ARL4D

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

Basic information

Region (hg38): 17:43398992-43401137

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.

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.

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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in ARL4D

This is a list of pathogenic ClinVar variants found in the ARL4D region.

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

Position	Type	Phenotype	Significance	ClinVar
17-43399758-C-T		not specified	Uncertain significance (Jan 04, 2024)
17-43399769-T-G		not specified	Likely benign (Dec 18, 2023)
17-43399824-C-T		not specified	Uncertain significance (Mar 28, 2024)
17-43399870-T-G		not specified	Uncertain significance (Mar 14, 2023)
17-43399874-C-G		not specified	Uncertain significance (Nov 30, 2021)
17-43399983-G-C		not specified	Uncertain significance (Apr 22, 2024)
17-43400018-G-A		not specified	Uncertain significance (Jun 29, 2023)
17-43400069-A-G		not specified	Uncertain significance (Sep 26, 2023)
17-43400082-A-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
17-43400196-G-C		not specified	Uncertain significance (Jun 02, 2023)

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