PI4KA p.Pro290=
c.870C>T · rs146943439 · VCV3044763
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.941%, afr)
Conditions
1
PI4KA-related disorder
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 -1.6 | |
| Overall | ||
| CADD | 4.907 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.941%
African / African-American · 706/75,026 alleles
Filtering AF
0.883%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.861%
Overall
0.0537%
866/1,613,834 alleles · rare
exomes 432/1,461,582 · genomes 434/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.941% | 106 |
| Admixed American | 0.138% | 722 |
| Remaining individualsnot grpmax-eligible | 0.0672% | 1,488 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0033% | 30,342 |
| European (non-Finnish) | 0.00263% | 38,060 |
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
- PI4KA
- Protein
- p.Pro290=
- Coding
- c.870C>T
- MANE Select
- NM_058004
- dbSNP
- rs146943439
- Type
- single nucleotide variant
- Location
- chr22:20813493 (GRCh38)
- Gene constraint
- LOEUF 0.548 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.42 · 4 PDB
Similar variants
- PI4KA p.Arg618Ter Likely pathogenic ★★ same condition
- PI4KA p.Asp1854Asn Pathogenic/Likely pathogenic ★★ same condition
- PI4KA p.Asp1713His Uncertain significance ★★ ⚠ same condition
- PI4KA c.156+5C>G Likely benign ★★ same condition
- PI4KA p.Leu1011= Benign ★★ same condition
- PI4KA p.Phe395= Likely benign ★★ same condition
- PI4KA p.Arg746Ter Likely pathogenic ★ same condition
- PI4KA p.Glu563Ter Likely 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/pi4ka-p-pro290 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown