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.

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.

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				8	8	16
missense			88	7	3	98
nonsense						0
start loss						0
frameshift						0
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	88	16	12

Variants in NCOA6

This is a list of pathogenic ClinVar variants found in the NCOA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-34708786-C-T		not specified	Uncertain significance (Nov 03, 2023)
20-34708788-G-C		not specified	Uncertain significance (Aug 28, 2021)
20-34708815-G-T		not specified	Uncertain significance (Sep 16, 2022)
20-34708845-C-G		not specified	Uncertain significance (Sep 26, 2023)
20-34709256-A-G		not specified	Uncertain significance (Dec 06, 2022)
20-34709257-G-A		not specified	Uncertain significance (Feb 03, 2022)
20-34709313-G-A		not specified	Uncertain significance (Dec 27, 2023)
20-34709316-G-C		not specified	Uncertain significance (Dec 21, 2021)
20-34709324-G-C		not specified	Uncertain significance (May 20, 2024)
20-34709371-G-C		not specified	Uncertain significance (Sep 17, 2021)
20-34709395-C-G		not specified	Uncertain significance (Jan 17, 2024)
20-34709427-A-T		not specified	Uncertain significance (Feb 17, 2024)
20-34709476-C-T		not specified	Uncertain significance (Mar 19, 2024)
20-34709508-G-A		not specified	Uncertain significance (Oct 26, 2022)
20-34710071-G-A		not specified	Uncertain significance (Mar 28, 2023)
20-34710075-G-A		not specified	Uncertain significance (Nov 08, 2022)
20-34710077-C-G		not specified	Uncertain significance (Apr 12, 2024)
20-34710080-G-A		not specified	Uncertain significance (Oct 24, 2023)
20-34710084-C-T		not specified	Uncertain significance (Jun 06, 2023)
20-34710110-C-G		not specified	Uncertain significance (Nov 17, 2022)
20-34710162-A-G		not specified	Uncertain significance (Dec 17, 2023)
20-34710165-G-A		not specified	Uncertain significance (Jun 17, 2024)
20-34710204-A-T		not specified	Uncertain significance (Aug 10, 2021)
20-34710207-C-A		not specified	Uncertain significance (Mar 04, 2024)
20-34710209-G-T		not specified	Uncertain significance (Jan 31, 2024)

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
0.999	0.000875	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

Haploinsufficiency Scores

• pHI: 0.887
• hipred: Y
• hipred_score: 0.765
• ghis: 0.587

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

Mouse Genome Informatics

• Gene name: Ncoa6
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); liver/biliary system phenotype; embryo phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; pigmentation phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

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