NR6A1

nuclear receptor subfamily 6 group A member 1, the group of Nuclear receptor subfamily 6 group A

Basic information

Region (hg38): 9:124517274-124771311

Previous symbols: [ "GCNF" ]

Links

ENSG00000148200 ∙ NCBI:2649 ∙ OMIM:602778 ∙ HGNC:7985 ∙ Uniprot:Q15406 ∙ 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 NR6A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR6A1 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					2	2
missense			28	1	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	3

Variants in NR6A1

This is a list of pathogenic ClinVar variants found in the NR6A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-124522721-C-T			Benign (Aug 17, 2018)
9-124524758-A-T		not specified	Uncertain significance (Sep 22, 2023)
9-124524793-A-G		not specified	Uncertain significance (Jan 04, 2022)
9-124524806-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
9-124526882-C-T		not specified	Uncertain significance (Nov 27, 2023)
9-124526885-C-G			Benign (Jun 04, 2018)
9-124526890-C-T		not specified	Uncertain significance (Aug 17, 2022)
9-124526900-T-G		not specified	Uncertain significance (Oct 19, 2021)
9-124535894-C-T		not specified	Uncertain significance (Jun 07, 2023)
9-124536026-G-C		not specified	Uncertain significance (Mar 29, 2023)
9-124536074-G-A		not specified	Uncertain significance (Jul 20, 2021)
9-124536084-G-A			Benign (Mar 29, 2018)
9-124536128-C-T		not specified	Uncertain significance (Jun 24, 2022)
9-124538101-A-G		not specified	Uncertain significance (Jun 16, 2023)
9-124538158-A-T		not specified	Uncertain significance (Aug 16, 2022)
9-124538198-G-A		not specified	Uncertain significance (Jun 30, 2022)
9-124538201-G-T		not specified	Uncertain significance (Aug 15, 2023)
9-124538246-G-T		not specified	Uncertain significance (Dec 21, 2023)
9-124538252-G-A		not specified	Uncertain significance (Mar 05, 2024)
9-124538277-C-A		not specified	Uncertain significance (Dec 15, 2022)
9-124538291-C-T		not specified	Uncertain significance (Dec 22, 2023)
9-124554357-T-C		not specified	Uncertain significance (Apr 28, 2023)
9-124554420-C-T		not specified	Uncertain significance (May 30, 2024)
9-124554471-T-C			Uncertain significance (Jul 01, 2022)
9-124554516-C-T		not specified	Uncertain significance (Nov 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NR6A1	protein_coding	protein_coding	ENST00000487099	10	254036

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.982	0.0183	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.83	176	259	0.681	0.0000149	3143
Missense in Polyphen		46	109.37	0.42058		1201
Synonymous	-0.456	109	103	1.06	0.00000603	911
Loss of Function	4.12	3	25.4	0.118	0.00000141	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Orphan nuclear receptor. Binds to a response element containing the sequence 5'-TCAAGGTCA-3'. May be involved in the regulation of gene expression in germ cell development during gametogenesis (By similarity). {ECO:0000250}.
• Pathway: NHR;Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.196

Intolerance Scores

• loftool: 0.0544
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.864
• hipred: Y
• hipred_score: 0.806
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nr6a1
• Phenotype: craniofacial phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland 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; digestive/alimentary phenotype; vision/eye phenotype; skeleton phenotype; embryo 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); 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)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;gamete generation;spermatogenesis;cell population proliferation;intracellular receptor signaling pathway;steroid hormone mediated signaling pathway;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;steroid hormone receptor activity;nuclear receptor activity;zinc ion binding;protein homodimerization activity;sequence-specific DNA binding