ARL6IP6

ADP ribosylation factor like GTPase 6 interacting protein 6

Basic information

Region (hg38): 2:152717646-152762396

Links

ENSG00000177917 ∙ NCBI:151188 ∙ OMIM:616495 ∙ HGNC:24048 ∙ Uniprot:Q8N6S5 ∙ 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 ARL6IP6 gene.

• Inborn genetic diseases (11 variants)
• not provided (3 variants)
• Bardet-Biedl syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL6IP6 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		1	12		1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	1	12	0	1

Highest pathogenic variant AF is 0.0000197

Variants in ARL6IP6

This is a list of pathogenic ClinVar variants found in the ARL6IP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-152718629-C-T		not specified	Uncertain significance (Mar 04, 2024)
2-152718713-C-T		not specified	Uncertain significance (Nov 09, 2023)
2-152718760-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-152718787-C-G		not specified	Uncertain significance (Feb 06, 2023)
2-152718788-T-G		not specified	Uncertain significance (Feb 28, 2024)
2-152718790-C-G		not specified	Uncertain significance (Jan 04, 2022)
2-152718791-G-T			Benign (Mar 01, 2023)
2-152718816-G-A			Uncertain significance (Aug 29, 2018)
2-152718824-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-152718833-G-C		not specified	Uncertain significance (May 04, 2023)
2-152718887-A-C		not specified	Uncertain significance (Dec 12, 2023)
2-152718901-G-T		not specified	Uncertain significance (Feb 15, 2023)
2-152718920-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-152718924-G-C		not specified	Uncertain significance (Jun 07, 2023)
2-152718956-T-C		not specified	Uncertain significance (Sep 20, 2023)
2-152718958-C-A		not specified	Uncertain significance (May 18, 2023)
2-152718965-C-T			Uncertain significance (Aug 25, 2020)
2-152718985-C-A		not specified	Uncertain significance (Jan 23, 2023)
2-152718997-C-T		Bardet-Biedl syndrome	Likely pathogenic (-)
2-152720525-A-G			Benign (Dec 31, 2019)
2-152735075-C-T		not specified	Uncertain significance (Jul 27, 2022)
2-152735113-C-T		not specified	Uncertain significance (Mar 14, 2023)
2-152735116-G-A		not specified	Uncertain significance (Jan 29, 2024)
2-152759764-C-G		not specified	Uncertain significance (Mar 24, 2023)
2-152759779-A-G		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL6IP6	protein_coding	protein_coding	ENST00000326446	4	43361

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0181	0.903	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.77	183	127	1.44	0.00000574	1438
Missense in Polyphen		65	50.595	1.2847		606
Synonymous	-2.24	75	54.1	1.39	0.00000262	485
Loss of Function	1.48	4	8.73	0.458	3.71e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.000166	0.000163
Finnish	0.0000480	0.0000462
European (Non-Finnish)	0.0000542	0.0000527
Middle Eastern	0.000166	0.000163
South Asian	0.000361	0.000359
Other	0.000342	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0951

Intolerance Scores

• loftool: 0.365
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.0908
• hipred: N
• hipred_score: 0.199
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.407

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arl6ip6

Gene ontology

• Cellular component: integral component of membrane