PRPF6 p.Phe8=
c.24C>T · rs751016032 · VCV783875
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.1%, 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 1.6 | GERP 0.33, phastCons 0.97 |
| Overall | ||
| CADD | 13.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.1%
African / African-American · 75/74,868 alleles
Filtering AF
0.0819%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0752%
Overall
0.0051%
82/1,609,064 alleles · rare
exomes 43/1,456,840 · genomes 39/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.1% | 998 |
| Remaining individualsnot grpmax-eligible | 0.00482% | 20,753 |
| Admixed American | 0.00337% | 29,716 |
| South Asian | 0.00111% | 90,250 |
| European (non-Finnish) | 8.49e-05% | 1,177,872 |
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
- PRPF6
- Protein
- p.Phe8=
- Coding
- c.24C>T
- MANE Select
- NM_012469
- dbSNP
- rs751016032
- Type
- single nucleotide variant
- Location
- chr20:63981269 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.07 · 33 PDB
- Residue 8
- the 'disordered' region
Similar variants
- PRPF6 c.2028+5G>A Uncertain significance ★★ same type
- PRPF6 c.2205+5G>A Uncertain significance ★★ same type
- PRPF6 c.439-19G>A Uncertain significance ★★ same type
- PRPF6 p.Ala246Val Uncertain significance ★★ ⚠ same type
- PRPF6 p.Ala380Thr Uncertain significance ★★ ⚠ same type
- PRPF6 p.Ala564Thr Uncertain significance ★★ ⚠ same type
- PRPF6 p.Ala65Thr Uncertain significance ★★ ⚠ same type
- PRPF6 p.Ala675Thr 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/prpf6-p-phe8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown