RAB9A

RAB9A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): X:13689128-13710504

Previous symbols: [ "RAB9" ]

Links

ENSG00000123595 ∙ NCBI:9367 ∙ OMIM:300284 ∙ HGNC:9792 ∙ Uniprot:P51151 ∙ 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 RAB9A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB9A 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				1	1	2
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	9	1	1

Variants in RAB9A

This is a list of pathogenic ClinVar variants found in the RAB9A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-13692854-G-A			Uncertain significance (Jun 24, 2023)
X-13708832-C-T		not specified	Uncertain significance (Jan 10, 2022)
X-13708883-A-G		not specified	Uncertain significance (Jun 16, 2024)
X-13708958-G-A		not specified	Uncertain significance (Dec 06, 2022)
X-13709062-A-C		not specified	Uncertain significance (May 31, 2023)
X-13709087-C-T		not specified	Uncertain significance (Jun 05, 2023)
X-13709181-C-T			Likely benign (Aug 01, 2022)
X-13709185-G-A		not specified	Uncertain significance (Jan 23, 2023)
X-13709306-C-A		not specified	Uncertain significance (Oct 05, 2023)
X-13709313-T-G		not specified	Uncertain significance (May 30, 2023)
X-13709340-A-T			Benign (Mar 29, 2018)
X-13709341-T-C		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB9A	protein_coding	protein_coding	ENST00000464506	1	21382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.832	0.165	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	45	76.4	0.589	0.00000569	1331
Missense in Polyphen		6	32.714	0.18341		625
Synonymous	0.957	23	29.6	0.776	0.00000239	380
Loss of Function	2.25	0	5.87	0.00	5.74e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the transport of proteins between the endosomes and the trans Golgi network. Involved in the recruitment of SGSM2 to melanosomes and is required for the proper trafficking of melanogenic enzymes TYR, TYRP1 and DCT/TYRP2 to melanosomes in melanocytes. {ECO:0000250|UniProtKB:P24408, ECO:0000250|UniProtKB:Q9R0M6}.
• Pathway: Measles - Homo sapiens (human);Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs;RAB geranylgeranylation;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.124
• hipred: Y
• hipred_score: 0.528
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rab9
• Phenotype: normal phenotype

Gene ontology

• Biological process: intracellular protein transport;Rab protein signal transduction;regulation of protein localization;retrograde transport, endosome to Golgi;positive regulation of exocytosis;negative regulation by host of symbiont molecular function
• Cellular component: lysosome;late endosome;endoplasmic reticulum membrane;cytosol;plasma membrane;transport vesicle;phagocytic vesicle membrane;trans-Golgi network membrane;melanosome;phagocytic vesicle;extracellular exosome
• Molecular function: GTPase activity;protein binding;GTP binding;GDP binding;identical protein binding