Is CLECL1 n.52A>G pathogenic?

CLECL1 n.52A>G is classified Uncertain significance in CLECL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-30). AlphaMissense: likely benign (0.103); Absent from gnomAD v4.1.

How common is CLECL1 n.52A>G in the general population?

CLECL1 n.52A>G is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CLECL1 n.52A>G?

AlphaMissense predicts likely benign (score 0.103) — an in-silico prediction, not a clinical call.

CLECL1 n.52A>G

VCV3493619

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.103 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.103	likely benign
REVEL	0.016	strongly benign-leaning
SaProt	LLR -5.80	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 -0.7	GERP -0.37
Non-coding constraint	Z 0.70	1 kb window · o/e 0.93 · regional · uncalibrated
Overall
CADD	3.61	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: CLECL1
Non-coding: n.52A>G
Type: single nucleotide variant
Location: chr12:9733245 (GRCh38)
Structure: AlphaFold pLDDT 53.91

Full CLECL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CLECL1 c.4-35C>A Uncertain significance ★ ⚠ same type
CLECL1 c.-27G>A Uncertain significance ★ ⚠ same type
CLECL1 c.-5G>C Uncertain significance ★ ⚠ same type
CLECL1 n.231T>C Uncertain significance ★ ⚠ same type
CLECL1 n.303G>A Uncertain significance ★ ⚠ same type
CLECL1 n.307G>A Uncertain significance ★ ⚠ same type
CLECL1 n.373A>C Uncertain significance ★ ⚠ same type
CLECL1 p.Ala8Val 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/clecl1-n-52a-g (accessed [today's date]).

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