ALPK2 p.Asp941=
c.2823T>C · rs753288154 · VCV1796479
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00669%, 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 -0.1 | GERP -4.7 |
| Overall | ||
| CADD | 4.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
East Asian · 3/44,848 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000892%
Overall
0.000274%
4/1,461,730 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00669% | 14,949 |
| European (non-Finnish) | 8.47e-05% | 1,179,944 |
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.Asp941=
- Coding
- c.2823T>C
- MANE Select
- NM_052947
- dbSNP
- rs753288154
- Type
- single nucleotide variant
- Location
- chr18:58537364 (GRCh38)
- Gene constraint
- LOEUF 0.862 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 40.99
- Residue 941
- the 'disordered' region
Similar variants
- ALPK2 p.Asp941His 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-asp941 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown