Is DES p.Thr442Ile (c.1325C>T) pathogenic?

DES p.Thr442Ile (c.1325C>T) is classified Pathogenic in DES (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-04-01). AlphaMissense: ambiguous (0.4558); Absent from gnomAD v4.1; Associated with myofibrillar myopathy 1.

What condition is associated with DES p.Thr442Ile (c.1325C>T)?

DES p.Thr442Ile (c.1325C>T) is associated with myofibrillar myopathy 1 (ClinVar).

How common is DES p.Thr442Ile (c.1325C>T) in the general population?

DES p.Thr442Ile (c.1325C>T) is absent from gnomAD v4.1 (gnomAD).

How is Desminopathy inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about DES p.Thr442Ile (c.1325C>T)?

AlphaMissense predicts ambiguous (score 0.4558) — an in-silico prediction, not a clinical call.

DES p.Thr442Ile

c.1325C>T · rs121913005 · VCV16834

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

ambiguous

0.4558 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

myofibrillar myopathy 1

Computational evidence

Protein change
AlphaMissense	0.4558	ambiguous
REVEL	0.77	pathogenic-leaning
SaProt	LLR -9.53	tolerated
⇒ REVEL calls this damaging; SaProt does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP -2.1, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 7,524 bp · p 0.05 · regional, not allelic
Overall
CADD	25.0	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: DES
Protein: p.Thr442Ile
Coding: c.1325C>T
MANE Select: NM_001927
dbSNP: rs121913005
Type: single nucleotide variant
Location: chr2:219425699 (GRCh38)
Gene constraint: LOEUF 0.81 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73
Residue 442: the 'tail' region; the 'interaction with cryab' region; a UniProt-annotated variant site (in mfm1; reveals a severe disturbance of filament-formation competence and filament-filament interactions)

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

Disease context

myofibrillar myopathy 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Desminopathy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy

Similar variants

DES p.Thr442Asn Uncertain significance ★★ ⚠ same residue
DES p.Thr442Pro Uncertain significance ★ ⚠ same residue
DES p.Thr442Ala Uncertain significance ★ ⚠ same residue
DES c.1289-2A>G Pathogenic/Likely pathogenic ★★ same condition
DES c.579-2A>C Likely pathogenic ★★ same condition
DES c.735+1G>A Pathogenic/Likely pathogenic ★★ same condition
DES c.735+1G>C Pathogenic/Likely pathogenic ★★ same condition
DES c.735+3A>G 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/des-p-thr442ile (accessed [today's date]).

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