LCA5 p.Arg218=
c.652C>A · rs1318750068 · VCV1568706
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Leber congenital amaurosis 5
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 5.5 | GERP 0.51, phastCons 1 |
| Overall | ||
| CADD | 8.321 | 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
- LCA5
- Protein
- p.Arg218=
- Coding
- c.652C>A
- MANE Select
- NM_001122769
- dbSNP
- rs1318750068
- Type
- single nucleotide variant
- Location
- chr6:79513280 (GRCh38)
- Gene constraint
- LOEUF 0.883 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.05
- Residue 218
- a UniProt-annotated variant site (in lca5; uncertain significance)
Disease context
Leber congenital amaurosis 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Leber congenital amaurosis (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- LCA5 p.Arg218Ter Pathogenic/Likely pathogenic ★★ same residue
- LCA5 p.Arg218Gln Uncertain significance ★ ⚠ same residue
- LCA5 c.190+1G>A Pathogenic/Likely pathogenic ★★ same condition
- LCA5 c.721-1G>A Pathogenic/Likely pathogenic ★★ same condition
- LCA5 c.721-2A>T Pathogenic/Likely pathogenic ★★ same condition
- LCA5 c.858+1G>C Likely pathogenic ★★ same condition
- LCA5 p.Ala319Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- LCA5 p.Arg255Ter 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/lca5-p-arg218 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown