PRR12 p.Pro301=
c.903A>C · rs892429498 · VCV2650254
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0471%, nfe)
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 -15 | GERP -3 |
| Overall | ||
| CADD | 0.075 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0471%
European (non-Finnish) · 349/741,512 alleles
Filtering AF
0.043%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0413%
Overall
0.0355%
390/1,099,844 alleles · ultra-rare
exomes 385/949,486 · genomes 5/150,358 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0471% | 2,125 |
| Remaining individualsnot grpmax-eligible | 0.0309% | 3,236 |
| African / African-American | 0.0187% | 5,356 |
| South Asian | 0.0147% | 6,820 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0116% | 8,588 |
| East Asian | 0.00258% | 38,744 |
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
- PRR12
- Protein
- p.Pro301=
- Coding
- c.903A>C
- MANE Select
- NM_020719
- dbSNP
- rs892429498
- Type
- single nucleotide variant
- Location
- chr19:49595238 (GRCh38)
- Gene constraint
- LOEUF 0.18 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.84
- Residue 301
- a UniProt-annotated variant site (in noc1)
Similar variants
- PRR12 p.Arg1169Trp Likely pathogenic ★★ ⚠ same type
- PRR12 p.Arg1320Ter Pathogenic ★★ same type
- PRR12 p.Gln264Ter Pathogenic ★★ same type
- PRR12 p.Gln919Ter Pathogenic ★★ same type
- PRR12 p.Glu640Ter Pathogenic ★★ same type
- PRR12 p.Ala1190Ser Uncertain significance ★★ ⚠ same type
- PRR12 p.Ala82Gly Uncertain significance ★★ ⚠ same type
- PRR12 p.Arg1755Gln 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/prr12-p-pro301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown