INPP5A p.Ser271=
c.813G>A · rs143990293 · VCV782211
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.973%, mid)
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 -7.7 | GERP -3.3 |
| Overall | ||
| CADD | 0.799 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.973%
Middle Eastern · 59/6,062 alleles
Filtering AF
0.775%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.703%
Overall
0.213%
3,428/1,612,986 alleles · rare
exomes 3,152/1,460,626 · genomes 276/152,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.973% | 103 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| South Asian | 0.262% | 381 |
| Remaining individualsnot grpmax-eligible | 0.253% | 395 |
| European (non-Finnish) | 0.239% | 418 |
| Admixed American | 0.15% | 667 |
| Finnishnot grpmax-eligible | 0.0414% | 2,418 |
| African / African-American | 0.04% | 2,502 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| East Asian | 0.00223% | 44,888 |
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
- INPP5A
- Protein
- p.Ser271=
- Coding
- c.813G>A
- MANE Select
- NM_005539
- dbSNP
- rs143990293
- Type
- single nucleotide variant
- Location
- chr10:132749597 (GRCh38)
- Gene constraint
- LOEUF 0.356 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 91.81
- Residue 271
- the 5-ppase domain
Similar variants
- INPP5A p.Ser271Leu Uncertain significance ★ ⚠ same residue
- INPP5A p.Leu237= Benign ★★ same type
- INPP5A c.1158+1G>A Uncertain significance ★ same type
- INPP5A c.828+1G>A Uncertain significance ★ same type
- INPP5A p.Ala333Thr Uncertain significance ★ ⚠ same type
- INPP5A p.Ala403Ser Uncertain significance ★ ⚠ same type
- INPP5A p.Ala7Val Uncertain significance ★ ⚠ same type
- INPP5A p.Arg206Trp Uncertain significance ★ ⚠ same type
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/inpp5a-p-ser271 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown