Is CLEC1A p.Asp154Glu (c.462C>A) pathogenic?

CLEC1A p.Asp154Glu (c.462C>A) is classified Likely benign in CLEC1A (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-26). AlphaMissense: likely benign (0.096); Very rare (popmax 8.48e-05%, nfe).

How common is CLEC1A p.Asp154Glu (c.462C>A) in the general population?

CLEC1A p.Asp154Glu (c.462C>A) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about CLEC1A p.Asp154Glu (c.462C>A)?

AlphaMissense predicts likely benign (score 0.096) — an in-silico prediction, not a clinical call.

CLEC1A p.Asp154Glu

c.462C>A · VCV3493547

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.096 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.096	likely benign
REVEL	0.024	moderately benign-leaning
SaProt	LLR -5.71	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 -1.7	GERP -2.8
Regional constraint	o/e 1.13	unconstrained · MANE · 28 kb · p 0.014 · regional, not allelic
Overall
CADD	0.103	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 8.48e-05% European (non-Finnish) · 1/1,179,868 alleles

Overall 6.84e-05% 1/1,461,656 alleles · very rare

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: CLEC1A
Protein: p.Asp154Glu
Coding: c.462C>A
MANE Select: NM_016511
Type: single nucleotide variant
Location: chr12:10075585 (GRCh38)
Gene constraint: LOEUF 1.529 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.51
Residue 154: the c-type lectin domain

Full CLEC1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CLEC1A p.Gly26Ala Benign ★★ same type
CLEC1A p.His32Arg Likely benign ★★ same type
CLEC1A p.Ala238Asp Uncertain significance ★ same type
CLEC1A p.Ala261Val Uncertain significance ★ ⚠ same type
CLEC1A p.Arg254His Uncertain significance ★ ⚠ same type
CLEC1A p.Arg31Trp Uncertain significance ★ ⚠ same type
CLEC1A p.Arg36Trp Uncertain significance ★ ⚠ same type
CLEC1A p.Asp10Glu 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/clec1a-p-asp154glu (accessed [today's date]).

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