NCOA5

nuclear receptor coactivator 5

Basic information

Region (hg38): 20:46060990-46089962

Links

ENSG00000124160 ∙ NCBI:57727 ∙ OMIM:616825 ∙ HGNC:15909 ∙ Uniprot:Q9HCD5 ∙ 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 NCOA5 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCOA5 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	1

Variants in NCOA5

This is a list of pathogenic ClinVar variants found in the NCOA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-46062393-C-G		not specified	Uncertain significance (Mar 29, 2022)
20-46062422-C-A		not specified	Uncertain significance (May 23, 2023)
20-46062458-C-T		not specified	Uncertain significance (May 10, 2022)
20-46062485-C-T		not specified	Uncertain significance (Oct 22, 2021)
20-46062595-T-C		not specified	Uncertain significance (Apr 26, 2023)
20-46062615-T-G		not specified	Uncertain significance (Sep 17, 2021)
20-46062674-C-G		not specified	Uncertain significance (Dec 27, 2022)
20-46062721-T-C		not specified	Uncertain significance (Sep 16, 2021)
20-46062813-C-A		not specified	Uncertain significance (Oct 25, 2023)
20-46062826-G-T		not specified	Uncertain significance (Jan 11, 2023)
20-46062853-C-A		not specified	Uncertain significance (Nov 13, 2023)
20-46062863-C-A		not specified	Uncertain significance (Jan 04, 2024)
20-46062866-C-T		not specified	Uncertain significance (Apr 25, 2023)
20-46063423-T-C		not specified	Uncertain significance (Aug 02, 2023)
20-46063456-T-C		not specified	Uncertain significance (Dec 28, 2022)
20-46063531-T-G			Benign (Dec 31, 2019)
20-46065092-T-C		not specified	Uncertain significance (Dec 16, 2023)
20-46065182-C-T		not specified	Uncertain significance (Jun 29, 2023)
20-46065196-C-G		not specified	Uncertain significance (Oct 26, 2022)
20-46067161-G-A		not specified	Uncertain significance (Feb 27, 2024)
20-46070259-T-C		not specified	Uncertain significance (Jan 22, 2024)
20-46070330-C-T		not specified	Uncertain significance (Jan 18, 2022)
20-46070334-C-T		not specified	Uncertain significance (Dec 13, 2023)
20-46070339-C-T		not specified	Uncertain significance (Jan 26, 2022)
20-46079417-G-A		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCOA5	protein_coding	protein_coding	ENST00000290231	7	28968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000739	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.994	309	362	0.853	0.0000230	3787
Missense in Polyphen		81	127.98	0.63291		1372
Synonymous	0.828	117	129	0.907	0.00000728	1184
Loss of Function	4.71	2	29.6	0.0675	0.00000235	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nuclear receptor coregulator that can have both coactivator and corepressor functions. Interacts with nuclear receptors for steroids (ESR1 and ESR2) independently of the steroid binding domain (AF-2) of the ESR receptors, and with the orphan nuclear receptor NR1D2. Involved in the coactivation of nuclear steroid receptors (ER) as well as the corepression of MYC in response to 17-beta-estradiol (E2). {ECO:0000269|PubMed:15073177}.

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.365
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.17

Haploinsufficiency Scores

• pHI: 0.456
• hipred: Y
• hipred_score: 0.543
• ghis: 0.656

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncoa5
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; neoplasm; immune system phenotype; liver/biliary system phenotype; reproductive 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)

Gene ontology

• Biological process: glucose homeostasis;negative regulation of insulin receptor signaling pathway
• Cellular component: extracellular space;nucleus;actin cytoskeleton
• Molecular function: chromatin binding;RNA binding;protein binding