PHKA2 p.Ser1044=
c.3132G>A · rs376018294 · VCV514799
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00702%, afr)
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 -6.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.637 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00702%
African / African-American · 4/56,948 alleles
Filtering AF
0.00234%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0014%
Overall
0.00199%
24/1,207,326 alleles · very rare
exomes 22/1,096,092 · genomes 2/111,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00702% | 14,237 |
| Admixed American | 0.00219% | 45,686 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,529 |
| European (non-Finnish) | 0.0019% | 52,617 |
| South Asian | 0.00177% | 56,623 |
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.Ser1044=
- Coding
- c.3132G>A
- MANE Select
- NM_000292
- dbSNP
- rs376018294
- Type
- single nucleotide variant
- Location
- chrX:18897313 (GRCh38)
- Structure
- AlphaFold pLDDT 81.36
- Residue 1044
- a modified residue (phosphoserine); the 'disordered' region
Similar variants
- 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
- PHKA2 p.Arg295Cys Pathogenic/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-ser1044 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown