NUPR2

nuclear protein 2, transcriptional regulator

Basic information

Region (hg38): 7:56114681-56116417

Previous symbols: [ "NUPR1L" ]

Links

ENSG00000185290 ∙ NCBI:389493 ∙ ∙ HGNC:44164 ∙ Uniprot:A6NF83 ∙ 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 NUPR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUPR2 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	1	0

Variants in NUPR2

This is a list of pathogenic ClinVar variants found in the NUPR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-56116298-T-A		not specified	Uncertain significance (Aug 10, 2021)
7-56116299-C-G		not specified	Uncertain significance (Aug 10, 2021)
7-56116300-T-A			Likely benign (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUPR2	protein_coding	protein_coding	ENST00000329309	1	1720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000507	0.273	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.191	45	48.7	0.923	0.00000365	598
Missense in Polyphen		4	5.0705	0.78887		56
Synonymous	0.496	18	20.9	0.862	0.00000143	215
Loss of Function	-0.977	4	2.38	1.68	1.02e-7	32

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor by inhibiting gene expression at the NUPR1 promoter in a p53/TP53-dependent manner in cancer cells (PubMed:25899918). Involved in the G1 cell cycle arrest, and in a decrease in cell viability and cell proliferation (PubMed:25899918). Plays a role as a negative regulator of the protumoral factor NUPR1 (PubMed:25899918). {ECO:0000269|PubMed:25899918}.

Haploinsufficiency Scores

• ghis: 0.438

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Nupr1l

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;cellular response to DNA damage stimulus;cell cycle arrest;negative regulation of cell population proliferation;cellular response to starvation;negative regulation of cell cycle;negative regulation of cell cycle arrest
• Cellular component: nucleus