RABEP2

rabaptin, RAB GTPase binding effector protein 2

Basic information

Region (hg38): 16:28904421-28936526

Links

ENSG00000177548 ∙ NCBI:79874 ∙ OMIM:611869 ∙ HGNC:24817 ∙ Uniprot:Q9H5N1 ∙ 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 RABEP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABEP2 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
missense			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		2	3
Total	0	0	33	2	3

Variants in RABEP2

This is a list of pathogenic ClinVar variants found in the RABEP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28904492-G-A		Brody myopathy	Uncertain significance (Jan 12, 2018)
16-28904503-C-T		Brody myopathy	Benign (Jan 13, 2018)
16-28905025-C-T		not specified	Uncertain significance (May 06, 2022)
16-28905032-G-A		not specified	Uncertain significance (Feb 23, 2023)
16-28905054-C-T			Benign (Dec 31, 2019)
16-28905420-C-T		not specified	Uncertain significance (Jan 11, 2023)
16-28905467-C-T		not specified	Uncertain significance (Jun 22, 2024)
16-28905724-C-A		not specified	Uncertain significance (Sep 01, 2021)
16-28905726-C-T		not specified	Uncertain significance (May 18, 2023)
16-28905873-G-C		not specified	Uncertain significance (Jul 13, 2022)
16-28906096-A-G		not specified	Uncertain significance (Jan 23, 2023)
16-28906121-G-A		not specified	Uncertain significance (Aug 26, 2022)
16-28906168-C-T		not specified	Likely benign (Mar 29, 2022)
16-28908610-G-T		not specified	Uncertain significance (May 06, 2024)
16-28908650-G-T		not specified	Uncertain significance (May 27, 2022)
16-28908692-G-A		not specified	Uncertain significance (Apr 25, 2023)
16-28908719-G-A		not specified	Uncertain significance (Dec 06, 2022)
16-28908723-T-C			Benign (Jan 30, 2018)
16-28908732-G-C		not specified	Uncertain significance (Mar 19, 2024)
16-28910938-T-A		not specified	Uncertain significance (Sep 15, 2021)
16-28911137-G-A		not specified	Uncertain significance (Feb 13, 2024)
16-28911149-C-G		not specified	Uncertain significance (Apr 20, 2023)
16-28911149-C-T		not specified	Likely benign (Nov 08, 2021)
16-28911171-C-G		not specified	Uncertain significance (Nov 09, 2023)
16-28914324-G-A		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABEP2	protein_coding	protein_coding	ENST00000358201	13	32106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00114	0.999	124731	0	74	124805	0.000297

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.432	337	360	0.936	0.0000243	3599
Missense in Polyphen		65	73.254	0.88732		740
Synonymous	0.626	156	166	0.938	0.0000109	1198
Loss of Function	3.43	11	31.9	0.344	0.00000162	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000684	0.000678
Ashkenazi Jewish	0.00402	0.00368
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000164	0.000150
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000659	0.0000654
Other	0.000186	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in membrane trafficking and in homotypic early endosome fusion. {ECO:0000269|PubMed:9524116}.

Recessive Scores

• pRec: 0.239

Intolerance Scores

• loftool: 0.502
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.246
• hipred: N
• hipred_score: 0.372
• ghis: 0.650

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.104

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rabep2

Gene ontology

• Biological process: endocytosis;regulation of signaling receptor activity;protein transport;positive regulation of GTPase activity
• Cellular component: early endosome;cytosol;intracellular membrane-bounded organelle
• Molecular function: GTPase activator activity;growth factor activity