Is DES p.Asp312Ala (c.935A>C) pathogenic?

DES p.Asp312Ala (c.935A>C) is classified Conflicting classifications of pathogenicity in DES (ClinVar, Conflicting submitters, 12 submitters; last evaluated 2026-02-24). AlphaMissense: ambiguous (0.5354); Rare (popmax 0.311%, afr); Associated with Cardiovascular phenotype.

What condition is associated with DES p.Asp312Ala (c.935A>C)?

DES p.Asp312Ala (c.935A>C) is associated with Cardiovascular phenotype, myofibrillar myopathy 1 (ClinVar).

How common is DES p.Asp312Ala (c.935A>C) in the general population?

DES p.Asp312Ala (c.935A>C) is rare (popmax 0.311%, afr) (gnomAD).

What do computational predictors say about DES p.Asp312Ala (c.935A>C)?

AlphaMissense predicts ambiguous (score 0.5354) — an in-silico prediction, not a clinical call.

DES p.Asp312Ala

c.935A>C · rs148947510 · VCV44275

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 12 submitters

AlphaMissense

ambiguous

0.5354 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.311%, afr)

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.5354	ambiguous
REVEL	0.721	pathogenic-leaning
SaProt	LLR -11.72	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 7,524 bp · p 0.05 · regional, not allelic
Overall
CADD	29.2	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

Grpmax group 0.311% African / African-American · 233/74,956 alleles

Filtering AF 0.278% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.265%

Overall 0.0208% 336/1,613,674 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.311%	322
Middle Eastern	0.0495%	2,021
Remaining individualsnot grpmax-eligible	0.0336%	2,976
Admixed American	0.03%	3,332
South Asian	0.00879%	11,382
European (non-Finnish)	0.00441%	22,692
East Asian	0.00223%	44,844

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: DES
Protein: p.Asp312Ala
Coding: c.935A>C
MANE Select: NM_001927
dbSNP: rs148947510
Type: single nucleotide variant
Location: chr2:219420865 (GRCh38)
Gene constraint: LOEUF 0.81 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73
Residue 312: the 'coil 2b' region; the if rod domain; the 'interaction with neb' region

Full DES 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: myofibrillar myopathy 1

Similar variants

DES p.Asp312= Likely benign ★★ same residue
DES p.Asp312Asn Conflicting classifications of pathogenicity ★ same residue
DES p.Asp312Glu 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-asp312ala (accessed [today's date]).

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