PRR12 p.Pro838=
c.2514G>C · rs776869714 · VCV2650260
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.43%, nfe)
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 0.78 | GERP -2.6, phastCons 0.24 |
| Overall | ||
| CADD | 0.639 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.43%
European (non-Finnish) · 4,907/342,050 alleles
Filtering AF
1.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.39%
Overall
0.912%
5,354/586,820 alleles · low-frequency
exomes 5,323/459,448 · genomes 31/127,372 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.43% | 70 |
| Remaining individualsnot grpmax-eligible | 0.745% | 134 |
| Middle Eastern | 0.394% | 254 |
| Ashkenazi Jewishnot grpmax-eligible | 0.279% | 359 |
| African / African-American | 0.21% | 476 |
| East Asian | 0.164% | 610 |
| South Asian | 0.141% | 708 |
| Admixed American | 0.0171% | 5,863 |
| Finnishnot grpmax-eligible | 0.00817% | 12,238 |
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.Pro838=
- Coding
- c.2514G>C
- MANE Select
- NM_020719
- dbSNP
- rs776869714
- Type
- single nucleotide variant
- Location
- chr19:49596849 (GRCh38)
- Gene constraint
- LOEUF 0.18 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.84
- Residue 838
- the 'disordered' region; 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-pro838 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown