CLEC16A p.Phe500=
c.1500C>T · VCV3905464
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.7 | GERP -4 |
| Overall | ||
| CADD | 2.665 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
African / African-American · 9/74,858 alleles
Filtering AF
0.00624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00468%
Overall
0.000683%
11/1,609,712 alleles · ultra-rare
exomes 8/1,457,548 · genomes 3/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.012% | 8,318 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,364 |
| South Asian | 0.00111% | 89,836 |
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
- CLEC16A
- Protein
- p.Phe500=
- Coding
- c.1500C>T
- MANE Select
- NM_015226
- Type
- single nucleotide variant
- Location
- chr16:11024884 (GRCh38)
- Gene constraint
- LOEUF 0.639 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.17
Similar variants
- CLEC16A p.Glu432= Benign/Likely benign ★★ same type
- CLEC16A p.His31= Likely benign ★★ same type
- CLEC16A p.Leu948Phe Benign ★★ same type
- CLEC16A p.Ser892Asn Likely benign ★★ same type
- CLEC16A p.Ser982Asn Likely benign ★★ same type
- CLEC16A p.Thr475Met Benign/Likely benign ★★ same type
- CLEC16A p.Ala1043Val Uncertain significance ★ ⚠ same type
- CLEC16A p.Ala347Thr 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/clec16a-p-phe500 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown