DZIP3

DAZ interacting zinc finger protein 3, the group of Ring finger proteins|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 3:108589705-108694840

Links

ENSG00000198919 ∙ NCBI:9666 ∙ OMIM:608672 ∙ HGNC:30938 ∙ Uniprot:Q86Y13 ∙ 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 DZIP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DZIP3 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			52	4	1	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	52	4	2

Variants in DZIP3

This is a list of pathogenic ClinVar variants found in the DZIP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-108605423-A-G			Benign (Jun 19, 2018)
3-108608103-A-G		not specified	Uncertain significance (Jan 09, 2024)
3-108608108-C-G		not specified	Uncertain significance (Nov 30, 2022)
3-108608112-G-A		not specified	Uncertain significance (Jan 29, 2024)
3-108608118-A-G		not specified	Uncertain significance (May 18, 2023)
3-108611313-C-G		not specified	Uncertain significance (Feb 23, 2023)
3-108616559-A-G		not specified	Uncertain significance (Oct 30, 2023)
3-108616599-G-A		not specified	Uncertain significance (Mar 26, 2024)
3-108616623-C-T		not specified	Uncertain significance (Jul 08, 2022)
3-108624511-G-A		not specified	Uncertain significance (Apr 25, 2022)
3-108624534-A-G			Benign (Jun 29, 2018)
3-108625845-G-T		not specified	Uncertain significance (Jan 26, 2022)
3-108625856-A-C		not specified	Uncertain significance (Jul 16, 2021)
3-108625942-G-A		not specified	Uncertain significance (Nov 29, 2023)
3-108625944-G-A		not specified	Uncertain significance (Sep 29, 2022)
3-108629109-G-C		not specified	Uncertain significance (Jul 17, 2024)
3-108632987-G-A		not specified	Uncertain significance (Jul 11, 2023)
3-108633005-C-T		not specified	Uncertain significance (Apr 26, 2023)
3-108633020-T-G		not specified	Uncertain significance (Jan 09, 2024)
3-108633022-G-C		not specified	Uncertain significance (Sep 26, 2023)
3-108633032-G-A		not specified	Uncertain significance (May 23, 2024)
3-108633046-G-A		not specified	Uncertain significance (Nov 08, 2024)
3-108633068-A-G		not specified	Uncertain significance (Jan 31, 2022)
3-108634887-T-C		not specified	Uncertain significance (May 10, 2024)
3-108634920-A-T		not specified	Uncertain significance (Jun 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DZIP3	protein_coding	protein_coding	ENST00000361582	31	105165

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.65e-13	1.00	125625	0	123	125748	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.712	549	598	0.918	0.0000290	8013
Missense in Polyphen		148	163.53	0.90501		2211
Synonymous	0.501	193	202	0.955	0.00000999	2117
Loss of Function	3.96	33	68.4	0.483	0.00000324	907

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000773	0.000758
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000509	0.000381
Finnish	0.00109	0.00106
European (Non-Finnish)	0.000487	0.000457
Middle Eastern	0.000509	0.000381
South Asian	0.000653	0.000588
Other	0.000536	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 Ubiquitin ligase proteins mediate ubiquitination and subsequent proteasomal degradation of target proteins. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin- conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. Able to specifically bind RNA. {ECO:0000269|PubMed:12538761}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.0953

Intolerance Scores

• loftool: 0.570
• rvis_EVS: -1.1
• rvis_percentile_EVS: 6.91

Haploinsufficiency Scores

• pHI: 0.0836
• hipred: N
• hipred_score: 0.372
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.439

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dzip3
• Phenotype: 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)

Gene ontology

• Biological process: protein polyubiquitination
• Cellular component: cytoplasm
• Molecular function: RNA binding;ubiquitin-protein transferase activity;protein binding;phosphatase binding;polyubiquitin modification-dependent protein binding;metal ion binding;ubiquitin protein ligase activity