenicity in DMD (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2024-12-12). AlphaMissense: likely benign (0.098); Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with DMD p.Ile245Thr (c.734T>C)?

DMD p.Ile245Thr (c.734T>C) is associated with Cardiovascular phenotype, Duchenne muscular dystrophy (ClinVar).

How common is DMD p.Ile245Thr (c.734T>C) in the general population?

DMD p.Ile245Thr (c.734T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DMD p.Ile245Thr (c.734T>C)?

AlphaMissense predicts likely benign (score 0.098) — an in-silico prediction, not a clinical call.

DMD p.Ile245Thr

c.734T>C · rs1234861163 · VCV2170595

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.098 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.098	likely benign
REVEL	0.185	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 5.4	GERP 6, phastCons 1
Regional constraint	o/e 1.36	unconstrained · MANE · 1,863 kb · p 2.4e-62 · regional, not allelic
Overall
CADD	22.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

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.Ile245Thr
Coding: c.734T>C
MANE Select: NM_004006
dbSNP: rs1234861163
Type: single nucleotide variant
Location: chrX:32699209 (GRCh38)
Residue 245: a β-strand

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: Duchenne muscular dystrophy

Similar variants

DMD p.Ile245= Likely benign ★★ same residue
DMD p.Ile245Val Conflicting classifications of pathogenicity ★ ⚠ same residue
DMD p.Ile245fs 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

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-ile245thr (accessed [today's date]).

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