PRPF6 p.Phe880=
c.2640C>T · rs746161407 · VCV1661399
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 2.6 | GERP 0.8, phastCons 1 |
| Overall | ||
| CADD | 12.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000372%
6/1,614,142 alleles · ultra-rare
exomes 6/1,461,786 · genomes 0/152,356 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Admixed American | 0.00333% | 30,014 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000169% | 590,016 |
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.Phe880=
- Coding
- c.2640C>T
- MANE Select
- NM_012469
- dbSNP
- rs746161407
- Type
- single nucleotide variant
- Location
- chr20:64032011 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.07 · 33 PDB
- Residue 880
- an α-helix
Similar variants
- PRPF6 p.Phe880Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
- PRPF6 p.Phe880Val Likely benign ★ ⚠ same residue
- PRPF6 p.Phe880Ala Uncertain significance ★★ same residue
- 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
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-phe880 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown