CLEC19A p.Asp106=
c.318C>T · rs1340826696 · VCV740596
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, mid)
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 · C>G here scores Δ0.31 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.19 | phastCons 0.32 |
| Overall | ||
| CADD | 12.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
Middle Eastern · 2/6,014 alleles
Filtering AF
0.00586%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00244%
Overall
0.00258%
40/1,550,476 alleles · ultra-rare
exomes 36/1,398,298 · genomes 4/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0333% | 3,007 |
| Finnishnot grpmax-eligible | 0.0085% | 11,758 |
| African / African-American | 0.00274% | 36,521 |
| European (non-Finnish) | 0.00262% | 38,232 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,108 |
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.Asp106=
- Coding
- c.318C>T
- MANE Select
- NM_001256720
- dbSNP
- rs1340826696
- Type
- single nucleotide variant
- Location
- chr16:19304125 (GRCh38)
- Gene constraint
- LOEUF 1.155 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.51
- Residue 106
- the c-type lectin domain
Similar variants
- CLEC19A p.Ser77= 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-asp106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown