Is RAB23 p.Arg59fs (c.177_183del) pathogenic?

RAB23 p.Arg59fs (c.177183del) is classified Likely pathogenic in RAB23 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-07). Associated with RAB23-related Carpenter syndrome.

What condition is associated with RAB23 p.Arg59fs (c.177_183del)?

RAB23 p.Arg59fs (c.177_183del) is associated with RAB23-related Carpenter syndrome (ClinVar).

RAB23 p.Arg59fs

c.177_183del · VCV4817033

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

RAB23-related Carpenter syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.9	GERP 1.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: RAB23
Protein: p.Arg59fs
Coding: c.177_183del
MANE Select: NM_016277
Type: Deletion
Location: chr6:57207686 (GRCh38)
Gene constraint: LOEUF 0.838 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 80.39 · 6 PDB
Residue 59: a β-strand

Full RAB23 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

RAB23-related Carpenter syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

RAB23 p.Leu2fs Pathogenic/Likely pathogenic ★★ same condition
RAB23 p.Gln171fs Likely pathogenic ★ same condition
RAB23 p.Glu70fs Pathogenic ★ same condition
RAB23 p.Gly203fs Likely pathogenic ★ same condition
RAB23 p.Lys174fs Likely pathogenic ★ same condition
RAB23 p.Ser187fs Likely pathogenic ★ same condition
RAB23 p.Arg59= Likely benign ★ same residue
RAB23 c.398+6del Conflicting classifications of pathogenicity 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-arg59fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown