LCORL

protein-coding

ligand dependent nuclear receptor corepressor like

Gene summary

This gene encodes a transcription factor that appears to function in spermatogenesis. Polymorphisms in this gene are associated with measures of skeletal frame size and adult height. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

MANE transcript

NM_001394446.1

Inheritance

—

ClinVar variants

U:41

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr4:17,841,187-18,021,876

External References & Databases

Ensembl (ENSG00000178177)

Transcript & Mutation Effects

hg38 • Region Span ~180.7 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 LCORL variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 76

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394446.1. 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			1 clinvar			1
missense			37 clinvar			37
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	41	0	0	41

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394446.1	RefSeq	NP_001381375.1	8	MANE Select
ENST00000635767.2	Ensembl	ENSP00000490600.1	8	MANE Select
NM_001166139.2	RefSeq	NP_001159611.1	7	Standard
NM_001365658.1	RefSeq	NP_001352587.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382226
Coding exons: 7
Length: 180678
Individuals with no LoFs: 124260
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 124284
p: 0.0000966

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.66	201	279	0.720	0.0000136	3902
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.00010	rare
East Asian	0	0.0	absent
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.619

Gene Damage Prediction

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