CLEC4D p.Glu59=
c.177G>A · rs138087450 · VCV1285021
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.389%, sas)
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 0.35 | |
| Overall | ||
| CADD | 0.704 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.389%
South Asian · 340/87,422 alleles
Filtering AF
0.355%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.342%
Overall
0.166%
2,402/1,451,264 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.389% | 257 |
| Middle Eastern | 0.243% | 412 |
| European (non-Finnish) | 0.181% | 554 |
| Remaining individualsnot grpmax-eligible | 0.147% | 681 |
| Admixed American | 0.0854% | 1,171 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0385% | 2,598 |
| African / African-American | 0.0291% | 3,431 |
| Finnishnot grpmax-eligible | 0.0282% | 3,547 |
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
- CLEC4D
- Protein
- p.Glu59=
- Coding
- c.177G>A
- MANE Select
- NM_080387
- dbSNP
- rs138087450
- Type
- single nucleotide variant
- Location
- chr12:8518219 (GRCh38)
- Gene constraint
- LOEUF 1.613 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.58 · 2 PDB
Similar variants
- CLEC4D p.Ser32Gly Benign ★★ same type
- CLEC4D p.Ala117Ser Uncertain significance ★ ⚠ same type
- CLEC4D p.Ala126Thr Uncertain significance ★ ⚠ same type
- CLEC4D p.Ala37Glu Uncertain significance ★ ⚠ same type
- CLEC4D p.Ala90Gly Uncertain significance ★ ⚠ same type
- CLEC4D p.Arg110Ser Uncertain significance ★ ⚠ same type
- CLEC4D p.Arg138Trp Uncertain significance ★ ⚠ same type
- CLEC4D p.Arg155Cys 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/clec4d-p-glu59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown