ARL6IP4

ADP ribosylation factor like GTPase 6 interacting protein 4

Basic information

Region (hg38): 12:122980060-122982913

Links

ENSG00000182196 ∙ NCBI:51329 ∙ OMIM:607668 ∙ HGNC:18076 ∙ Uniprot:Q66PJ3 ∙ 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 ARL6IP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL6IP4 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15			15
Total	0	0	37	1	0

Variants in ARL6IP4

This is a list of pathogenic ClinVar variants found in the ARL6IP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-122980428-G-A		not specified	Uncertain significance (May 18, 2022)
12-122980445-C-T		not specified	Uncertain significance (Dec 17, 2023)
12-122980467-T-C		not specified	Uncertain significance (Mar 14, 2023)
12-122980490-G-T		not specified	Uncertain significance (Sep 16, 2021)
12-122980523-A-G		not specified	Uncertain significance (Jun 29, 2022)
12-122980551-G-A		not specified	Uncertain significance (Mar 22, 2022)
12-122980554-C-G		not specified	Uncertain significance (May 10, 2024)
12-122980592-C-G		not specified	Uncertain significance (Aug 31, 2022)
12-122980647-G-A		not specified	Uncertain significance (Feb 03, 2022)
12-122980674-C-T		not specified	Uncertain significance (Jun 22, 2023)
12-122980682-T-G		not specified	Uncertain significance (Aug 17, 2022)
12-122980718-G-A		not specified	Uncertain significance (Jul 13, 2022)
12-122980718-G-C		not specified	Uncertain significance (Dec 01, 2022)
12-122980722-T-C		not specified	Uncertain significance (Feb 21, 2024)
12-122980737-G-A		not specified	Uncertain significance (Dec 28, 2023)
12-122981137-G-A		not specified	Uncertain significance (Apr 26, 2023)
12-122981195-G-A		not specified	Uncertain significance (Jun 07, 2024)
12-122981204-A-C		not specified	Uncertain significance (Mar 03, 2022)
12-122981204-A-T		not specified	Uncertain significance (Jun 05, 2024)
12-122981230-G-A		not specified	Uncertain significance (Apr 22, 2022)
12-122981287-C-T		not specified	Likely benign (Jul 13, 2021)
12-122981612-G-A		not specified	Uncertain significance (Jun 24, 2022)
12-122981673-C-T		not specified	Uncertain significance (Sep 22, 2023)
12-122981679-C-T		not specified	Uncertain significance (Jan 31, 2023)
12-122981685-C-T		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL6IP4	protein_coding	protein_coding	ENST00000315580	6	2850

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000908	0.945	125656	0	31	125687	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.808	188	159	1.18	0.00000884	2220
Missense in Polyphen		44	47.503	0.92626		503
Synonymous	-1.32	81	67.2	1.20	0.00000365	786
Loss of Function	1.70	7	13.8	0.506	8.56e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000548	0.000547
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000450	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.000425	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in modulating alternative pre-mRNA splicing with either 5' distal site activation or preferential use of 3' proximal site. In case of infection by Herpes simplex virus (HSVI), may act as a splicing inhibitor of HSVI pre-mRNA. {ECO:0000269|PubMed:19582790}.

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.145
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.388

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arl6ip4

Gene ontology

• Biological process: mRNA processing;RNA splicing
• Cellular component: nucleus;nucleolus;nuclear speck
• Molecular function: RNA binding;protein binding