CLEC19A p.Ser77=
c.231C>T · rs181126361 · VCV715677
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.5%, afr)
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 -10 | GERP -2.9 |
| Overall | ||
| CADD | 4.733 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.5%
African / African-American · 1,100/73,158 alleles
Filtering AF
1.43%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4%
Overall
0.0847%
1,314/1,550,470 alleles · low-frequency
exomes 691/1,398,196 · genomes 623/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.5% | 67 |
| Middle Eastern | 0.2% | 500 |
| Remaining individualsnot grpmax-eligible | 0.158% | 633 |
| Admixed American | 0.149% | 671 |
| East Asian | 0.0122% | 8,182 |
| South Asian | 0.00952% | 10,504 |
| European (non-Finnish) | 0.00157% | 63,718 |
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
- CLEC19A
- Protein
- p.Ser77=
- Coding
- c.231C>T
- MANE Select
- NM_001256720
- dbSNP
- rs181126361
- Type
- single nucleotide variant
- Location
- chr16:19298815 (GRCh38)
- Gene constraint
- LOEUF 1.155 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.51
- Residue 77
- the c-type lectin domain
Similar variants
- CLEC19A p.Asp106= Likely benign ★ 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/clec19a-p-ser77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown