PHKA1 p.Pro1180=
c.3540C>T · rs782121327 · VCV387009
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00297%, eas)
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 -1.1 | GERP -3.1 |
| Overall | ||
| CADD | 1.235 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00297%
East Asian · 1/33,699 alleles
Filtering AF
3.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000334%
4/1,198,211 alleles · very rare
exomes 3/1,086,842 · genomes 1/111,369 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00297% | 33,699 |
| Admixed American | 0.00219% | 45,682 |
| European (non-Finnish) | 0.000226% | 442,423 |
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
- PHKA1
- Protein
- p.Pro1180=
- Coding
- c.3540C>T
- MANE Select
- NM_002637
- dbSNP
- rs782121327
- Type
- single nucleotide variant
- Location
- chrX:72581134 (GRCh38)
- Structure
- AlphaFold pLDDT 81.84 · 10 PDB
- Residue 1180
- a turn
Similar variants
- PHKA1 p.Pro1180Thr Uncertain significance ★★ ⚠ same residue
- PHKA1 c.2137+1G>A Likely pathogenic ★★ same type
- PHKA1 c.2527-1G>T Likely pathogenic ★★ same type
- PHKA1 c.2606+1G>A Pathogenic/Likely pathogenic ★★ same type
- PHKA1 c.537+1G>A Likely pathogenic ★★ same type
- PHKA1 p.Arg298Ter Pathogenic ★★ same type
- PHKA1 p.Arg392Ter Pathogenic/Likely pathogenic ★★ same type
- PHKA1 p.Arg739Ter 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/phka1-p-pro1180 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown