PRPF31 p.Ser44=
c.132C>T · rs150968066 · VCV1910149
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -15 | GERP -2.4 |
| Overall | ||
| CADD | 3.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,070 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.00285%
46/1,613,904 alleles · ultra-rare
exomes 42/1,461,858 · genomes 4/152,046 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,070 |
| Admixed American | 0.00667% | 14,996 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| East Asian | 0.00445% | 22,449 |
| European (non-Finnish) | 0.00305% | 32,778 |
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.Ser44=
- Coding
- c.132C>T
- MANE Select
- NM_015629
- dbSNP
- rs150968066
- Type
- single nucleotide variant
- Location
- chr19:54118410 (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-ser44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown