PHKA2 p.Pro1115=
c.3345G>A · rs201620564 · VCV385816
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0152%, amr)
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 -15 | GERP -3.5 |
| Overall | ||
| CADD | 0.034 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0152%
Admixed American · 7/45,940 alleles
Filtering AF
0.00711%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00505%
Overall
0.00306%
37/1,208,036 alleles · ultra-rare
exomes 33/1,095,275 · genomes 4/112,761 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0152% | 6,563 |
| Remaining individualsnot grpmax-eligible | 0.00631% | 15,858 |
| European (non-Finnish) | 0.00291% | 34,377 |
| South Asian | 0.00176% | 56,846 |
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
- PHKA2
- Protein
- p.Pro1115=
- Coding
- c.3345G>A
- MANE Select
- NM_000292
- dbSNP
- rs201620564
- Type
- single nucleotide variant
- Location
- chrX:18894396 (GRCh38)
- Structure
- AlphaFold pLDDT 81.36
Similar variants
- PHKA2 p.Pro1115Ser Uncertain significance ★ ⚠ same residue
- PHKA2 c.1325-2A>G Likely pathogenic ★★ same type
- PHKA2 c.2597+1G>A Pathogenic/Likely pathogenic ★★ same type
- PHKA2 c.537+2T>C Pathogenic/Likely pathogenic ★★ same type
- PHKA2 c.918+1G>A Pathogenic/Likely pathogenic ★★ same type
- PHKA2 p.Arg1111Ter Pathogenic ★★ same type
- PHKA2 p.Arg186Cys Pathogenic/Likely pathogenic ★★ same type
- PHKA2 p.Arg186His Likely pathogenic ★★ 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/phka2-p-pro1115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown