Is RAB23 p.Ser202= (c.606C>T) pathogenic?

RAB23 p.Ser202= (c.606C>T) is classified Likely benign in RAB23 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-02-28). Very rare (popmax 0.00439%, sas); Associated with Carpenter syndrome.

What condition is associated with RAB23 p.Ser202= (c.606C>T)?

RAB23 p.Ser202= (c.606C>T) is associated with Carpenter syndrome (ClinVar).

How common is RAB23 p.Ser202= (c.606C>T) in the general population?

RAB23 p.Ser202= (c.606C>T) is very rare (popmax 0.00439%, sas) (gnomAD).

RAB23 p.Ser202=

c.606C>T · rs771204930 · VCV1158043

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00439%, sas)

Conditions

Carpenter syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.20	acceptor loss · deltas
Constraint at this position
Conservation	phyloP -0.11	GERP -2.8
Overall
CADD	5.42	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00439% South Asian · 4/91,078 alleles

Filtering AF 0.00231% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00202%

Overall 0.00273% 44/1,613,768 alleles · very rare exomes 43/1,461,610 · genomes 1/152,158 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00439%	22,769
European (non-Finnish)	0.00314%	31,887
East Asian	0.00223%	44,882
Admixed American	0.00167%	59,992
Remaining individualsnot grpmax-eligible	0.0016%	62,474

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.Ser202=
Coding: c.606C>T
MANE Select: NM_016277
dbSNP: rs771204930
Type: single nucleotide variant
Location: chr6:57190569 (GRCh38)
Gene constraint: LOEUF 0.838 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 80.39 · 6 PDB
Residue 202: the 'disordered' region; a UniProt-annotated variant site (in crpt1; pathogenic; homozygous patient-derived neuronal cells exhibit impaired formation of the primary cilium)

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

Disease context

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

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-ser202 (accessed [today's date]).

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