ARL5C

ADP ribosylation factor like GTPase 5C, the group of ARF GTPase family

Basic information

Region (hg38): 17:39156893-39167484

Previous symbols: [ "ARL12" ]

Links

ENSG00000141748 ∙ NCBI:390790 ∙ ∙ HGNC:31111 ∙ Uniprot:A6NH57 ∙ 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 ARL5C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL5C 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			3	3		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	3	0

Variants in ARL5C

This is a list of pathogenic ClinVar variants found in the ARL5C region.

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

Position	Type	Phenotype	Significance	ClinVar
17-39156935-C-T		not specified	Uncertain significance (May 07, 2024)
17-39160595-C-T		not specified	Uncertain significance (Apr 05, 2023)
17-39160630-G-A		not specified	Uncertain significance (Jul 14, 2021)
17-39161308-A-G		not specified	Uncertain significance (May 14, 2024)
17-39161315-G-A		not specified	Likely benign (Jan 30, 2024)
17-39161326-G-A		not specified	Likely benign (Dec 07, 2021)
17-39165082-C-T		not specified	Likely benign (Jul 26, 2022)
17-39165729-A-T		not specified	Uncertain significance (Oct 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL5C	protein_coding	protein_coding	ENST00000444555	6	10591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.310	0.674	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.899	76	101	0.749	0.00000522	1181
Missense in Polyphen		19	27.781	0.68393		382
Synonymous	1.69	25	38.3	0.653	0.00000216	327
Loss of Function	2.02	2	8.29	0.241	3.52e-7	101

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: Binds and exchanges GTP and GDP. {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 1.73
• rvis_percentile_EVS: 96.5

Haploinsufficiency Scores

• pHI: 0.143

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arl5c
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: intracellular protein transport;vesicle-mediated transport;protein localization to Golgi membrane
• Cellular component: cytoplasm;trans-Golgi network
• Molecular function: GTP binding