ARL9

ADP ribosylation factor like GTPase 9, the group of ARF GTPase family

Basic information

Region (hg38): 4:56505209-56524959

Links

ENSG00000196503 ∙ NCBI:132946 ∙ OMIM:612405 ∙ HGNC:23592 ∙ Uniprot:Q6T311 ∙ 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 ARL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARL9 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in ARL9

This is a list of pathogenic ClinVar variants found in the ARL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-56518742-C-G		not specified	Uncertain significance (Apr 25, 2022)
4-56518755-T-C		not specified	Uncertain significance (Jun 10, 2024)
4-56518845-A-G		not specified	Uncertain significance (Nov 09, 2023)
4-56518847-C-A		not specified	Uncertain significance (Nov 08, 2024)
4-56518851-C-G		not specified	Uncertain significance (Dec 31, 2024)
4-56523707-C-A		not specified	Uncertain significance (Nov 20, 2023)
4-56523710-C-T		not specified	Uncertain significance (Nov 20, 2023)
4-56523767-G-A		not specified	Uncertain significance (Jan 06, 2025)
4-56523796-A-G		not specified	Uncertain significance (Mar 29, 2024)
4-56523818-C-G		not specified	Uncertain significance (Aug 11, 2022)
4-56523818-C-T		not specified	Uncertain significance (Nov 18, 2023)
4-56523838-A-G		not specified	Uncertain significance (Dec 14, 2024)
4-56523856-C-G		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARL9	protein_coding	protein_coding	ENST00000360096	3	19106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.445	0.529	124633	0	20	124653	0.0000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0742	60	61.6	0.973	0.00000273	798
Missense in Polyphen		30	28.853	1.0398		364
Synonymous	0.953	18	23.9	0.752	0.00000103	245
Loss of Function	1.78	1	5.50	0.182	3.17e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000491	0.000361
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000621	0.0000619
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0857

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.255
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0117

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arl9
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Molecular function: GTP binding