NUPR1

nuclear protein 1, transcriptional regulator

Basic information

Region (hg38): 16:28532708-28539008

Links

ENSG00000176046 ∙ NCBI:26471 ∙ OMIM:614812 ∙ HGNC:29990 ∙ Uniprot:O60356 ∙ 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 NUPR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUPR1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in NUPR1

This is a list of pathogenic ClinVar variants found in the NUPR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28538023-C-T		not specified	Uncertain significance (Jan 14, 2025)
16-28538024-G-A		not specified	Uncertain significance (Sep 26, 2023)
16-28538027-G-A		not specified	Uncertain significance (Jan 08, 2025)
16-28538032-C-T		not specified	Uncertain significance (Mar 06, 2025)
16-28538043-C-G		not specified	Uncertain significance (Nov 30, 2021)
16-28538048-C-T		not specified	Uncertain significance (Jan 17, 2023)
16-28538081-C-T		not specified	Uncertain significance (Jan 30, 2024)
16-28538102-G-A		not specified	Uncertain significance (Dec 09, 2024)
16-28538134-C-T		not specified	Uncertain significance (Dec 28, 2024)
16-28538135-G-A		not specified	Uncertain significance (Oct 25, 2022)
16-28538143-C-T		not specified	Uncertain significance (Jul 09, 2024)
16-28538144-G-A		not specified	Uncertain significance (Jun 13, 2024)
16-28538171-G-A		not specified	Uncertain significance (Jan 27, 2025)
16-28538843-G-C		not specified	Uncertain significance (Nov 22, 2024)
16-28538851-G-C		not specified	Uncertain significance (Mar 15, 2024)
16-28538858-G-A		not specified	Uncertain significance (Jul 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUPR1	protein_coding	protein_coding	ENST00000395641	2	1890

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00415	0.438	125732	0	10	125742	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.120	68	65.3	1.04	0.00000400	628
Missense in Polyphen		13	6.6371	1.9587		55
Synonymous	0.0222	25	25.1	0.994	0.00000143	225
Loss of Function	-0.414	3	2.32	1.29	9.67e-8	32

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000272	0.000272
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chromatin-binding protein that converts stress signals into a program of gene expression that empowers cells with resistance to the stress induced by a change in their microenvironment. Interacts with MSL1 and inhibits its activity on histone H4 'Lys-16' acetylation (H4K16ac). Binds the RELB promoter and activates its transcription, leading to the transactivation of IER3. The NUPR1/RELB/IER3 survival pathway may provide pancreatic ductal adenocarcinoma with remarkable resistance to cell stress, such as starvation or gemcitabine treatment. In breast cancer cells, NUPR1 overexpression leads to the activation of PI3K/AKT signaling pathway, CDKN1A/p21 phosphorylation and relocalization from the nucleus to the cytoplasm, leading to resistance to chemotherapeutic agents, such as doxorubicin. {ECO:0000269|PubMed:19650074, ECO:0000269|PubMed:22565310, ECO:0000269|PubMed:22858377}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);TNFalpha (Consensus)

Intolerance Scores

• loftool: 0.433
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.749

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nupr1
• Phenotype: reproductive system phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: acute inflammatory response;protein acetylation;cell population proliferation;negative regulation of cell population proliferation;male gonad development;response to toxic substance;positive regulation of protein modification process;skeletal muscle cell differentiation;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;positive regulation of apoptotic process;negative regulation of cell cycle;negative regulation of fibroblast proliferation;protein-containing complex assembly;regulation of female gonad development
• Cellular component: nucleus;cytosol;protein-DNA complex
• Molecular function: DNA binding;chromatin binding;protein binding