ZUP1

zinc finger containing ubiquitin peptidase 1, the group of ZUP1 deubiquitinase|Zinc fingers C2H2-type

Basic information

Region (hg38): 6:116635618-116668794

Previous symbols: [ "C6orf113", "ZUFSP" ]

Links

ENSG00000153975 ∙ NCBI:221302 ∙ ∙ HGNC:21224 ∙ Uniprot:Q96AP4 ∙ 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 ZUP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZUP1 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in ZUP1

This is a list of pathogenic ClinVar variants found in the ZUP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-116635852-T-A		not specified	Uncertain significance (Jun 05, 2023)
6-116645734-G-C		not specified	Uncertain significance (Feb 27, 2023)
6-116645920-C-T		not specified	Uncertain significance (Jan 20, 2023)
6-116647476-A-G		not specified	Uncertain significance (Jun 01, 2023)
6-116647504-T-C		not specified	Uncertain significance (Oct 12, 2022)
6-116647557-C-T		not specified	Uncertain significance (Dec 16, 2023)
6-116647558-G-A		not specified	Uncertain significance (Apr 07, 2023)
6-116647582-T-C		not specified	Uncertain significance (Apr 09, 2024)
6-116651647-T-C		not specified	Uncertain significance (Oct 26, 2022)
6-116652072-C-A		not specified	Uncertain significance (Aug 04, 2023)
6-116652090-T-C		not specified	Uncertain significance (Jan 10, 2023)
6-116652144-A-G		not specified	Uncertain significance (Apr 17, 2023)
6-116652180-G-T		not specified	Uncertain significance (Apr 19, 2024)
6-116656843-C-T		not specified	Uncertain significance (May 02, 2024)
6-116658873-T-C		not specified	Uncertain significance (May 07, 2024)
6-116660841-C-G		not specified	Uncertain significance (Jul 27, 2021)
6-116666719-G-C		not specified	Uncertain significance (Nov 18, 2022)
6-116666736-G-A		not specified	Uncertain significance (Jun 30, 2022)
6-116666780-C-A		not specified	Uncertain significance (May 30, 2023)
6-116666822-G-T		not specified	Uncertain significance (Dec 05, 2022)
6-116666948-T-G		not specified	Uncertain significance (Apr 22, 2024)
6-116666969-T-G		not specified	Uncertain significance (Apr 05, 2023)
6-116666999-A-C		not specified	Uncertain significance (Nov 09, 2023)
6-116667048-C-T		not specified	Uncertain significance (Jun 29, 2023)
6-116667150-G-T		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZUP1	protein_coding	protein_coding	ENST00000368576	9	33177

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.12e-9	0.874	125678	0	65	125743	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0812	286	290	0.987	0.0000135	3817
Missense in Polyphen		84	98.19	0.85548		1290
Synonymous	-0.250	102	98.8	1.03	0.00000479	1024
Loss of Function	1.73	18	27.9	0.646	0.00000132	383

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000893	0.000886
Ashkenazi Jewish	0.00	0.00
East Asian	0.000166	0.000163
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000285	0.000281
Middle Eastern	0.000166	0.000163
South Asian	0.000168	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinase with endodeubiquitinase activity that specifically interacts with and cleaves 'Lys-63'-linked long polyubiquitin chains. Shows only weak activity against 'Lys-11' and 'Lys-48'-linked chains (PubMed:29576528, PubMed:29563501, PubMed:29476094). Plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage (PubMed:29576528, PubMed:29576527). Modulates the ubiquitination status of replication protein A (RPA) complex proteins in response to replication stress (PubMed:29563501). {ECO:0000269|PubMed:29476094, ECO:0000269|PubMed:29563501, ECO:0000269|PubMed:29576527, ECO:0000269|PubMed:29576528}.

Recessive Scores

• pRec: 0.0895

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.231
• ghis: 0.544

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Zup1

Gene ontology

• Biological process: proteolysis
• Cellular component: nucleus;cytoplasm
• Molecular function: nucleic acid binding;protein binding;thiol-dependent ubiquitinyl hydrolase activity;metal ion binding