ALPK2 p.Gln2000=
c.6000G>A · VCV3531612
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 3.3 | GERP 0.67, phastCons 1 |
| Overall | ||
| CADD | 10.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ALPK2
- Protein
- p.Gln2000=
- Coding
- c.6000G>A
- MANE Select
- NM_052947
- Type
- single nucleotide variant
- Location
- chr18:58515022 (GRCh38)
- Gene constraint
- LOEUF 0.862 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 40.99
- Residue 2000
- the alpha-type protein kinase domain
Similar variants
- ALPK2 p.Gln2000Lys 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-gln2000 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown