PRPF31 p.Phe328=
c.984C>T · rs202206056 · VCV1901722
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00954%, afr)
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 -7.5 | GERP -2.5 |
| Overall | ||
| CADD | 0.589 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00954%
African / African-American · 7/73,378 alleles
Filtering AF
0.00445%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00314%
Overall
0.00316%
49/1,550,348 alleles · very rare
exomes 44/1,398,186 · genomes 5/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00954% | 10,483 |
| Remaining individualsnot grpmax-eligible | 0.005% | 19,987 |
| European (non-Finnish) | 0.00322% | 31,014 |
| East Asian | 0.0024% | 41,628 |
| Admixed American | 0.00196% | 50,982 |
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.Phe328=
- Coding
- c.984C>T
- MANE Select
- NM_015629
- dbSNP
- rs202206056
- Type
- single nucleotide variant
- Location
- chr19:54128111 (GRCh38)
- Gene constraint
- LOEUF 0.347 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.69 · 30 PDB
- Residue 328
- the nop domain; an α-helix
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-phe328 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown