RABEP1

rabaptin, RAB GTPase binding effector protein 1

Basic information

Region (hg38): 17:5282264-5386340

Links

ENSG00000029725 ∙ NCBI:9135 ∙ OMIM:603616 ∙ HGNC:17677 ∙ Uniprot:Q15276 ∙ 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 RABEP1 gene.

• Inborn genetic diseases (26 variants)
• not provided (4 variants)
• Fetal akinesia deformation sequence 4 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABEP1 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				2		2
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1		2	3
Total	0	0	25	3	2

Variants in RABEP1

This is a list of pathogenic ClinVar variants found in the RABEP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-5282491-C-A		not specified	Uncertain significance (Sep 27, 2022)
17-5282508-T-C		not specified	Likely benign (Apr 07, 2023)
17-5308728-A-C		not specified	Uncertain significance (Dec 16, 2022)
17-5332113-T-G		not specified	Uncertain significance (Jun 24, 2022)
17-5335213-C-T		not specified	Uncertain significance (Sep 17, 2021)
17-5335264-G-A		not specified	Uncertain significance (Dec 28, 2022)
17-5335289-G-C		not specified	Uncertain significance (Dec 27, 2023)
17-5335301-C-A		not specified	Uncertain significance (Mar 22, 2023)
17-5335301-C-G		not specified	Uncertain significance (Dec 05, 2022)
17-5338059-C-T		not specified	Uncertain significance (Dec 15, 2021)
17-5338079-G-A		not specified	Uncertain significance (Aug 12, 2021)
17-5338113-A-C		not specified	Uncertain significance (Oct 26, 2021)
17-5338123-G-C		not specified	Uncertain significance (Jul 19, 2023)
17-5346796-G-A		not specified	Uncertain significance (Mar 14, 2023)
17-5346805-C-A		not specified	Uncertain significance (Mar 29, 2023)
17-5350586-C-T		not specified	Uncertain significance (Jun 22, 2023)
17-5361214-T-G		not specified	Uncertain significance (Feb 27, 2024)
17-5361291-G-A			Likely benign (May 01, 2022)
17-5361318-C-T			Likely benign (Oct 17, 2017)
17-5361473-C-T		not specified	Uncertain significance (Nov 23, 2022)
17-5361511-A-T		not specified	Uncertain significance (Dec 19, 2023)
17-5362953-G-A		not specified	Uncertain significance (Jun 07, 2023)
17-5365201-A-G		not specified	Uncertain significance (May 17, 2023)
17-5365221-G-A		Teratoma	Uncertain significance (Jan 01, 2023)
17-5365235-C-A		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABEP1	protein_coding	protein_coding	ENST00000262477	18	103572

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00149	124776	0	16	124792	0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	330	439	0.751	0.0000233	5655
Missense in Polyphen		109	183.47	0.59412		2319
Synonymous	0.491	154	162	0.951	0.00000854	1534
Loss of Function	5.82	8	54.2	0.148	0.00000272	656

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.000167	0.000167
South Asian	0.000229	0.000229
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rab effector protein acting as linker between gamma- adaptin, RAB4A and RAB5A. Involved in endocytic membrane fusion and membrane trafficking of recycling endosomes. Involved in KCNH1 channels trafficking to and from the cell membrane (PubMed:22841712). Stimulates RABGEF1 mediated nucleotide exchange on RAB5A. {ECO:0000269|PubMed:10698684, ECO:0000269|PubMed:11452015, ECO:0000269|PubMed:12773381, ECO:0000269|PubMed:22841712, ECO:0000269|PubMed:8521472}.
• Pathway: Endocytosis - Homo sapiens (human);Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• rvis_EVS: -1.2
• rvis_percentile_EVS: 5.83

Haploinsufficiency Scores

• pHI: 0.626
• hipred: Y
• hipred_score: 0.528
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.837

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rabep1

Zebrafish Information Network

• Gene name: rabep1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: Golgi to plasma membrane transport;endocytosis;apoptotic process;regulation of signaling receptor activity;protein transport;vesicle-mediated transport;positive regulation of GTPase activity;membrane fusion;protein localization to ciliary membrane
• Cellular component: endosome;early endosome;endocytic vesicle;early endosome membrane;protein-containing complex;intracellular membrane-bounded organelle;recycling endosome
• Molecular function: GTPase activator activity;protein binding;growth factor activity;protein domain specific binding;protein homodimerization activity