RCE1

Ras converting CAAX endopeptidase 1

Basic information

Region (hg38): 11:66842834-66846552

Previous symbols: [ "RCE1A", "RCE1B" ]

Links

ENSG00000173653 ∙ NCBI:9986 ∙ OMIM:605385 ∙ HGNC:13721 ∙ Uniprot:Q9Y256 ∙ 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 RCE1 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCE1 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in RCE1

This is a list of pathogenic ClinVar variants found in the RCE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66842871-CAA-C		Hydatidiform mole, recurrent, 4	Likely pathogenic (-)
11-66842947-G-A		TOP6BL-related disorder	Benign/Likely benign (Apr 18, 2019)
11-66843021-C-T		TOP6BL-related disorder	Likely benign (Mar 19, 2019)
11-66843174-G-C		TOP6BL-related disorder	Benign (Oct 21, 2019)
11-66843468-G-A		not specified	Uncertain significance (Nov 14, 2023)
11-66843471-G-A		not specified	Uncertain significance (Apr 25, 2023)
11-66843474-G-A		not specified	Uncertain significance (Dec 19, 2023)
11-66843499-C-T		not specified	Uncertain significance (Jun 09, 2022)
11-66843519-G-C		not specified	Uncertain significance (Aug 17, 2022)
11-66843570-G-C		not specified	Uncertain significance (May 31, 2023)
11-66843630-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-66843814-C-T		not specified	Uncertain significance (Oct 22, 2021)
11-66843821-C-T		not specified	Uncertain significance (Jul 31, 2023)
11-66843829-G-A		not specified	Uncertain significance (Jan 04, 2022)
11-66843966-C-G		not specified	Uncertain significance (Jan 19, 2024)
11-66844341-C-T		not specified	Uncertain significance (Oct 29, 2021)
11-66845000-C-T		not specified	Uncertain significance (Aug 13, 2021)
11-66845013-C-T		not specified	Uncertain significance (Sep 26, 2023)
11-66845213-G-C		not specified	Uncertain significance (Dec 21, 2022)
11-66845213-G-T		not specified	Uncertain significance (Feb 08, 2023)
11-66845547-C-T		not specified	Uncertain significance (Jun 29, 2022)
11-66845970-G-T		not specified	Uncertain significance (Nov 06, 2023)
11-66846061-G-A		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCE1	protein_coding	protein_coding	ENST00000309657	8	3712

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.160	0.838	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.782	158	188	0.840	0.0000104	2062
Missense in Polyphen		37	59.755	0.6192		624
Synonymous	-2.43	110	82.0	1.34	0.00000439	731
Loss of Function	2.59	4	14.8	0.271	6.29e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000994	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proteolytically removes the C-terminal three residues of farnesylated and geranylated proteins. Seems to be able to process K-Ras, N-Ras, H-Ras, RAP1B and G-gamma-1 (PubMed:10085068). {ECO:0000269|PubMed:10085068, ECO:0000269|PubMed:11038283, ECO:0000269|PubMed:19188362}.
• Pathway: Terpenoid backbone biosynthesis - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.205
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.419
• hipred: Y
• hipred_score: 0.523
• ghis: 0.691

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.584

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rce1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; muscle phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: proteolysis;protein deubiquitination;CAAX-box protein processing
• Cellular component: endoplasmic reticulum membrane;cytosol;integral component of plasma membrane;membrane;integral component of endoplasmic reticulum membrane
• Molecular function: endopeptidase activity;cysteine-type endopeptidase activity;metalloendopeptidase activity