RABL2B

RAB, member of RAS oncogene family like 2B, the group of RAB like GTPases

Basic information

Region (hg38): 22:50767501-50783667

Links

ENSG00000079974 ∙ NCBI:11158 ∙ OMIM:605413 ∙ HGNC:9800 ∙ Uniprot:Q9UNT1 ∙ 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 RABL2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABL2B 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			16			16
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	16	1	0

Variants in RABL2B

This is a list of pathogenic ClinVar variants found in the RABL2B region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50768810-G-A		not specified	Uncertain significance (Nov 09, 2023)
22-50769034-G-T			Benign (Dec 31, 2019)
22-50769106-G-A			Likely benign (Jul 06, 2018)
22-50769451-A-G		not specified	Uncertain significance (Aug 02, 2021)
22-50769465-T-C		not specified	Uncertain significance (Jul 14, 2022)
22-50769487-C-T		not specified	Uncertain significance (Mar 21, 2023)
22-50769533-T-G		not specified	Uncertain significance (Jan 24, 2024)
22-50769916-T-C		not specified	Uncertain significance (Jan 09, 2024)
22-50769988-T-C		not specified	Uncertain significance (Jan 04, 2022)
22-50775783-C-T		not specified	Uncertain significance (Sep 27, 2022)
22-50775840-T-G		not specified	Uncertain significance (Oct 04, 2022)
22-50776679-T-G		not specified	Uncertain significance (Mar 30, 2024)
22-50776693-A-C		not specified	Uncertain significance (May 21, 2024)
22-50776706-G-A		not specified	Uncertain significance (Aug 13, 2021)
22-50777956-C-T		not specified	Uncertain significance (Jan 12, 2024)
22-50777972-C-A		not specified	Uncertain significance (Jul 26, 2022)
22-50777976-A-G		not specified	Uncertain significance (Aug 03, 2022)
22-50782204-C-T		not specified	Uncertain significance (Nov 22, 2022)
22-50782243-C-T		not specified	Uncertain significance (Dec 06, 2022)
22-50782258-G-T		not specified	Uncertain significance (Mar 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABL2B	protein_coding	protein_coding	ENST00000395593	8	16163

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.72e-7	0.300	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0204	129	128	1.01	0.00000706	1596
Missense in Polyphen		32	35.707	0.89619		448
Synonymous	-0.0181	51	50.8	1.00	0.00000327	407
Loss of Function	0.340	10	11.2	0.890	5.14e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000620	0.000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000943	0.0000924
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.00	0.00
South Asian	0.000458	0.000457
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Small GTPase required for ciliation. Activated in a guanine nucleotide exchange factor (GEF)-independent manner via its intrinsic GDP for GTP nucleotide exchange ability (PubMed:28625565). Involved in ciliary assembly by binding the intraflagellar transport (IFT) complex B from the large pool pre- docked at the base of the cilium and thus triggers its entry into the cilia (PubMed:28625565, PubMed:28428259). {ECO:0000269|PubMed:28428259, ECO:0000269|PubMed:28625565}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.829
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.0961
• hipred: N
• hipred_score: 0.380
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.669

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rabl2
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: intracellular protein transport;Rab protein signal transduction;intraciliary transport;cilium assembly
• Cellular component: pericentriolar material;cytoplasm;centriole;ciliary basal body
• Molecular function: GTPase activity;protein binding;GTP binding