LCORL

ligand dependent nuclear receptor corepressor like

Basic information

Region (hg38): 4:17841186-18021876

Links

ENSG00000178177 ∙ NCBI:254251 ∙ OMIM:611799 ∙ HGNC:30776 ∙ Uniprot:Q8N3X6 ∙ 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 LCORL gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCORL 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10			10
Total	0	0	20	0	0

Variants in LCORL

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

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

Position	Type	Phenotype	Significance	ClinVar
4-17842327-G-C		not specified	Uncertain significance (Jan 17, 2024)
4-17842337-G-A		not specified	Uncertain significance (Jan 08, 2024)
4-17842369-G-A		not specified	Uncertain significance (Sep 29, 2022)
4-17843348-C-T		not specified	Uncertain significance (Jan 25, 2023)
4-17843357-G-A		not specified	Uncertain significance (Aug 10, 2021)
4-17884108-C-T		not specified	Uncertain significance (Sep 14, 2022)
4-17884221-C-T		not specified	Uncertain significance (Mar 01, 2024)
4-17884243-C-G		not specified	Uncertain significance (May 09, 2023)
4-17884269-A-C		not specified	Uncertain significance (Feb 05, 2024)
4-17884306-G-A		not specified	Uncertain significance (Mar 27, 2023)
4-17884307-G-A		not specified	Uncertain significance (Mar 27, 2023)
4-17884565-A-G		not specified	Uncertain significance (Nov 22, 2023)
4-17884665-C-G		not specified	Uncertain significance (Feb 15, 2023)
4-17884711-G-C		not specified	Uncertain significance (Jun 09, 2022)
4-17884739-T-G		not specified	Uncertain significance (Aug 02, 2023)
4-17884750-C-T		not specified	Uncertain significance (Nov 22, 2023)
4-17886072-C-T		not specified	Uncertain significance (Apr 05, 2023)
4-17909194-T-G		not specified	Uncertain significance (Mar 07, 2023)
4-17909205-T-C		not specified	Uncertain significance (Jan 18, 2022)
4-17909222-C-A		not specified	Uncertain significance (Jun 16, 2023)
4-17909343-G-A		not specified	Uncertain significance (Sep 15, 2021)
4-17961911-C-T		not specified	Uncertain significance (Sep 16, 2021)
4-17963008-T-G		not specified	Uncertain significance (Dec 21, 2022)
4-17972847-G-C		not specified	Uncertain significance (Oct 13, 2023)
4-18021683-C-G		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCORL	protein_coding	protein_coding	ENST00000382226	7	180678

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.924	0.0763	124260	0	24	124284	0.0000966

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	201	279	0.720	0.0000136	3902
Missense in Polyphen		67	130.2	0.5146		1793
Synonymous	0.334	91	95.1	0.956	0.00000434	1155
Loss of Function	3.98	4	25.9	0.155	0.00000149	351

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000130	0.000123
Ashkenazi Jewish	0.000103	0.000100
East Asian	0.00	0.00
Finnish	0.000330	0.000324
European (Non-Finnish)	0.000128	0.000124
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as transcription activator that binds DNA elements with the sequence 5'-CCCTATCGATCGATCTCTACCT-3'. May play a role in spermatogenesis (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.109
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.321
• hipred: Y
• hipred_score: 0.549
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.619

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lcorl

Gene ontology

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