ARL6IP5

ADP ribosylation factor like GTPase 6 interacting protein 5, the group of YIP family

Basic information

Region (hg38): 3:69084936-69106092

Links

ENSG00000144746 ∙ NCBI:10550 ∙ OMIM:605709 ∙ HGNC:16937 ∙ Uniprot:O75915 ∙ 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 ARL6IP5 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL6IP5 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in ARL6IP5

This is a list of pathogenic ClinVar variants found in the ARL6IP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-69085067-C-A		not specified	Uncertain significance (Jun 07, 2023)
3-69101888-G-A		not specified	Uncertain significance (Feb 21, 2024)
3-69101898-G-C		not specified	Uncertain significance (Dec 06, 2021)
3-69101936-C-T		not specified	Uncertain significance (Oct 21, 2021)
3-69101948-C-T		not specified	Uncertain significance (Mar 28, 2023)
3-69102022-G-A		not specified	Uncertain significance (Feb 03, 2022)
3-69104470-T-C		not specified	Uncertain significance (May 25, 2022)
3-69104503-A-C		not specified	Uncertain significance (Jun 27, 2022)
3-69104507-C-A		not specified	Uncertain significance (May 11, 2022)
3-69104575-T-A		not specified	Uncertain significance (Oct 12, 2022)
3-69104614-A-G		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL6IP5	protein_coding	protein_coding	ENST00000273258	3	21123

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.104	0.784	125745	0	3	125748	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.374	104	115	0.902	0.00000634	1253
Missense in Polyphen		37	42.57	0.86915		510
Synonymous	0.194	43	44.7	0.963	0.00000263	364
Loss of Function	1.23	2	4.96	0.403	2.09e-7	63

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)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates intracellular concentrations of taurine and glutamate. Negatively modulates SLC1A1/EAAC1 glutamate transport activity by decreasing its affinity for glutamate in a PKC activity-dependent manner. May be involved in membrane traffic. {ECO:0000250|UniProtKB:Q8R5J9, ECO:0000250|UniProtKB:Q9ES40}.
• Pathway: Neuronal System;Glutamate Neurotransmitter Release Cycle;Neurotransmitter release cycle;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.406
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.218
• hipred: N
• hipred_score: 0.398
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.975

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arl6ip5
• Phenotype: neoplasm; normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of L-glutamate import across plasma membrane;intrinsic apoptotic signaling pathway in response to oxidative stress;negative regulation of mitochondrial membrane potential;L-glutamate transmembrane transport;positive regulation of stress-activated MAPK cascade;positive regulation of apoptotic process;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process
• Cellular component: endoplasmic reticulum membrane;cytoskeleton;plasma membrane;membrane;integral component of membrane
• Molecular function: molecular_function;protein binding