NPAS3

neuronal PAS domain protein 3, the group of PAS domain containing|Basic helix-loop-helix proteins

Basic information

Region (hg38): 14:32934395-33820863

Links

ENSG00000151322 ∙ NCBI:64067 ∙ OMIM:609430 ∙ HGNC:19311 ∙ Uniprot:Q8IXF0 ∙ 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 NPAS3 gene.

• Inborn genetic diseases (35 variants)
• not provided (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPAS3 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				6	5	11
missense			35	2	1	38
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	36	9	7

Variants in NPAS3

This is a list of pathogenic ClinVar variants found in the NPAS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-33215174-G-A			Likely benign (Oct 10, 2018)
14-33215287-A-C			Likely benign (Aug 01, 2023)
14-33215335-T-C			Benign (Nov 16, 2018)
14-33215391-G-A		not specified	Uncertain significance (Jun 03, 2022)
14-33676202-G-A			Benign (Sep 24, 2018)
14-33676268-A-C		not specified	Uncertain significance (Apr 04, 2023)
14-33676298-C-A		not specified	Uncertain significance (Jan 23, 2023)
14-33676349-G-A		not specified	Uncertain significance (Sep 14, 2023)
14-33774351-A-G			Likely benign (Aug 09, 2018)
14-33774364-C-G		not specified	Uncertain significance (May 08, 2023)
14-33774373-T-G		not specified	Uncertain significance (Dec 21, 2023)
14-33774418-G-A		not specified	Uncertain significance (Sep 15, 2021)
14-33774490-C-T			Uncertain significance (Nov 01, 2022)
14-33774509-A-G		not specified	Uncertain significance (Apr 04, 2023)
14-33778542-G-C		not specified	Uncertain significance (Nov 17, 2022)
14-33797523-C-T			Benign (Dec 31, 2019)
14-33797565-C-A		not specified	Uncertain significance (Feb 27, 2024)
14-33799745-A-G		not specified	Uncertain significance (Apr 12, 2022)
14-33799775-T-A		not specified	Uncertain significance (Jun 30, 2022)
14-33799786-C-T			Benign (Jul 31, 2018)
14-33799807-G-C			Likely benign (Nov 01, 2022)
14-33799812-A-C		not specified	Uncertain significance (Mar 01, 2023)
14-33799838-A-G		not specified	Uncertain significance (Feb 05, 2024)
14-33799877-G-A			Uncertain significance (Feb 12, 2022)
14-33799946-T-C		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPAS3	protein_coding	protein_coding	ENST00000356141	12	869244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000263	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.14	364	576	0.632	0.0000364	6016
Missense in Polyphen		107	176.12	0.60755		1802
Synonymous	0.445	251	260	0.965	0.0000199	1873
Loss of Function	5.16	3	36.8	0.0815	0.00000204	405

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a broad role in neurogenesis. May control regulatory pathways relevant to schizophrenia and to psychotic illness (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.347
• rvis_EVS: -1.35
• rvis_percentile_EVS: 4.6

Haploinsufficiency Scores

• pHI: 0.301
• hipred: Y
• hipred_score: 0.752
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npas3
• Phenotype: respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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); 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); immune system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytosol
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein heterodimerization activity