NCOA6

nuclear receptor coactivator 6

Basic information

Region (hg38): 20:34689097-34825651

Links

ENSG00000198646 ∙ NCBI:23054 ∙ OMIM:605299 ∙ HGNC:15936 ∙ Uniprot:Q14686 ∙ 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 NCOA6 gene.

• not_specified (247 variants)
• not_provided (26 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCOA6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014071.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			5	9	8	22
missense			244	10	3	257
nonsense			4			4
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7			7
Total	0	0	260	19	11

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCOA6	protein_coding	protein_coding	ENST00000374796	13	128731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.954	1035	1.13e+3	0.920	0.0000583	13520
Missense in Polyphen		332	419.52	0.79138		5220
Synonymous	-1.02	449	422	1.06	0.0000236	4273
Loss of Function	6.80	13	77.7	0.167	0.00000413	793

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000164	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000164	0.000163
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Coactivates expression in an agonist- and AF2-dependent manner. Involved in the coactivation of different nuclear receptors, such as for steroids (GR and ERs), retinoids (RARs and RXRs), thyroid hormone (TRs), vitamin D3 (VDR) and prostanoids (PPARs). Probably functions as a general coactivator, rather than just a nuclear receptor coactivator. May also be involved in the coactivation of the NF-kappa-B pathway. May coactivate expression via a remodeling of chromatin and its interaction with histone acetyltransferase proteins.
• Pathway: Constitutive Androstane Receptor Pathway;Nuclear Receptors Meta-Pathway;Liver steatosis AOP;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;Metabolism;AndrogenReceptor;Coregulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.355

Intolerance Scores

• loftool: 0.354
• rvis_EVS: -2.02
• rvis_percentile_EVS: 1.71

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.864

Gene Damage Prediction

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

Gene ontology

• Biological process: DNA replication;DNA repair;DNA recombination;DNA-templated transcription, initiation;cellular response to DNA damage stimulus;brain development;heart development;response to hormone;regulation of lipid metabolic process;myeloid cell differentiation;intracellular estrogen receptor signaling pathway;glucocorticoid receptor signaling pathway;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;transcription factor complex;cytosol;histone methyltransferase complex;intracellular membrane-bounded organelle
• Molecular function: chromatin binding;transcription coactivator activity;protein binding;enzyme binding;estrogen receptor binding;nuclear receptor transcription coactivator activity;retinoid X receptor binding;thyroid hormone receptor binding