PASK p.Pro101=
c.303G>A · rs13392516 · VCV767879
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.11%, 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 -0.69 | GERP -2.4 |
| Overall | ||
| CADD | 6.391 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.11%
African / African-American · 3,081/75,020 alleles
Filtering AF
3.99%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.94%
Overall
0.23%
3,715/1,613,946 alleles · low-frequency
exomes 1,962/1,461,646 · genomes 1,753/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.11% | 24 |
| Middle Eastern | 0.627% | 159 |
| Remaining individualsnot grpmax-eligible | 0.374% | 267 |
| Admixed American | 0.298% | 335 |
| South Asian | 0.0758% | 1,320 |
| European (non-Finnish) | 0.00949% | 10,534 |
| Finnishnot grpmax-eligible | 0.00312% | 32,017 |
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.Pro101=
- Coding
- c.303G>A
- MANE Select
- NM_015148
- dbSNP
- rs13392516
- Type
- single nucleotide variant
- Location
- chr2:241140647 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.14 · 2 PDB
Similar variants
- PASK p.Pro101Leu 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.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-pro101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown