PRR12 p.Pro304=
c.912G>A · VCV4821658
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.173%, sas)
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 -4.8 | GERP -3 |
| Overall | ||
| CADD | 2.937 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.173%
South Asian · 125/72,052 alleles
Filtering AF
0.149%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.139%
Overall
0.037%
357/965,530 alleles · rare
exomes 345/814,500 · genomes 12/151,030 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.173% | 576 |
| European (non-Finnish) | 0.0345% | 2,900 |
| Remaining individualsnot grpmax-eligible | 0.0341% | 2,931 |
| African / African-American | 0.00802% | 12,474 |
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.Pro304=
- Coding
- c.912G>A
- MANE Select
- NM_020719
- Type
- single nucleotide variant
- Location
- chr19:49595247 (GRCh38)
- Gene constraint
- LOEUF 0.18 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.84
- Residue 304
- a UniProt-annotated variant site (in noc1)
Similar variants
- PRR12 p.Pro304fs Pathogenic ★★ same residue
- 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
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-pro304 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown