SPATA7 p.Pro129=
c.387G>A · rs199727517 · VCV314781
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.19 | GERP -3.9 |
| Overall | ||
| CADD | 3.263 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Ashkenazi Jewishnot grpmax-eligible | 0.243% | 411 |
| Admixed Americangrpmax | 0.0484% | 2,066 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,083 |
| European (non-Finnish) | 0.0207% | 4,834 |
| South Asian | 0.0187% | 5,356 |
| African / African-American | 0.0173% | 5,770 |
Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- SPATA7
- Protein
- p.Pro129=
- Coding
- c.387G>A
- MANE Select
- NM_018418
- dbSNP
- rs199727517
- Type
- single nucleotide variant
- Location
- chr14:88426246 (GRCh38)
- Gene constraint
- LOEUF 1.22 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 58.28
Disease context
Leber congenital amaurosis 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: retinitis pigmentosa
For Leber congenital amaurosis (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- SPATA7 p.Pro129Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- SPATA7 c.94+2T>C Likely pathogenic ★★ same condition
- SPATA7 p.Arg108Ter Pathogenic/Likely pathogenic ★★ same condition
- SPATA7 p.Arg391Ter Pathogenic/Likely pathogenic ★★ same condition
- SPATA7 p.Arg395Ter Pathogenic/Likely pathogenic ★★ same condition
- SPATA7 p.Arg85Ter Pathogenic/Likely pathogenic ★★ same condition
- SPATA7 p.Cys96Ter Pathogenic/Likely pathogenic ★★ same condition
- SPATA7 p.Lys163Ter Pathogenic ★★ 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/spata7-p-pro129 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown