ARL16

protein-coding

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

Gene summary

The protein encoded by this gene belongs to the ARL (ADP-ribosylation factor-like) family of proteins, which are structurally related to ADP-ribosylation factors (ARFs). This protein has been shown to have an inhibitory role in the cellular antiviral response. This gene product interacts with the C-terminal domain of the DEXD/H-box helicase 58 (DDX58) gene product. This interaction was found to suppress the association between the DDX58 gene product and RNA, thereby negatively regulating the activity of the DDX58 gene product. [provided by RefSeq, Jul 2016]

MANE transcript

NM_001040025.3

Inheritance

—

ClinVar variants

U:36B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.22

Max pathogenic AF

—

Genomic locus

chr17:81,681,165-81,683,797

External References & Databases

Ensembl (ENSG00000214087)

Transcript & Mutation Effects

hg38 • Region Span ~2.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARL16 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 34

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040025.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			33 clinvar	1 clinvar		34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	36	1	0	37

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040025.3	RefSeq	NP_001035114.2	5	MANE Select
ENST00000622299.5	Ensembl	ENSP00000483183.1	5	MANE Select
NM_001329608.2	RefSeq	NP_001316537.1	2	Standard
NM_001329609.2	RefSeq	NP_001316538.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
GTP binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397498
Coding exons: 5
Length: 2751
Individuals with no LoFs: 124552
Homozygous LoFs: 0
Heterozygous LoFs: 82
Defined: 124634
p: 0.000329

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.720	134	113	1.19	0.00000568	1234
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0.00057	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00058	0.00056	rare
Finnish	0.000059	0.000046	rare
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.0010	0.00098	notable
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.633
RVIS EVS: -0.01
RVIS percentile EVS: 53.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.347

Gene Damage Prediction

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