Is CLEC17A p.Val232Leu (c.694G>T) pathogenic?

CLEC17A p.Val232Leu (c.694G>T) is classified Uncertain significance in CLEC17A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-13). AlphaMissense: likely benign (0.1148); Absent from gnomAD v4.1.

How common is CLEC17A p.Val232Leu (c.694G>T) in the general population?

CLEC17A p.Val232Leu (c.694G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CLEC17A p.Val232Leu (c.694G>T)?

AlphaMissense predicts likely benign (score 0.1148) — an in-silico prediction, not a clinical call.

CLEC17A p.Val232Leu

c.694G>T · VCV4003511

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1148 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1148	likely benign
REVEL	0.052	moderately benign-leaning
SaProt	LLR -3.84	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.7	GERP -3
Regional constraint	o/e 0.90	unconstrained · MANE · 27 kb · p 0.03 · regional, not allelic
Overall
CADD	0.113	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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: CLEC17A
Protein: p.Val232Leu
Coding: c.694G>T
MANE Select: NM_001204118
Type: single nucleotide variant
Location: chr19:14599764 (GRCh38)
Gene constraint: LOEUF 0.776 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 71.08

Full CLEC17A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CLEC17A p.Arg158Met Uncertain significance ★ ⚠ same type
CLEC17A p.Arg250Cys Uncertain significance ★ ⚠ same type
CLEC17A p.Arg250His Uncertain significance ★ ⚠ same type
CLEC17A p.Arg250Pro Uncertain significance ★ ⚠ same type
CLEC17A p.Asn137Lys Uncertain significance ★ ⚠ same type
CLEC17A p.Asn3Asp Uncertain significance ★ ⚠ same type
CLEC17A p.Asp123Gly Uncertain significance ★ ⚠ same type
CLEC17A p.Asp228Asn Uncertain significance ★ ⚠ same type

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/clec17a-p-val232leu (accessed [today's date]).

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