STRA6 p.Asp612=
c.1836C>T · rs142048815 · VCV317098
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.93%, 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 -0.6 | GERP -2, phastCons 0.074 |
| Overall | ||
| CADD | 4.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.93%
African / African-American · 1,442/74,822 alleles
Filtering AF
1.84%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.81%
Overall
0.133%
2,128/1,604,706 alleles · low-frequency
exomes 1,277/1,452,504 · genomes 851/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.93% | 52 |
| Middle Eastern | 0.366% | 273 |
| Ashkenazi Jewishnot grpmax-eligible | 0.279% | 359 |
| Remaining individualsnot grpmax-eligible | 0.244% | 411 |
| Admixed American | 0.201% | 497 |
| European (non-Finnish) | 0.0259% | 3,857 |
| East Asian | 0.0112% | 8,918 |
| South Asian | 0.0022% | 45,415 |
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.Asp612=
- Coding
- c.1836C>T
- MANE Select
- NM_022369
- dbSNP
- rs142048815
- Type
- single nucleotide variant
- Location
- chr15:74180786 (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-asp612 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown