STRA6 p.Val333=
c.999C>G · VCV4925830
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
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 1.5 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 3.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,082 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0114%
Overall
0.00229%
37/1,613,102 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,041 |
| South Asian | 0.0209% | 4,776 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,940 |
| European (non-Finnish) | 0.000593% | 168,528 |
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
- STRA6
- Protein
- p.Val333=
- Coding
- c.999C>G
- MANE Select
- NM_022369
- Type
- single nucleotide variant
- Location
- chr15:74189206 (GRCh38)
- Gene constraint
- LOEUF 0.725 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.18
Similar variants
- STRA6 c.267-1G>T Pathogenic/Likely pathogenic ★★ same type
- STRA6 p.Arg532Ter Pathogenic ★★ same type
- STRA6 p.Thr644Met Pathogenic ★★ ⚠ same type
- STRA6 c.1840+4C>T Uncertain significance ★★ same type
- STRA6 c.*10A>C Uncertain significance ★★ same type
- STRA6 p.Ala54Ser Uncertain significance ★★ ⚠ same type
- STRA6 p.Ala557Thr Uncertain significance ★★ ⚠ same type
- STRA6 p.Ala557Val 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/stra6-p-val333 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown