STRA6 p.Thr447=
c.1341G>A · rs368073018 · VCV884903
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
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 -1.2 | GERP -4.4 |
| Overall | ||
| CADD | 7.885 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,040 alleles
Filtering AF
0.002%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00176%
Overall
0.00248%
40/1,612,350 alleles · ultra-rare
exomes 33/1,460,022 · genomes 7/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,040 |
| Admixed American | 0.00502% | 19,917 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,219 |
| European (non-Finnish) | 0.0028% | 35,734 |
| African / African-American | 0.00133% | 75,020 |
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.Thr447=
- Coding
- c.1341G>A
- MANE Select
- NM_022369
- dbSNP
- rs368073018
- Type
- single nucleotide variant
- Location
- chr15:74182420 (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 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
- STRA6 p.Arg655Cys 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-thr447 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown