ARL4C

ADP ribosylation factor like GTPase 4C, the group of ARF GTPase family

Basic information

Region (hg38): 2:234493041-234497081

Previous symbols: [ "ARL7" ]

Links

ENSG00000188042 ∙ NCBI:10123 ∙ OMIM:604787 ∙ HGNC:698 ∙ Uniprot:P56559 ∙ 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 ARL4C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL4C 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	8	0	0

Variants in ARL4C

This is a list of pathogenic ClinVar variants found in the ARL4C region.

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

Position	Type	Phenotype	Significance	ClinVar
2-234496004-C-A			Benign (May 29, 2018)
2-234496040-T-C		not specified	Uncertain significance (May 06, 2022)
2-234496138-A-G		not specified	Uncertain significance (Mar 30, 2024)
2-234496217-C-T		not specified	Uncertain significance (Dec 21, 2023)
2-234496249-T-C		not specified	Uncertain significance (Oct 25, 2024)
2-234496426-A-G		not specified	Uncertain significance (May 16, 2022)
2-234496428-C-G		not specified	Uncertain significance (Mar 30, 2024)
2-234496429-T-C		not specified	Uncertain significance (Mar 30, 2024)
2-234496430-T-G		not specified	Uncertain significance (Mar 30, 2024)
2-234496473-G-T		not specified	Uncertain significance (Mar 09, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL4C	protein_coding	protein_coding	ENST00000390645	1	4013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.761	0.231	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	39	112	0.348	0.00000507	1243
Missense in Polyphen		8	52.937	0.15112		578
Synonymous	-0.199	54	52.2	1.04	0.00000256	396
Loss of Function	2.02	0	4.74	0.00	2.03e-7	56

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Small GTP-binding protein which cycles between an inactive GDP-bound and an active GTP-bound form, and the rate of cycling is regulated by guanine nucleotide exchange factors (GEF) and GTPase-activating proteins (GAP). GTP-binding protein that does not act as an allosteric activator of the cholera toxin catalytic subunit. May be involved in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Recruits CYTH1, CYTH2, CYTH3 and CYTH4 to the plasma membrane in the GDP- bound form. Regulates the microtubule-dependent intracellular vesicular transport from early endosome to recycling endosome process. {ECO:0000269|PubMed:15147902, ECO:0000269|PubMed:17398095, ECO:0000269|PubMed:19409876}.

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.0900
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.678
• hipred: Y
• hipred_score: 0.546
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Arl4c

Gene ontology

• Biological process: intracellular protein transport;vesicle-mediated transport;endocytic recycling
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;filopodium
• Molecular function: GTPase activity;protein binding;GTP binding;alpha-tubulin binding