ARL1

ADP ribosylation factor like GTPase 1, the group of ARF GTPase family

Basic information

Region (hg38): 12:101393116-101407772

Links

ENSG00000120805

∙ NCBI:400 ∙ OMIM:603425 ∙ HGNC:692 ∙ Uniprot:P40616 ∙ 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 ARL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL1 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in ARL1

This is a list of pathogenic ClinVar variants found in the ARL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-101395644-T-G		not specified	Uncertain significance (Dec 20, 2022)	2337776
12-101396497-C-T		not specified	Uncertain significance (Mar 27, 2023)	2517031

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL1	protein_coding	protein_coding	ENST00000261636	6	14701

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0937	0.899	124630	0	6	124636	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.18	33	91.8	0.360	0.00000455	1158
Missense in Polyphen		5	37.232	0.13429		464
Synonymous	0.929	26	32.8	0.794	0.00000178	336
Loss of Function	2.34	4	13.1	0.304	8.13e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000331	0.000331

dbNSFP

Source: dbNSFP

Function: FUNCTION: GTP-binding protein that has very low efficiency as allosteric activator of the cholera toxin catalytic subunit, an ADP-ribosyltransferase. Can activate phospholipase D with very low efficiency. Important for normal function of the Golgi apparatus. {ECO:0000269|PubMed:9624189}.;
Pathway: Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.285

Intolerance Scores

loftool
rvis_EVS: 0.06
rvis_percentile_EVS: 58

Haploinsufficiency Scores

pHI: 0.298
hipred: Y
hipred_score: 0.775
ghis: 0.672

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Arl1
Phenotype

Gene ontology

Biological process: intracellular protein transport;Golgi organization;toxin metabolic process;vesicle-mediated transport;activation of phospholipase D activity;protein localization to Golgi apparatus;retrograde transport, endosome to Golgi;Golgi vesicle transport
Cellular component: cytoplasm;Golgi apparatus;trans-Golgi network;cytosol;trans-Golgi network membrane
Molecular function: GTPase activity;GTP binding;enzyme activator activity;protein domain specific binding;metal ion binding