CLEC2B p.Ala68=
c.204C>T · VCV4654287
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0318%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.14 | GERP -4.2 |
| Overall | ||
| CADD | 5.649 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0318%
Admixed American · 19/59,746 alleles
Filtering AF
0.0208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0172%
Overall
0.00255%
41/1,609,600 alleles · ultra-rare
exomes 34/1,457,718 · genomes 7/151,882 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0318% | 3,145 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,152 |
| African / African-American | 0.00268% | 37,372 |
| East Asian | 0.00224% | 44,738 |
| European (non-Finnish) | 0.00144% | 69,219 |
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
- CLEC2B
- Protein
- p.Ala68=
- Coding
- c.204C>T
- MANE Select
- NM_005127
- Type
- single nucleotide variant
- Location
- chr12:9857507 (GRCh38)
- Gene constraint
- LOEUF 1.404 · pLI 0.52 (gnomAD)
- Structure
- AlphaFold pLDDT 92.25
- Residue 68
- the c-type lectin domain
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-ala68 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown