PPRC1 p.Pro1353=
c.4059G>A · rs529047644 · VCV2640783
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.81 | GERP -2.8, phastCons 0.98 |
| Overall | ||
| CADD | 4.415 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.0021%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00136%
Overall
0.00155%
25/1,614,034 alleles · ultra-rare
exomes 23/1,461,832 · genomes 2/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| South Asian | 0.00549% | 18,214 |
| African / African-American | 0.00267% | 37,508 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| European (non-Finnish) | 0.00136% | 73,748 |
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
- PPRC1
- Protein
- p.Pro1353=
- Coding
- c.4059G>A
- MANE Select
- NM_015062
- dbSNP
- rs529047644
- Type
- single nucleotide variant
- Location
- chr10:102147051 (GRCh38)
- Gene constraint
- LOEUF 0.248 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 42.49
- Residue 1353
- the 'disordered' region
Similar variants
- PPRC1 p.Pro1353Leu Benign same residue
- PPRC1 p.Arg1428His Uncertain significance ★★ ⚠ same type
- PPRC1 c.4551-5G>A Benign/Likely benign ★★ same type
- PPRC1 p.Ala1005Val Uncertain significance ★ ⚠ same type
- PPRC1 p.Ala1134Val Uncertain significance ★ ⚠ same type
- PPRC1 p.Ala1192Val Uncertain significance ★ ⚠ same type
- PPRC1 p.Ala1243Val Uncertain significance ★ ⚠ same type
- PPRC1 p.Ala1258Thr 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/pprc1-p-pro1353 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown