CRX c.252+18_252+24del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
2
Leber congenital amaurosis 7
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +18 | near-intronic (+18 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.005 | GERP -0.85, phastCons 0.001 |
| Non-coding constraint | Z 3.59 | 1 kb window · o/e 0.73 · regional · uncalibrated |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CRX
- Coding
- c.252+18_252+24del
- MANE Select
- NM_000554
- dbSNP
- rs2123740025
- Type
- Deletion
- Location
- chr19:47836409 (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
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- CRX p.Gln39_Glu42del Pathogenic/Likely pathogenic ★★ same condition
- CRX p.Leu146fs Pathogenic/Likely pathogenic ★★ same condition
- CRX p.Pro108fs Pathogenic/Likely pathogenic ★★ same condition
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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-c-252-plus-18-252-plus-24del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown