Is CLEC2B p.Ser120Asn (c.359G>A) pathogenic?

CLEC2B p.Ser120Asn (c.359G>A) is classified Likely benign in CLEC2B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-15). AlphaMissense: likely benign (0.102); Absent from gnomAD v4.1.

How common is CLEC2B p.Ser120Asn (c.359G>A) in the general population?

CLEC2B p.Ser120Asn (c.359G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CLEC2B p.Ser120Asn (c.359G>A)?

AlphaMissense predicts likely benign (score 0.102) — an in-silico prediction, not a clinical call.

CLEC2B p.Ser120Asn

c.359G>A · rs2497561573 · VCV2485001

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.102 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.102	likely benign
REVEL	0.005	strongly benign-leaning
SaProt	LLR -5.45	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 -6.4	GERP -3.5
Regional constraint	o/e 0.91	unconstrained · MANE · 9,268 bp · p 0.23 · regional, not allelic
Overall
CADD	0.015	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

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: CLEC2B
Protein: p.Ser120Asn
Coding: c.359G>A
MANE Select: NM_005127
dbSNP: rs2497561573
Type: single nucleotide variant
Location: chr12:9853391 (GRCh38)
Gene constraint: LOEUF 1.404 · pLI 0.52 (gnomAD)
Structure: AlphaFold pLDDT 92.25
Residue 120: the c-type lectin domain; a disulfide bond

Full CLEC2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CLEC2B p.Arg145Lys Uncertain significance ★ ⚠ same type
CLEC2B p.Arg147Gly Uncertain significance ★ ⚠ same type
CLEC2B p.Arg84Trp Uncertain significance ★ ⚠ same type
CLEC2B p.Asn100Lys Uncertain significance ★ ⚠ same type
CLEC2B p.Asn44Lys Uncertain significance ★ ⚠ same type
CLEC2B p.Cys123Tyr Uncertain significance ★ ⚠ same type
CLEC2B p.Glu53Gly Uncertain significance ★ ⚠ same type
CLEC2B p.Glu53Val 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/clec2b-p-ser120asn (accessed [today's date]).

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