PASK p.Thr858=
c.2574G>A · rs56043607 · VCV788483
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.21%, 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 -3.9 | GERP -2.7 |
| Overall | ||
| CADD | 0.557 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.21%
European (non-Finnish) · 14,319/1,180,038 alleles
Filtering AF
1.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.19%
Overall
0.979%
15,802/1,614,222 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.21% | 82 |
| Remaining individualsnot grpmax-eligible | 0.709% | 141 |
| Finnishnot grpmax-eligible | 0.693% | 144 |
| Ashkenazi Jewishnot grpmax-eligible | 0.493% | 203 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| African / African-American | 0.22% | 455 |
| Admixed American | 0.205% | 488 |
| South Asian | 0.167% | 599 |
| Middle Eastern | 0.0825% | 1,212 |
| East Asian | 0.00446% | 22,442 |
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.Thr858=
- Coding
- c.2574G>A
- MANE Select
- NM_015148
- dbSNP
- rs56043607
- Type
- single nucleotide variant
- Location
- chr2:241126341 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.14 · 2 PDB
Similar variants
- PASK p.Thr858Met 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.Ser582= 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-thr858 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown