PRPF6 p.Arg669=
c.2007G>C · rs962201507 · VCV1633629
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.7 | GERP 0.87, phastCons 1 |
| Overall | ||
| CADD | 13.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,028 alleles
Overall
0.000124%
2/1,607,994 alleles · very rare
exomes 1/1,455,642 · genomes 1/152,352 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,028 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,432 |
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.Arg669=
- Coding
- c.2007G>C
- MANE Select
- NM_012469
- dbSNP
- rs962201507
- Type
- single nucleotide variant
- Location
- chr20:64026037 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.07 · 33 PDB
- Residue 669
- an α-helix
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-arg669 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown