RAB22A

RAB22A, member RAS oncogene family, the group of RAB, member RAS oncogene GTPases

Basic information

Region (hg38): 20:58309715-58367507

Links

ENSG00000124209 ∙ NCBI:57403 ∙ OMIM:612966 ∙ HGNC:9764 ∙ Uniprot:Q9UL26 ∙ 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 RAB22A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB22A 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in RAB22A

This is a list of pathogenic ClinVar variants found in the RAB22A region.

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

Position	Type	Phenotype	Significance	ClinVar
20-58343729-T-C		not specified	Uncertain significance (Oct 16, 2023)
20-58343744-A-G		not specified	Uncertain significance (Mar 17, 2023)
20-58343797-C-G		not specified	Uncertain significance (Feb 12, 2025)
20-58353277-G-A		not specified	Uncertain significance (Sep 02, 2024)
20-58353327-T-C		not specified	Uncertain significance (Dec 03, 2024)
20-58353528-A-G		not specified	Uncertain significance (Dec 24, 2024)
20-58353531-G-C		not specified	Uncertain significance (May 04, 2022)
20-58354233-C-G		not specified	Uncertain significance (Aug 08, 2023)
20-58354241-A-G		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB22A	protein_coding	protein_coding	ENST00000244040	7	57812

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.103	0.891	125711	0	6	125717	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	62	112	0.552	0.00000641	1271
Missense in Polyphen		15	37.418	0.40088		439
Synonymous	-0.00728	42	41.9	1.00	0.00000269	365
Loss of Function	2.38	4	13.4	0.298	8.63e-7	134

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in endocytosis and intracellular protein transport. Mediates trafficking of TF from early endosomes to recycling endosomes (PubMed:16537905). Required for NGF-mediated endocytosis of NTRK1, and subsequent neurite outgrowth (PubMed:21849477). Binds GTP and GDP and has low GTPase activity. Alternates between a GTP-bound active form and a GDP-bound inactive form (PubMed:16537905). {ECO:0000269|PubMed:16537905, ECO:0000269|PubMed:21849477}.
• Pathway: Endocytosis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;RAB geranylgeranylation (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.453
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.675
• ghis: 0.656

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	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rab22a

Gene ontology

• Biological process: intracellular protein transport;endocytosis;endosome organization;Rab protein signal transduction;regulation of vesicle size
• Cellular component: ruffle;early endosome;late endosome;plasma membrane;endosome membrane;actin cytoskeleton;phagocytic vesicle membrane;phagocytic vesicle;extracellular exosome
• Molecular function: GTPase activity;protein binding;GTP binding;GDP binding