ARL13A

ADP ribosylation factor like GTPase 13A, the group of ARF GTPase family

Basic information

Region (hg38): X:100969708-100990831

Previous symbols: [ "ARL13" ]

Links

ENSG00000174225

∙ NCBI:392509 ∙ ∙ HGNC:31709 ∙ Uniprot:Q5H913 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARL13A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL13A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in ARL13A

This is a list of pathogenic ClinVar variants found in the ARL13A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-100985885-G-C		Neurodevelopmental disorder	Uncertain significance (Jan 01, 2019)	982929

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL13A	protein_coding	protein_coding	ENST00000450049	7	21122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000592	0.734	124624	6	7	124637	0.0000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	61	88.8	0.687	0.00000662	1635
Missense in Polyphen		11	24.297	0.45272		465
Synonymous	0.209	32	33.5	0.954	0.00000239	501
Loss of Function	0.917	6	8.96	0.669	7.08e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000814	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000116	0.0000796
Middle Eastern	0.00	0.00
South Asian	0.000165	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool: 0.622
rvis_EVS: 0.06
rvis_percentile_EVS: 58.26

Haploinsufficiency Scores

pHI: 0.129
hipred: N
hipred_score: 0.112
ghis: 0.381

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.257

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Arl13a
Phenotype

Gene ontology

Biological process: receptor localization to non-motile cilium;non-motile cilium assembly
Cellular component: cilium;ciliary membrane;non-motile cilium
Molecular function: GTP binding