REP15

RAB15 effector protein

Basic information

Region (hg38): 12:27696447-27697596

Links

ENSG00000174236 ∙ NCBI:387849 ∙ OMIM:610848 ∙ HGNC:33748 ∙ Uniprot:Q6BDI9 ∙ 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 REP15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REP15 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in REP15

This is a list of pathogenic ClinVar variants found in the REP15 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-27696645-T-C		not specified	Uncertain significance (Apr 23, 2024)
12-27696730-T-A		not specified	Uncertain significance (Apr 28, 2023)
12-27696751-C-A		not specified	Uncertain significance (Dec 21, 2022)
12-27696823-C-G		not specified	Likely benign (Oct 10, 2023)
12-27696866-A-C		not specified	Uncertain significance (Dec 22, 2023)
12-27696924-T-C		not specified	Uncertain significance (Jan 26, 2022)
12-27697044-G-A		not specified	Uncertain significance (Oct 27, 2021)
12-27697067-C-T		not specified	Uncertain significance (Mar 30, 2024)
12-27697068-C-T		not specified	Uncertain significance (Feb 09, 2023)
12-27697101-T-G		not specified	Uncertain significance (Jul 29, 2023)
12-27697112-A-G		not specified	Uncertain significance (Jul 07, 2022)
12-27697185-G-C		not specified	Uncertain significance (Mar 16, 2024)
12-27697186-T-G		not specified	Uncertain significance (Dec 11, 2023)
12-27697223-A-G		not specified	Uncertain significance (Jun 18, 2021)
12-27697232-G-A		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REP15	protein_coding	protein_coding	ENST00000310791	1	1139

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000191	0.281	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.439	106	120	0.887	0.00000549	1551
Missense in Polyphen		25	30.718	0.81384		410
Synonymous	-0.283	48	45.6	1.05	0.00000228	451
Loss of Function	-0.0877	7	6.75	1.04	2.86e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates transferrin receptor recycling from the endocytic recycling compartment. {ECO:0000269|PubMed:16195351}.

Intolerance Scores

• loftool: 0.817
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.201

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0191

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rep15

Gene ontology

• Biological process: receptor recycling;transferrin transport
• Cellular component: endosome membrane;early endosome membrane;perinuclear region of cytoplasm;recycling endosome
• Molecular function: protein binding