ARL13A

Chr X

ARF like GTPase 13A

Also known as: ARL13, dJ341D10.2

NCBI Gene: 392509ENSG00000174225UniProt: Q5H913

Predicted to enable GTP binding activity and GTPase activity. Predicted to be involved in non-motile cilium assembly and receptor localization to non-motile cilium. Predicted to be active in ciliary membrane; motile cilium; and non-motile cilium. [provided by Alliance of Genome Resources, Jul 2025]

Research Assistant →
0
Active trials
2
Pubs (1 yr)
66
P/LP submissions
—
P/LP missense
1.32
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— ARL13A
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
64 unique Pathogenic / Likely Pathogenic· 21 VUS of 100 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.32LOEUF
pLI 0.001
Z-score 0.92
OE 0.67 (0.36–1.32)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
1.05Z-score
OE missense 0.69 (0.56–0.85)
61 obs / 88.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.67 (0.36–1.32)
0≤0.351.4
Missense OE0.69 (0.56–0.85)
0≤0.61.4
Synonymous OE0.95
0≤1.21.6
LoF obs/exp: 6 / 9.0Missense obs/exp: 61 / 88.8Syn Z: 0.21
DN
0.76top 25%
GOF
0.74top 25%
LOF
0.2678th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

100 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic63
Likely Pathogenic1
VUS21
63
Pathogenic
1
Likely Pathogenic
21
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
————63
Likely Pathogenic
————1
VUS
————21
Likely Benign
————0
Benign
————0
Total—85

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ARL13A · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients