INPP5A p.Ser203=
c.609G>A · VCV4681403
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0387%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.022 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -3 |
| Overall | ||
| CADD | 6.958 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0387%
African / African-American · 29/74,948 alleles
Filtering AF
0.0277%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0239%
Overall
0.00359%
58/1,613,916 alleles · ultra-rare
exomes 30/1,461,662 · genomes 28/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0387% | 2,584 |
| Middle Eastern | 0.0168% | 5,966 |
| Admixed American | 0.0117% | 8,572 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,617 |
| South Asian | 0.00329% | 30,360 |
| European (non-Finnish) | 0.00119% | 84,289 |
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.Ser203=
- Coding
- c.609G>A
- MANE Select
- NM_005539
- Type
- single nucleotide variant
- Location
- chr10:132710418 (GRCh38)
- Gene constraint
- LOEUF 0.356 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 91.81
- Residue 203
- the 5-ppase domain
Similar variants
- INPP5A p.Leu237= Benign ★★ same type
- INPP5A p.Ser271= 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-ser203 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown