Is DES p.Val56Leu (c.166G>C) pathogenic?

DES p.Val56Leu (c.166G>C) is classified Conflicting classifications of pathogenicity in DES (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-01-26). AlphaMissense: likely benign (0.3375); Ultra-rare (popmax 0.0842%, afr); Associated with Cardiovascular phenotype.

What condition is associated with DES p.Val56Leu (c.166G>C)?

DES p.Val56Leu (c.166G>C) is associated with Cardiovascular phenotype, neurogenic scapuloperoneal syndrome, Kaeser type, myofibrillar myopathy 1 (ClinVar).

How common is DES p.Val56Leu (c.166G>C) in the general population?

DES p.Val56Leu (c.166G>C) is ultra-rare (popmax 0.0842%, afr) (gnomAD).

What do computational predictors say about DES p.Val56Leu (c.166G>C)?

AlphaMissense predicts likely benign (score 0.3375) — an in-silico prediction, not a clinical call.

DES p.Val56Leu

c.166G>C · rs578066781 · VCV201713

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

AlphaMissense

likely benign

0.3375 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0842%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.3375	likely benign
REVEL	0.494	indeterminate
SaProt	LLR -9.29	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP -0.85, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 7,524 bp · p 0.05 · regional, not allelic
Overall
CADD	22.2	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 0.0842% African / African-American · 63/74,810 alleles

Filtering AF 0.0675% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0615%

Overall 0.0045% 72/1,601,674 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0842%	1,187
Middle Eastern	0.0332%	3,010
Remaining individualsnot grpmax-eligible	0.00485%	20,638
Admixed American	0.0034%	29,373
European (non-Finnish)	0.00017%	587,227

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.Val56Leu
Coding: c.166G>C
MANE Select: NM_001927
dbSNP: rs578066781
Type: single nucleotide variant
Location: chr2:219418628 (GRCh38)
Gene constraint: LOEUF 0.81 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.73
Residue 56: the 'head' 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: neurogenic scapuloperoneal syndrome, Kaeser type myofibrillar myopathy 1 dilated cardiomyopathy 1I

Similar variants

DES p.Val56Glu Uncertain significance ★★ ⚠ same residue
DES p.Val56Met 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
DES p.Ala120Pro 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-val56leu (accessed [today's date]).

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