PASK p.Pro1182=
c.3546G>A · rs143703586 · VCV725051
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0551%, nfe)
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 -14 | GERP -3.4 |
| Overall | ||
| CADD | 0.706 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0551%
European (non-Finnish) · 650/1,179,962 alleles
Filtering AF
0.0515%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0502%
Overall
0.0415%
670/1,614,082 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0551% | 1,815 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,250 |
| African / African-American | 0.00799% | 12,510 |
| East Asian | 0.00446% | 22,435 |
| Admixed American | 0.00333% | 30,013 |
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.Pro1182=
- Coding
- c.3546G>A
- MANE Select
- NM_015148
- dbSNP
- rs143703586
- Type
- single nucleotide variant
- Location
- chr2:241108288 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.14 · 2 PDB
- Residue 1182
- the protein kinase domain; an α-helix
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.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-pro1182 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown