ALPK2 p.Ser163=
c.489C>T · rs73961633 · VCV710666
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.41%, 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 1.5 | GERP 0.82, phastCons 1 |
| Overall | ||
| CADD | 7.629 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.41%
African / African-American · 1,811/75,028 alleles
Filtering AF
2.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.28%
Overall
0.124%
1,994/1,614,164 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.41% | 41 |
| Remaining individualsnot grpmax-eligible | 0.149% | 672 |
| Admixed American | 0.107% | 938 |
| Middle Eastern | 0.066% | 1,516 |
| European (non-Finnish) | 0.00178% | 56,192 |
| South Asian | 0.0011% | 91,076 |
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
- ALPK2
- Protein
- p.Ser163=
- Coding
- c.489C>T
- MANE Select
- NM_052947
- dbSNP
- rs73961633
- Type
- single nucleotide variant
- Location
- chr18:58580287 (GRCh38)
- Gene constraint
- LOEUF 0.862 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 40.99
- Residue 163
- the 'disordered' region
Similar variants
- ALPK2 p.Ser163Phe Uncertain significance ★ ⚠ same residue
- ALPK2 p.Ser163Pro Uncertain significance ★ ⚠ same residue
- ALPK2 p.Thr2079Met Uncertain significance ★★ ⚠ same type
- ALPK2 p.Arg1913Cys Benign/Likely benign ★★ same type
- ALPK2 p.Asp390= Likely benign ★★ same type
- ALPK2 p.Glu1525= Benign/Likely benign ★★ same type
- ALPK2 p.Glu2056= Benign/Likely benign ★★ same type
- ALPK2 p.Gly696= Likely benign ★★ 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/alpk2-p-ser163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown