RPGRIP1L p.Val552=
c.1656T>G · rs2151150242 · VCV1078724
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
Joubert syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>T here scores Δ0.48 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 0.33, phastCons 1 |
| Overall | ||
| CADD | 6.901 | 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
- RPGRIP1L
- Protein
- p.Val552=
- Coding
- c.1656T>G
- MANE Select
- NM_015272
- dbSNP
- rs2151150242
- Type
- single nucleotide variant
- Location
- chr16:53656515 (GRCh38)
- Gene constraint
- LOEUF 0.907 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.02 · 1 PDB
Similar variants
- RPGRIP1L p.Val552Leu Uncertain significance ⚠ same residue
- RPGRIP1L c.1030-1G>T Likely pathogenic ★★ same condition
- RPGRIP1L c.1104-2A>G Likely pathogenic ★★ same condition
- RPGRIP1L c.1243+1G>A Pathogenic/Likely pathogenic ★★ same condition
- RPGRIP1L c.1244-1G>T Likely pathogenic ★★ same condition
- RPGRIP1L c.1582-1G>C Likely pathogenic ★★ same condition
- RPGRIP1L c.1700-1G>A Pathogenic/Likely pathogenic ★★ same condition
- RPGRIP1L c.2152+1G>A 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/rpgrip1l-p-val552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown