RAB23 p.Leu165=
c.495G>A · rs1172417830 · VCV2909119
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Conditions
1
Carpenter syndrome
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 2.6 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 12.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,788 alleles
Overall
6.2e-05%
1/1,611,896 alleles · very rare
exomes 0/1,460,030 · genomes 1/151,866 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- RAB23
- Protein
- p.Leu165=
- Coding
- c.495G>A
- MANE Select
- NM_016277
- dbSNP
- rs1172417830
- Type
- single nucleotide variant
- Location
- chr6:57193921 (GRCh38)
- Gene constraint
- LOEUF 0.838 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 80.39 · 6 PDB
- Residue 165
- a UniProt-annotated variant site (in crpt1; pathogenic; homozygous patient-derived neuronal cells exhibit impaired formation of the primary cilium); an α-helix
Similar variants
- RAB23 p.Arg28Ter Pathogenic/Likely pathogenic ★★ same condition
- RAB23 p.Arg49Ter Pathogenic/Likely pathogenic ★★ same condition
- RAB23 p.Arg80Ter Pathogenic/Likely pathogenic ★★ same condition
- RAB23 p.Leu145Ter Pathogenic ★★ same condition
- RAB23 c.481+4A>C Uncertain significance ★★ same condition
- RAB23 p.Cys30Trp Uncertain significance ★★ ⚠ same condition
- RAB23 p.Gly203Ser Uncertain significance ★★ ⚠ same condition
- RAB23 p.Thr116Ala Uncertain significance ★★ ⚠ 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/rab23-p-leu165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown