PASK p.Arg438=
c.1314G>A · rs150978020 · VCV730983
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.043%, 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 -0.41 | GERP -1.5 |
| Overall | ||
| CADD | 1.444 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.043%
European (non-Finnish) · 507/1,180,014 alleles
Filtering AF
0.0398%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0386%
Overall
0.0329%
531/1,614,040 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.043% | 2,327 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,676 |
| African / African-American | 0.00667% | 14,984 |
| Admixed American | 0.00333% | 30,002 |
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.Arg438=
- Coding
- c.1314G>A
- MANE Select
- NM_015148
- dbSNP
- rs150978020
- Type
- single nucleotide variant
- Location
- chr2:241133023 (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.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-arg438 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown