Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.91%, 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 -10 | GERP -4.1 |
| Overall | ||
| CADD | 0.052 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.91%
African / African-American · 2,183/75,018 alleles
Filtering AF
2.81%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.77%
Overall
0.159%
2,566/1,614,066 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.91% | 34 |
| Remaining individualsnot grpmax-eligible | 0.253% | 396 |
| Admixed American | 0.227% | 441 |
| Middle Eastern | 0.132% | 758 |
| South Asian | 0.00659% | 15,179 |
| European (non-Finnish) | 0.00619% | 16,164 |
| East Asian | 0.00446% | 22,437 |
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.Ser472=
- Coding
- c.1416G>A
- MANE Select
- NM_022369
- dbSNP
- rs351241
- Type
- single nucleotide variant
- Location
- chr15:74182345 (GRCh38)
- Gene constraint
- LOEUF 0.725 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.18
Similar variants
- STRA6 p.Ser472Leu 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-ser472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown