Is DES p.Pro419Leu (c.1256C>T) pathogenic?

DES p.Pro419Leu (c.1256C>T) is classified Conflicting classifications of pathogenicity in DES (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2024-04-04). AlphaMissense: likely pathogenic (0.8313); Absent from gnomAD v4.1; Associated with myofibrillar myopathy 1.

What condition is associated with DES p.Pro419Leu (c.1256C>T)?

DES p.Pro419Leu (c.1256C>T) is associated with myofibrillar myopathy 1 (ClinVar).

How common is DES p.Pro419Leu (c.1256C>T) in the general population?

DES p.Pro419Leu (c.1256C>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.Pro419Leu (c.1256C>T)?

AlphaMissense predicts likely pathogenic (score 0.8313) — an in-silico prediction, not a clinical call.

DES p.Pro419Leu

c.1256C>T · rs796667045 · VCV287812

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.8313 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

myofibrillar myopathy 1

Computational evidence

Protein change
AlphaMissense	0.8313	likely pathogenic
REVEL	0.742	pathogenic-leaning
SaProt	LLR -13.53	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 7,524 bp · p 0.05 · regional, not allelic
Overall
CADD	28.5	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.Pro419Leu
Coding: c.1256C>T
MANE Select: NM_001927
dbSNP: rs796667045
Type: single nucleotide variant
Location: chr2:219423788 (GRCh38)
Gene constraint: LOEUF 0.81 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73
Residue 419: the 'tail' region; a UniProt-annotated variant site (in mfm1; found in a family with myofibrillar myopathy and arrhythmogenic right ventricular cardiomyopathy)

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.Pro419Ser Pathogenic/Likely pathogenic ★★ same residue
DES p.Pro419= Conflicting classifications of pathogenicity ★ same residue
DES p.Pro419Thr Uncertain significance ★ ⚠ same residue
DES p.Pro419fs Pathogenic ★★ 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

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-pro419leu (accessed [today's date]).

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