PRPF6 p.Pro774=
c.2322A>G · rs201710977 · VCV1102496
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.323%, eas)
Conditions
1
inherited retinal dystrophy
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 -10 | GERP -4 |
| Overall | ||
| CADD | 0.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.323%
East Asian · 145/44,888 alleles
Filtering AF
0.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.264%
Overall
0.00911%
147/1,613,994 alleles · rare
exomes 144/1,461,690 · genomes 3/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.323% | 310 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,253 |
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.Pro774=
- Coding
- c.2322A>G
- MANE Select
- NM_012469
- dbSNP
- rs201710977
- Type
- single nucleotide variant
- Location
- chr20:64027719 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.07 · 33 PDB
Similar variants
- PRPF6 p.Pro774Leu Uncertain significance ★ ⚠ same residue
- PRPF6 p.Ala65Thr Uncertain significance ★★ ⚠ same condition
- PRPF6 p.Ile919Val Uncertain significance ★★ ⚠ same condition
- PRPF6 p.Pro282Leu Uncertain significance ★★ ⚠ same condition
- PRPF6 p.Val411Ile Uncertain significance ★★ ⚠ same condition
- PRPF6 p.Arg936Cys Benign/Likely benign ★★ same condition
- PRPF6 p.Asp832= Benign/Likely benign ★★ same condition
- PRPF6 p.Pro14= Benign ★★ same condition
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-pro774 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown