CRX p.Ser262=
c.786C>T · rs2514256733 · VCV2109546
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
Leber congenital amaurosis 7
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 0.41 | GERP 0.68, phastCons 0.99 |
| Overall | ||
| CADD | 7.968 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CRX
- Protein
- p.Ser262=
- Coding
- c.786C>T
- MANE Select
- NM_000554
- dbSNP
- rs2514256733
- Type
- single nucleotide variant
- Location
- chr19:47839853 (GRCh38)
- Gene constraint
- LOEUF 0.673 · pLI 0.72 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.78 · 1 PDB
Disease context
Leber congenital amaurosis 7 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: cone-rod dystrophy 2
For Leber congenital amaurosis (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- CRX p.Ser262Gly Uncertain significance ★ ⚠ same residue
- 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.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-ser262 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown