RCOR1

REST corepressor 1, the group of Myb/SANT domain containing

Basic information

Region (hg38): 14:102592649-102730561

Previous symbols: [ "RCOR" ]

Links

ENSG00000089902 ∙ NCBI:23186 ∙ OMIM:607675 ∙ HGNC:17441 ∙ Uniprot:Q9UKL0 ∙ 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 RCOR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RCOR1 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				11	3	14
missense			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel			7	1		8
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				6	3	9
Total	0	0	23	18	7

Variants in RCOR1

This is a list of pathogenic ClinVar variants found in the RCOR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-102592894-C-A			Uncertain significance (Apr 01, 2022)
14-102592921-C-T			Uncertain significance (Aug 09, 2022)
14-102592949-GGCCGCCTCCGCCTCCGCCGCC-G			Likely benign (Jan 22, 2024)
14-102592950-GCCGCCT-G			Uncertain significance (Sep 10, 2022)
14-102592954-C-T			Uncertain significance (Apr 11, 2023)
14-102592955-C-T			Likely benign (Nov 28, 2023)
14-102592956-TCCGCCTCCGCCGCCG-T			Uncertain significance (Apr 30, 2023)
14-102592956-T-TCCGCCTCCGCCGCCG			Uncertain significance (Dec 24, 2021)
14-102592962-T-G			Uncertain significance (Apr 01, 2022)
14-102592962-T-TCCG			Uncertain significance (Nov 03, 2023)
14-102592979-C-T			Likely benign (Jan 22, 2024)
14-102592993-C-T		not specified	Uncertain significance (Jan 27, 2022)
14-102593019-G-A		not specified	Uncertain significance (Sep 14, 2022)
14-102593024-C-T			Likely benign (Aug 16, 2021)
14-102593029-GCGCCGCCGCCTCCTCAGCCTCGGCCGCCGCCGCCTCAGC-G			Uncertain significance (Jul 12, 2022)
14-102593037-GCCT-G			Uncertain significance (Dec 18, 2023)
14-102593051-GGCCGCCGCCGCCTCAGCC-G			Uncertain significance (Dec 09, 2022)
14-102593067-G-T		not specified	Uncertain significance (Nov 09, 2023)
14-102593078-C-T			Likely benign (May 21, 2022)
14-102593083-A-G			Uncertain significance (Nov 03, 2022)
14-102593090-C-T			Likely benign (Jul 17, 2022)
14-102593169-T-A			Uncertain significance (Oct 26, 2023)
14-102593334-CGG-C			Benign (Nov 14, 2023)
14-102681933-G-T		not specified	Uncertain significance (Sep 29, 2023)
14-102681965-G-C			Likely benign (Jan 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RCOR1	protein_coding	protein_coding	ENST00000262241	12	137916

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000783	123794	0	1	123795	0.00000404

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	152	232	0.655	0.0000125	3142
Missense in Polyphen		41	96.82	0.42347		1142
Synonymous	-0.750	89	80.4	1.11	0.00000417	891
Loss of Function	4.80	0	26.8	0.00	0.00000145	314

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000999	0.0000999
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: Essential component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it serves as a molecular beacon for the recruitment of molecular machinery, including MeCP2 and SUV39H1, that imposes silencing across a chromosomal interval. Plays a central role in demethylation of Lys-4 of histone H3 by promoting demethylase activity of KDM1A on core histones and nucleosomal substrates. It also protects KDM1A from the proteasome. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development and controls hematopoietic differentiation. {ECO:0000269|PubMed:11171972, ECO:0000269|PubMed:11516394, ECO:0000269|PubMed:12032298, ECO:0000269|PubMed:12399542, ECO:0000269|PubMed:12493763, ECO:0000269|PubMed:16079794, ECO:0000269|PubMed:16140033}.
• Pathway: Huntington,s disease - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;Signal Transduction;Factors involved in megakaryocyte development and platelet production;HDACs deacetylate histones;Chromatin modifying enzymes;Regulation of PTEN gene transcription;Hemostasis;PTEN Regulation;PIP3 activates AKT signaling;Chromatin organization;Intracellular signaling by second messengers (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.159
• hipred: Y
• hipred_score: 0.755
• ghis: 0.647

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.764

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rcor1
• Phenotype: embryo phenotype; normal 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); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: rcor1
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;blood coagulation;viral process;negative regulation of transcription, DNA-templated;histone H4 deacetylation
• Cellular component: nucleus;nucleoplasm;transcription factor complex;transcriptional repressor complex;DNA repair complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;histone deacetylase activity;protein binding;transcription factor binding;transcription regulatory region DNA binding