PRPF31 p.Val407=
c.1221G>A · rs2516206180 · VCV1904444
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000257%, 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 0.74 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 7.224 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000257%
European (non-Finnish) · 3/1,165,082 alleles
Filtering AF
6.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.00019%
3/1,582,440 alleles · very rare
exomes 3/1,430,148 · genomes 0/152,292 · joint denominator
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.Val407=
- Coding
- c.1221G>A
- MANE Select
- NM_015629
- dbSNP
- rs2516206180
- Type
- single nucleotide variant
- Location
- chr19:54129131 (GRCh38)
- Gene constraint
- LOEUF 0.347 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.69 · 30 PDB
Similar variants
- PRPF31 p.Val407fs Likely pathogenic ★ same residue
- 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
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-val407 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown