RPGRIP1L p.Pro992=
c.2976T>C · rs2151040617 · VCV1575064
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,565,888)
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 Δ0.32 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -4, phastCons 0.94 |
| Overall | ||
| CADD | 4.819 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,565,888). 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
- RPGRIP1L
- Protein
- p.Pro992=
- Coding
- c.2976T>C
- MANE Select
- NM_015272
- dbSNP
- rs2151040617
- Type
- single nucleotide variant
- Location
- chr16:53638394 (GRCh38)
- Gene constraint
- LOEUF 0.907 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.02 · 1 PDB
Similar variants
- RPGRIP1L p.Pro992Ala Uncertain significance ★ ⚠ same residue
- RPGRIP1L p.Pro992fs Pathogenic/Likely pathogenic ★★ same residue
- RPGRIP1L p.Pro992del Uncertain significance ★★ same residue
- RPGRIP1L p.Pro992Ser 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
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-pro992 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown