NPAS1

neuronal PAS domain protein 1, the group of PAS domain containing|Basic helix-loop-helix proteins

Basic information

Region (hg38): 19:47019837-47045775

Links

ENSG00000130751 ∙ NCBI:4861 ∙ OMIM:603346 ∙ HGNC:7894 ∙ Uniprot:Q99742 ∙ 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 NPAS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPAS1 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						0
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in NPAS1

This is a list of pathogenic ClinVar variants found in the NPAS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47021066-G-A		not specified	Likely benign (Nov 08, 2022)
19-47021096-G-T		not specified	Uncertain significance (Jun 09, 2022)
19-47021150-A-G		not specified	Uncertain significance (Jan 16, 2024)
19-47021156-C-G		not specified	Uncertain significance (May 04, 2022)
19-47021166-C-A		not specified	Uncertain significance (Jun 02, 2023)
19-47021664-G-C		not specified	Uncertain significance (Apr 24, 2024)
19-47021736-G-C		not specified	Uncertain significance (Oct 27, 2022)
19-47032287-G-A		not specified	Uncertain significance (Oct 20, 2024)
19-47032298-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-47032307-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-47032316-G-C		not specified	Uncertain significance (Jul 05, 2023)
19-47032664-G-A		not specified	Uncertain significance (Feb 06, 2024)
19-47036007-G-C		not specified	Uncertain significance (Mar 29, 2023)
19-47036037-G-A		not specified	Uncertain significance (Jun 06, 2023)
19-47036037-G-C		not specified	Uncertain significance (Apr 08, 2024)
19-47036057-G-A		not specified	Uncertain significance (Oct 16, 2024)
19-47036076-C-T		not specified	Uncertain significance (Apr 20, 2023)
19-47039426-G-A		not specified	Uncertain significance (May 12, 2024)
19-47039432-G-A		not specified	Uncertain significance (Aug 28, 2023)
19-47039446-G-A		not specified	Uncertain significance (Nov 25, 2024)
19-47039468-C-T		not specified	Uncertain significance (Apr 25, 2022)
19-47039474-C-A		not specified	Uncertain significance (Sep 29, 2022)
19-47039518-G-A		not specified	Uncertain significance (Feb 21, 2024)
19-47039525-G-A		not specified	Uncertain significance (Nov 21, 2024)
19-47040461-A-G		not specified	Uncertain significance (Jun 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPAS1	protein_coding	protein_coding	ENST00000602212	11	25957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.971	0.0293	125703	0	10	125713	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	239	331	0.722	0.0000203	3651
Missense in Polyphen		58	110.38	0.52544		1383
Synonymous	0.923	143	158	0.907	0.0000108	1292
Loss of Function	3.70	2	19.7	0.101	8.40e-7	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000636	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May control regulatory pathways relevant to schizophrenia and to psychotic illness. May play a role in late central nervous system development by modulating EPO expression in response to cellular oxygen level (By similarity). Forms a heterodimer that binds core DNA sequence 5'-TACGTG-3' within the hypoxia response element (HRE) leading to transcriptional repression on its target gene TH (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:P97459}.

Recessive Scores

• pRec: 0.132

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.789
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npas1
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;startle response;regulation of transcription by RNA polymerase II;central nervous system development;maternal behavior;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein heterodimerization activity