ARL15

ADP ribosylation factor like GTPase 15, the group of ARF GTPase family|MicroRNA protein coding host genes

Basic information

Region (hg38): 5:53883942-54310582

Previous symbols: [ "ARFRP2" ]

Links

ENSG00000185305 ∙ NCBI:54622 ∙ ∙ HGNC:25945 ∙ Uniprot:Q9NXU5 ∙ 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 ARL15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL15 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					1	1
missense			7			7
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	7	0	1

Variants in ARL15

This is a list of pathogenic ClinVar variants found in the ARL15 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-53886677-C-T		not specified	Uncertain significance (Feb 27, 2024)
5-53886692-C-G		not specified	Uncertain significance (Feb 28, 2023)
5-54113239-T-C		not specified	Uncertain significance (Feb 28, 2023)
5-54113317-A-G		not specified	Uncertain significance (Dec 22, 2023)
5-54154577-T-A		ARL15-related disorder	Uncertain significance (Aug 24, 2023)
5-54171853-C-T		not specified	Uncertain significance (Apr 27, 2023)
5-54171882-T-A		not specified	Uncertain significance (Jan 31, 2024)
5-54171888-C-T		not specified	Uncertain significance (Jun 05, 2023)
5-54310465-T-C		ARL15-related disorder	Benign (Oct 30, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL15	protein_coding	protein_coding	ENST00000504924	5	426638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000936	0.819	124623	0	15	124638	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.715	82	102	0.801	0.00000529	1304
Missense in Polyphen		30	33.379	0.89876		410
Synonymous	0.242	35	36.9	0.949	0.00000181	381
Loss of Function	1.15	6	9.89	0.606	5.17e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000117	0.000117
Ashkenazi Jewish	0.0000997	0.0000994
East Asian	0.0000558	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000534	0.0000531
Middle Eastern	0.0000558	0.0000556
South Asian	0.0000668	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.707
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.612
• hipred: N
• hipred_score: 0.253
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arl15

Zebrafish Information Network

• Gene name: arl15b
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular exosome
• Molecular function: molecular_function;GTP binding