ARL16

ADP ribosylation factor like GTPase 16, the group of ARF GTPase family

Basic information

Region (hg38): 17:81681186-81683797

Links

ENSG00000214087 ∙ NCBI:339231 ∙ OMIM:619117 ∙ HGNC:27902 ∙ Uniprot:Q0P5N6 ∙ 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 ARL16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL16 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1	2			3
Total	0	1	16	0	0

Variants in ARL16

This is a list of pathogenic ClinVar variants found in the ARL16 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-81681730-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-81681773-G-A		not specified	Uncertain significance (Oct 14, 2023)
17-81681776-C-T		not specified	Uncertain significance (Jan 23, 2023)
17-81681793-G-A		not specified	Uncertain significance (Apr 03, 2023)
17-81681862-A-G		not specified	Uncertain significance (Jan 23, 2024)
17-81682044-A-G		not specified	Uncertain significance (Feb 28, 2023)
17-81682086-G-A		not specified	Uncertain significance (May 11, 2022)
17-81683041-C-T		not specified	Uncertain significance (Oct 06, 2022)
17-81683046-C-A		not specified	Uncertain significance (Jul 14, 2023)
17-81683111-T-C		not specified	Uncertain significance (May 24, 2023)
17-81683113-A-C		not specified	Uncertain significance (Oct 06, 2021)
17-81683555-G-T		not specified	Uncertain significance (Nov 29, 2021)
17-81683716-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-81683735-C-G		not specified	Uncertain significance (Mar 25, 2024)
17-81683746-A-G		not specified	Uncertain significance (Feb 15, 2023)
17-81683756-C-T		not specified	Uncertain significance (Dec 18, 2023)
17-81683773-G-T		not specified	Uncertain significance (Aug 02, 2021)
17-81683794-C-A		Childhood-onset schizophrenia	Likely pathogenic (Jan 01, 2014)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL16	protein_coding	protein_coding	ENST00000397498	5	2751

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000169	0.140	124552	0	82	124634	0.000329

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.720	134	113	1.19	0.00000568	1234
Missense in Polyphen		58	46.579	1.2452		547
Synonymous	-2.83	71	46.5	1.53	0.00000229	425
Loss of Function	-0.523	8	6.55	1.22	2.75e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000762	0.000761
Ashkenazi Jewish	0.00	0.00
East Asian	0.000584	0.000556
Finnish	0.0000585	0.0000464
European (Non-Finnish)	0.000157	0.000150
Middle Eastern	0.000584	0.000556
South Asian	0.00100	0.000981
Other	0.000337	0.000330

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.633
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.0861
• hipred: N
• hipred_score: 0.201
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.347

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arl16

Gene ontology

• Molecular function: protein binding;GTP binding