PASK p.Ser789=
c.2367G>A · rs115388023 · VCV787249
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.19%, 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 -4 | GERP -2 |
| Overall | ||
| CADD | 0.198 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.19%
African / African-American · 1,643/75,060 alleles
Filtering AF
2.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.07%
Overall
0.121%
1,948/1,614,152 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.19% | 46 |
| Admixed American | 0.267% | 375 |
| Remaining individualsnot grpmax-eligible | 0.142% | 702 |
| East Asian | 0.0579% | 1,726 |
| Middle Eastern | 0.0495% | 2,021 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.00178% | 56,189 |
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
- PASK
- Protein
- p.Ser789=
- Coding
- c.2367G>A
- MANE Select
- NM_015148
- dbSNP
- rs115388023
- Type
- single nucleotide variant
- Location
- chr2:241126548 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.14 · 2 PDB
Similar variants
- PASK c.3533+1G>A Uncertain significance ★★ same type
- PASK p.Arg1319His Benign ★★ same type
- PASK p.Arg937His Benign ★★ same type
- PASK p.Gly782Arg Benign ★★ same type
- PASK p.Pro101= Benign ★★ same type
- PASK p.Pro844= Benign ★★ same type
- PASK p.Ser582= Benign ★★ same type
- PASK p.Thr850Met 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/pask-p-ser789 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown