Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.38%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Overall | ||
| CADD | 0.869 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.38%
South Asian · 1,260/91,086 alleles
Filtering AF
1.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.29%
Overall
0.652%
10,528/1,614,104 alleles · low-frequency
exomes 9,862/1,461,756 · genomes 666/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.38% | 72 |
| Middle Eastern | 0.792% | 126 |
| European (non-Finnish) | 0.7% | 143 |
| Remaining individualsnot grpmax-eligible | 0.667% | 150 |
| Admixed American | 0.478% | 209 |
| Ashkenazi Jewishnot grpmax-eligible | 0.294% | 340 |
| African / African-American | 0.121% | 825 |
| Finnishnot grpmax-eligible | 0.113% | 888 |
| East Asian | 0.00668% | 14,960 |
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.Ser582=
- Coding
- c.1746C>T
- MANE Select
- NM_015148
- dbSNP
- rs9677402
- Type
- single nucleotide variant
- Location
- chr2:241127169 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.14 · 2 PDB
- Residue 582
- a modified residue (phosphoserine)
Similar variants
- PASK p.Ser582Arg Uncertain significance ★ ⚠ same residue
- 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.Ser789= 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-ser582 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown