PRUNE1 p.Thr153=
c.459C>T · rs139698394 · VCV2080273
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, 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 -15 | GERP -3 |
| Overall | ||
| CADD | 0.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,898 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000929%
15/1,613,960 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,724 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,829 |
| South Asian | 0.00439% | 22,768 |
| Admixed American | 0.00167% | 59,976 |
| European (non-Finnish) | 0.000254% | 393,338 |
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.Thr153=
- Coding
- c.459C>T
- MANE Select
- NM_021222
- dbSNP
- rs139698394
- Type
- single nucleotide variant
- Location
- chr1:151024734 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.61
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-thr153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown