RABEPK

Rab9 effector protein with kelch motifs

Basic information

Region (hg38): 9:125200542-125234161

Links

ENSG00000136933 ∙ NCBI:10244 ∙ OMIM:605962 ∙ HGNC:16896 ∙ Uniprot:Q7Z6M1 ∙ 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 RABEPK gene.

Variants pathogenicity by type

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

Variants in RABEPK

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

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

Position	Type	Phenotype	Significance	ClinVar
9-125203020-C-A		not specified	Uncertain significance (May 03, 2023)
9-125207602-G-A		not specified	Uncertain significance (Apr 12, 2024)
9-125207628-C-A		not specified	Uncertain significance (Nov 29, 2023)
9-125207650-G-C		not specified	Uncertain significance (Jan 24, 2024)
9-125207674-G-T		not specified	Uncertain significance (Apr 07, 2022)
9-125207707-A-G		not specified	Uncertain significance (Dec 20, 2023)
9-125207712-A-G		not specified	Uncertain significance (Oct 14, 2023)
9-125213414-C-T		High myopia	Uncertain significance (Dec 17, 2018)
9-125213456-C-T		not specified	Uncertain significance (Oct 03, 2023)
9-125213463-G-C		not specified	Uncertain significance (Feb 27, 2024)
9-125220548-C-A		not specified	Uncertain significance (Sep 28, 2022)
9-125220572-G-T		not specified	Uncertain significance (Mar 06, 2023)
9-125220578-C-A		not specified	Uncertain significance (Nov 10, 2022)
9-125220580-C-T		not specified	Uncertain significance (Mar 01, 2023)
9-125220589-A-G		not specified	Uncertain significance (Dec 20, 2022)
9-125220623-A-G		not specified	Uncertain significance (Jan 10, 2022)
9-125220646-G-A		not specified	Uncertain significance (May 14, 2024)
9-125220667-G-A		not specified	Uncertain significance (Sep 17, 2021)
9-125220697-G-A		not specified	Uncertain significance (Jan 22, 2024)
9-125220697-G-C		not specified	Uncertain significance (Dec 11, 2023)
9-125227946-A-G		not specified	Uncertain significance (Aug 23, 2021)
9-125227952-C-T		not specified	Uncertain significance (Feb 21, 2024)
9-125227958-C-G		not specified	Uncertain significance (Nov 04, 2023)
9-125227961-G-A		not specified	Uncertain significance (Mar 21, 2023)
9-125227970-A-C		not specified	Uncertain significance (Apr 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABEPK	protein_coding	protein_coding	ENST00000373538	7	33617

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.84e-11	0.0806	124519	7	1220	125746	0.00489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0477	207	209	0.991	0.0000107	2423
Missense in Polyphen		77	76.219	1.0102		866
Synonymous	0.157	78	79.8	0.978	0.00000441	741
Loss of Function	0.284	17	18.3	0.928	0.00000101	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00637	0.00637
Ashkenazi Jewish	0.00338	0.00338
East Asian	0.000381	0.000381
Finnish	0.000970	0.000971
European (Non-Finnish)	0.00665	0.00662
Middle Eastern	0.000381	0.000381
South Asian	0.00582	0.00573
Other	0.00723	0.00719

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rab9 effector required for endosome to trans-Golgi network (TGN) transport. {ECO:0000269|PubMed:9230071}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.0851

Intolerance Scores

• loftool: 0.995
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.0785
• hipred: N
• hipred_score: 0.197
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.887

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rabepk

Gene ontology

• Biological process: receptor-mediated endocytosis;vesicle docking involved in exocytosis
• Cellular component: endosome;cytosol;endosome membrane;transport vesicle;trans-Golgi network membrane