PRUNE1 p.Lys193=
c.579G>A · rs776842998 · VCV2985330
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, eas)
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 3.7 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 7.687 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,886 alleles
Filtering AF
0.00434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.000496%
8/1,613,668 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0111% | 8,977 |
| South Asian | 0.0022% | 45,529 |
| European (non-Finnish) | 8.48e-05% | 1,179,834 |
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.Lys193=
- Coding
- c.579G>A
- MANE Select
- NM_021222
- dbSNP
- rs776842998
- Type
- single nucleotide variant
- Location
- chr1:151025573 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.61
- Residue 193
- 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-lys193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown