ARL4D

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

Basic information

Region (hg38): 17:43398993-43401137

Previous symbols: [ "ARF4L" ]

Links

ENSG00000175906

∙ NCBI:379 ∙ OMIM:600732 ∙ HGNC:656 ∙ Uniprot:P49703 ∙ 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 ARL4D gene.

not_specified (24 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL4D gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001661.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			23 clinvar	2 clinvar		25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL4D	protein_coding	protein_coding	ENST00000320033	1	2179

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0376	0.846	125500	0	3	125503	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.98	67	131	0.512	0.00000866	1267
Missense in Polyphen		19	53.461	0.3554		530
Synonymous	1.35	46	59.3	0.776	0.00000400	455
Loss of Function	1.26	3	6.45	0.465	5.32e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000634	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
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. Recruits CYTH1, CYTH2, CYTH3 and CYTH4 to the plasma membrane in GDP-bound form. {ECO:0000269|PubMed:17398095}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

loftool: 0.412
rvis_EVS: -0.27
rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

pHI: 0.0593
hipred: Y
hipred_score: 0.588
ghis: 0.594

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.932

Mouse Genome Informatics

Gene name: Arl4d
Phenotype: skeleton phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: intracellular protein transport;protein secretion;vesicle-mediated transport
Cellular component: nucleolus;cytoplasm;plasma membrane
Molecular function: GTPase activity;protein binding;GTP binding