CLEC16A p.Thr429=
c.1287G>A · rs200082818 · VCV740046
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0033%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.37 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.46 | GERP -2.2, phastCons 0.001 |
| Overall | ||
| CADD | 9.462 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0033%
South Asian · 3/90,958 alleles
Filtering AF
0.000876%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.00137%
22/1,611,716 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0033% | 30,319 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,144 |
| African / African-American | 0.00267% | 37,395 |
| Admixed American | 0.00167% | 59,978 |
| European (non-Finnish) | 0.00119% | 84,258 |
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.Thr429=
- Coding
- c.1287G>A
- MANE Select
- NM_015226
- dbSNP
- rs200082818
- Type
- single nucleotide variant
- Location
- chr16:11003289 (GRCh38)
- Gene constraint
- LOEUF 0.639 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.17
- Residue 429
- the 'disordered' region
Similar variants
- CLEC16A p.Thr429Met Uncertain significance ★ ⚠ same residue
- 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
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-thr429 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown