ARL11

protein-coding

ADP ribosylation factor like GTPase 11, the group of ARF GTPase family

Gene summary

This gene encodes a tumor suppressor related to the ADP-ribosylation factor (ARF) family of proteins. The encoded protein may play a role in apoptosis in a caspase-dependent manner. Polymorphisms in this gene have been associated with some familial cancers. [provided by RefSeq, May 2010]

MANE transcript

NM_138450.6

Inheritance

ClinVar variants

U:33B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.12

Max pathogenic AF

—

Genomic locus

chr13:49,628,507-49,633,872

External References & Databases

Ensembl (ENSG00000152213)

Transcript & Mutation Effects

hg38 • Region Span ~5.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hereditary neoplastic syndromeLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0015356

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ARL11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 33

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138450.6. 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 clinvar		2
missense			30 clinvar	2 clinvar		32
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	33	4	0	37

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138450.6	RefSeq	NP_612459.1	1	MANE Select
ENST00000282026.2	Ensembl	ENSP00000282026.1	1	MANE Select
ENST00000920918.1	Ensembl	ENSP00000590977.1	1	Standard
ENST00000958145.1	Ensembl	ENSP00000628204.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

hematopoietic progenitor cell differentiation
intracellular protein transport
vesicle-mediated transport

Molecular Function

protein binding
GTP binding

Cellular Component

cytoplasm
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000282026
Coding exons: 1
Length: 5574
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125738
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0945	121	118	1.02	0.00000709	1253
Missense (PolyPhen)		44	44.013	0.99969		487
Synonymous	1.31	44	56.5	0.778	0.00000392	423
Loss of Function	-0.180	3	2.68	1.12	1.13e-7	34

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in apoptosis. May act as a tumor suppressor. {ECO:0000269|PubMed:15843669}.;

Recessive Scores

pRec: 0.0996

Intolerance Scores

LoFtool: 0.470
RVIS EVS: 0.7
RVIS percentile EVS: 85.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.910

Gene Damage Prediction

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