LCOR

ligand dependent nuclear receptor corepressor

Basic information

Region (hg38): 10:96832254-96995956

Previous symbols: [ "C10orf12" ]

Links

ENSG00000196233 ∙ NCBI:84458 ∙ OMIM:607698 ∙ HGNC:29503 ∙ Uniprot:Q96JN0 ∙ 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 LCOR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCOR 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in LCOR

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

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

Position	Type	Phenotype	Significance	ClinVar
10-96949175-A-G		not specified	Uncertain significance (Mar 30, 2024)
10-96949199-A-G		not specified	Uncertain significance (Mar 30, 2024)
10-96949209-C-T		not specified	Uncertain significance (Apr 26, 2024)
10-96949224-T-C		not specified	Uncertain significance (Jul 12, 2022)
10-96952154-C-A		not specified	Uncertain significance (Feb 28, 2023)
10-96955129-C-T		not specified	Uncertain significance (May 09, 2023)
10-96955180-T-C		not specified	Uncertain significance (Feb 22, 2023)
10-96955294-C-T		not specified	Uncertain significance (Sep 14, 2022)
10-96955330-C-G		not specified	Uncertain significance (May 26, 2023)
10-96955417-A-G		not specified	Uncertain significance (Jun 25, 2024)
10-96955441-G-A		not specified	Uncertain significance (Nov 26, 2024)
10-96955459-T-C		not specified	Uncertain significance (Dec 20, 2021)
10-96955471-C-T		not specified	Uncertain significance (Mar 03, 2023)
10-96955488-A-C		not specified	Uncertain significance (Feb 12, 2024)
10-96955527-A-G		not specified	Uncertain significance (Jan 26, 2023)
10-96955537-A-G		not specified	Uncertain significance (Dec 19, 2023)
10-96955576-C-T		not specified	Uncertain significance (Dec 01, 2022)
10-96955618-A-G		not specified	Uncertain significance (Oct 12, 2022)
10-96955851-G-A		not specified	Uncertain significance (Jan 04, 2022)
10-96955888-C-G		not specified	Uncertain significance (Dec 20, 2023)
10-96981898-A-G		not specified	Uncertain significance (Oct 05, 2021)
10-96982243-C-T		not specified	Uncertain significance (Nov 09, 2021)
10-96982768-A-G		not specified	Uncertain significance (Nov 15, 2021)
10-96983024-G-A		Malignant tumor of prostate	Uncertain significance (-)
10-96983271-T-G			Likely benign (Mar 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCOR	protein_coding	protein_coding	ENST00000371097	3	148784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.950	0.0498	125738	0	3	125741	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	190	239	0.796	0.0000126	2822
Missense in Polyphen		19	38.557	0.49278		507
Synonymous	1.36	72	88.3	0.815	0.00000486	863
Loss of Function	3.53	2	18.3	0.110	0.00000108	198

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	0.0000463	0.0000462
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as transcription activator that binds DNA elements with the sequence 5'-CCCTATCGATCGATCTCTACCT-3' (By similarity). Repressor of ligand-dependent transcription activation by target nuclear receptors. Repressor of ligand- dependent transcription activation by ESR1, ESR2, NR3C1, PGR, RARA, RARB, RARG, RXRA and VDR. {ECO:0000250, ECO:0000269|PubMed:12535528}.
• Pathway: Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.0883

Intolerance Scores

• loftool: 0.0127
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.124
• hipred: Y
• hipred_score: 0.748
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lcor

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;transcription factor binding