RAB23 p.Arg104=
c.312A>G · rs2533184602 · VCV2745418
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000339%, nfe)
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 3.5 | GERP -0.55, phastCons 1 |
| Overall | ||
| CADD | 11.61 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,179,980 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,614,048 alleles · very rare
exomes 4/1,461,754 · genomes 0/152,294 · 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.Arg104=
- Coding
- c.312A>G
- MANE Select
- NM_016277
- dbSNP
- rs2533184602
- Type
- single nucleotide variant
- Location
- chr6:57196536 (GRCh38)
- Gene constraint
- LOEUF 0.838 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 80.39 · 6 PDB
- Residue 104
- 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-arg104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown