RCOR3

protein-coding

REST corepressor 3, the group of Myb/SANT domain containing

Gene summary

Predicted to enable enzyme binding activity and transcription corepressor activity. Predicted to be involved in negative regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001136223.3

Inheritance

—

ClinVar variants

U:51B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr1:211,258,377-211,316,385

External References & Databases

Ensembl (ENSG00000117625)

Transcript & Mutation Effects

hg38 • Region Span ~58.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RCOR3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001136223.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	3 clinvar		5
missense			45 clinvar			45
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	51	3	0	54

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 89 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001136223.3	RefSeq	NP_001129695.1	12	MANE Select
ENST00000419091.7	Ensembl	ENSP00000413929.2	12	MANE Select
NM_001136224.4	RefSeq	NP_001129696.2	11	Standard
NM_001136225.3	RefSeq	NP_001129697.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
negative regulation of nucleic acid-templated transcription

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription factor activity
transcription corepressor activity
protein binding
transcription factor binding

Cellular Component

nucleus
transcription factor complex
transcriptional repressor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000419091
Coding exons: 12
Length: 58009
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125746
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.72	172	306	0.563	0.0000167	3632
Missense (PolyPhen)		68	157.21	0.43255		1779
Synonymous	1.99	77	103	0.750	0.00000493	1068
Loss of Function	4.24	3	26.6	0.113	0.00000114	329

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a component of a corepressor complex that represses transcription. {ECO:0000305}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.457
RVIS EVS: -0.41
RVIS percentile EVS: 26.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.968

Gene Damage Prediction

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