PRUNE1 p.Lys236=
c.708A>G · rs11204762 · VCV2002792
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 44.7%, eas) — too common for a highly-penetrant pathogenic allele
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 0.94 | GERP 0.71, phastCons 1 |
| Overall | ||
| CADD | 7.631 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
44.7%
East Asian · 20,009/44,766 alleles
Filtering AF
44.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 44%
Overall
24.2%
389,750/1,607,318 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 44.7% | 2 |
| South Asian | 25.9% | 4 |
| African / African-American | 24.6% | 4 |
| European (non-Finnish) | 23.8% | 4 |
| Remaining individualsnot grpmax-eligible | 23.6% | 4 |
| Finnishnot grpmax-eligible | 22.7% | 4 |
| Admixed American | 20.5% | 5 |
| Amishnot grpmax-eligible | 19.2% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 18.2% | 5 |
| Middle Eastern | 17.2% | 6 |
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
- PRUNE1
- Protein
- p.Lys236=
- Coding
- c.708A>G
- MANE Select
- NM_021222
- dbSNP
- rs11204762
- Type
- single nucleotide variant
- Location
- chr1:151027261 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.61
- Residue 236
- a UniProt-annotated variant site (in nmihba)
Similar variants
- PRUNE1 c.132+2T>C Pathogenic ★★ same type
- PRUNE1 c.521-2A>G Pathogenic/Likely pathogenic ★★ same type
- PRUNE1 p.Arg128Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- PRUNE1 p.Arg66Ter Pathogenic/Likely pathogenic ★★ same type
- PRUNE1 p.Asp106Asn Pathogenic/Likely pathogenic ★★ same type
- PRUNE1 p.Asp30Asn Pathogenic/Likely pathogenic ★★ same type
- PRUNE1 p.Ala39Pro Uncertain significance ★★ ⚠ same type
- PRUNE1 p.Asp87Asn Uncertain significance ★★ ⚠ 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/prune1-p-lys236 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown