ALPK2 p.Ala29=
c.87T>C · rs2052132352 · VCV1764731
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -11 | GERP -4.6 |
| Overall | ||
| CADD | 0.125 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,058 alleles
Overall
6.85e-05%
1/1,460,774 alleles · ultra-rare
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.Ala29=
- Coding
- c.87T>C
- MANE Select
- NM_052947
- dbSNP
- rs2052132352
- Type
- single nucleotide variant
- Location
- chr18:58611711 (GRCh38)
- Gene constraint
- LOEUF 0.862 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 40.99
- Residue 29
- the ig-like 1 domain; a UniProt-annotated variant site (in)
Similar variants
- ALPK2 p.Ala29Val 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
- ALPK2 p.Ser163= Benign/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-ala29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown