PRPF31 p.Ser451=
c.1353C>T · rs1196306452 · VCV1896531
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00135%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.375 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -2.5 |
| Overall | ||
| CADD | 2.009 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00135%
African / African-American · 1/74,270 alleles
Filtering AF
0.000767%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000608%
Overall
0.001%
16/1,600,166 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00135% | 74,270 |
| European (non-Finnish) | 0.00128% | 78,301 |
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
- PRPF31
- Protein
- p.Ser451=
- Coding
- c.1353C>T
- MANE Select
- NM_015629
- dbSNP
- rs1196306452
- Type
- single nucleotide variant
- Location
- chr19:54129349 (GRCh38)
- Gene constraint
- LOEUF 0.347 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.69 · 30 PDB
Similar variants
- PRPF31 c.1073+1G>A Pathogenic ★★ same type
- PRPF31 c.1074-1G>C Likely pathogenic ★★ same type
- PRPF31 c.1074-2A>G Pathogenic ★★ same type
- PRPF31 c.1074-2A>T Pathogenic ★★ same type
- PRPF31 c.1146+2T>C Pathogenic ★★ same type
- PRPF31 c.1146+5G>T Likely pathogenic ★★ same type
- PRPF31 c.1374+654C>G Pathogenic ★★ same type
- PRPF31 c.178-2A>G Pathogenic ★★ 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/prpf31-p-ser451 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown