RABL2A

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

Basic information

Region (hg38): 2:113627229-113643396

Links

ENSG00000144134 ∙ NCBI:11159 ∙ OMIM:605412 ∙ HGNC:9799 ∙ Uniprot:Q9UBK7 ∙ 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 RABL2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABL2A 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in RABL2A

This is a list of pathogenic ClinVar variants found in the RABL2A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-113628611-C-T		not specified	Uncertain significance (Dec 20, 2023)
2-113628616-G-A		not specified	Uncertain significance (Mar 17, 2023)
2-113628629-C-T		not specified	Uncertain significance (Feb 04, 2025)
2-113628632-G-A		not specified	Uncertain significance (Jun 23, 2023)
2-113628683-G-A		not specified	Uncertain significance (Oct 13, 2021)
2-113628703-G-C		not specified	Uncertain significance (Oct 03, 2024)
2-113632919-A-C		not specified	Uncertain significance (Sep 01, 2021)
2-113634181-C-G		not specified	Uncertain significance (Jan 17, 2024)
2-113635076-G-T		not specified	Uncertain significance (Jul 20, 2021)
2-113635102-A-C		not specified	Uncertain significance (Mar 03, 2025)
2-113635128-A-G		not specified	Uncertain significance (Feb 06, 2023)
2-113640930-C-A		not specified	Uncertain significance (Mar 05, 2025)
2-113640946-C-A		not specified	Uncertain significance (Jan 07, 2025)
2-113640994-A-G		not specified	Uncertain significance (Feb 15, 2023)
2-113641356-A-C		not specified	Uncertain significance (Nov 08, 2022)
2-113641364-G-A		not specified	Uncertain significance (Dec 11, 2024)
2-113641440-A-G		not specified	Uncertain significance (Sep 23, 2023)
2-113641459-G-A			Likely benign (Apr 01, 2025)
2-113641800-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-113642068-A-C		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABL2A	protein_coding	protein_coding	ENST00000393167	8	16168

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.25e-8	0.155	118174	295	7279	125748	0.0306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.436	106	119	0.888	0.00000638	1530
Missense in Polyphen		43	43.095	0.99779		543
Synonymous	0.795	40	46.9	0.852	0.00000278	386
Loss of Function	0.0229	11	11.1	0.993	5.08e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0307	0.0306
Ashkenazi Jewish	0.0298	0.0297
East Asian	0.104	0.103
Finnish	0.0109	0.0109
European (Non-Finnish)	0.0159	0.0159
Middle Eastern	0.104	0.103
South Asian	0.0793	0.0782
Other	0.0333	0.0324

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in male fertility, sperm intra- flagellar transport, and tail assembly. Binds, in a GTP-regulated manner, to a specific set of effector proteins including key proteins involved in cilia development and function and delivers them into the growing sperm tail. {ECO:0000250|UniProtKB:E9Q9D5}.

Recessive Scores

• pRec: 0.0982

Intolerance Scores

• loftool: 0.669
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.380
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000365

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular protein transport;Rab protein signal transduction
• Cellular component: cell
• Molecular function: GTPase activity;GTP binding