STRA6 p.Thr321=
c.963T>C · rs144062660 · VCV719878
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0655%, afr)
Conditions
1
microphthalmia, syndromic 9
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 0.063 | GERP -3.9 |
| Overall | ||
| CADD | 5.093 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0655%
African / African-American · 49/74,842 alleles
Filtering AF
0.0508%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0456%
Overall
0.00479%
77/1,607,720 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0655% | 1,527 |
| Admixed American | 0.0407% | 2,458 |
| Remaining individualsnot grpmax-eligible | 0.00642% | 15,568 |
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.Thr321=
- Coding
- c.963T>C
- MANE Select
- NM_022369
- dbSNP
- rs144062660
- Type
- single nucleotide variant
- Location
- chr15:74189242 (GRCh38)
- Gene constraint
- LOEUF 0.725 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.18
- Residue 321
- a UniProt-annotated variant site (in mcops9)
Similar variants
- STRA6 p.Thr321Pro Uncertain significance ★★ ⚠ same residue
- STRA6 c.267-1G>T Pathogenic/Likely pathogenic ★★ same condition
- STRA6 p.Arg532Ter Pathogenic ★★ same condition
- STRA6 p.Thr644Met Pathogenic ★★ ⚠ same condition
- STRA6 c.*10A>C Uncertain significance ★★ same condition
- STRA6 p.Ala54Ser Uncertain significance ★★ ⚠ same condition
- STRA6 p.Ala557Val Uncertain significance ★★ ⚠ same condition
- STRA6 p.Arg467Cys Uncertain significance ★★ ⚠ same condition
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-thr321 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown