CRX p.Phe215=
c.645C>T · rs191794330 · VCV1595814
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.163%, eas)
Conditions
3
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 2.5 | GERP 0.66, phastCons 1 |
| Overall | ||
| CADD | 10.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.163%
East Asian · 73/44,854 alleles
Filtering AF
0.133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.122%
Overall
0.00496%
80/1,614,034 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.163% | 614 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,500 |
| Admixed American | 0.00167% | 60,010 |
| European (non-Finnish) | 8.47e-05% | 1,180,006 |
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
- CRX
- Protein
- p.Phe215=
- Coding
- c.645C>T
- MANE Select
- NM_000554
- dbSNP
- rs191794330
- Type
- single nucleotide variant
- Location
- chr19:47839712 (GRCh38)
- Gene constraint
- LOEUF 0.673 · pLI 0.72 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.78 · 1 PDB
Similar variants
- CRX c.101-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CRX p.Arg40Gln Pathogenic/Likely pathogenic ★★ same condition
- CRX p.Arg40Trp Pathogenic/Likely pathogenic ★★ same condition
- CRX p.Arg41Gln Pathogenic/Likely pathogenic ★★ same condition
- CRX p.Arg41Pro Likely pathogenic ★★ same condition
- CRX p.Arg43Cys Pathogenic ★★ same condition
- CRX p.Arg43His Pathogenic/Likely pathogenic ★★ same condition
- CRX p.Arg69Cys Pathogenic/Likely pathogenic ★★ 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/crx-p-phe215 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown