REEP3

receptor accessory protein 3, the group of Receptor accessory proteins

Basic information

Region (hg38): 10:63521400-63625128

Previous symbols: [ "C10orf74" ]

Links

ENSG00000165476 ∙ NCBI:221035 ∙ OMIM:609348 ∙ HGNC:23711 ∙ Uniprot:Q6NUK4 ∙ 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 REEP3 gene.

• Inborn genetic diseases (8 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the REEP3 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			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	1

Variants in REEP3

This is a list of pathogenic ClinVar variants found in the REEP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-63566399-G-A		not specified	Uncertain significance (Sep 14, 2022)
10-63566403-A-C		not specified	Uncertain significance (Mar 20, 2023)
10-63594794-A-T		not specified	Uncertain significance (Oct 12, 2021)
10-63598124-C-G		not specified	Uncertain significance (Oct 25, 2023)
10-63599278-G-A		not specified	Uncertain significance (Dec 08, 2023)
10-63610208-C-T		not specified	Uncertain significance (Jan 17, 2023)
10-63610281-A-G			Benign (Dec 31, 2019)
10-63610304-A-G		not specified	Uncertain significance (Aug 08, 2023)
10-63619660-G-A		not specified	Uncertain significance (Dec 19, 2022)
10-63619741-A-G		not specified	Uncertain significance (Dec 19, 2022)
10-63619755-A-G			Likely benign (Jun 22, 2018)
10-63619757-C-T		not specified	Uncertain significance (Jan 30, 2024)
10-63619784-C-G		not specified	Uncertain significance (May 23, 2023)
10-63620817-G-A		not specified	Uncertain significance (Mar 21, 2023)
10-63620850-G-A		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
REEP3	protein_coding	protein_coding	ENST00000373758	8	103761

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0151	0.980	124620	0	15	124635	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	94	129	0.731	0.00000663	1617
Missense in Polyphen		21	36.284	0.57876		495
Synonymous	0.734	36	42.1	0.856	0.00000215	470
Loss of Function	2.45	6	16.8	0.356	9.40e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000194	0.000194
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000815	0.0000796
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000370	0.0000327
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Microtubule-binding protein required to ensure proper cell division and nuclear envelope reassembly by sequestering the endoplasmic reticulum away from chromosomes during mitosis. Probably acts by clearing the endoplasmic reticulum membrane from metaphase chromosomes. {ECO:0000269|PubMed:23911198}.
• Pathway: Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.0919

Intolerance Scores

• loftool: 0.523
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.250
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0588

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Reep3

Gene ontology

• Biological process: nuclear envelope organization;mitotic nuclear envelope reassembly;cell division
• Cellular component: endoplasmic reticulum membrane;microtubule;integral component of membrane