DZIP1

DAZ interacting zinc finger protein 1

Basic information

Region (hg38): 13:95578202-95644706

Links

ENSG00000134874 ∙ NCBI:22873 ∙ OMIM:608671 ∙ HGNC:20908 ∙ Uniprot:Q86YF9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 47 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitral valve prolapse 3	AD	Cardiovascular	The condition can involve increased risk of mitral valve prolapse, and awareness may allow early diagnosis and management (eg, some individuals have required surgical management)	Cardiovascular; Genitourinary	16172273; 31118289; 32051257

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DZIP1 gene.

• not_specified (113 variants)
• not_provided (5 variants)
• Spermatogenic_failure_47 (4 variants)
• DZIP1-related_disorder (2 variants)
• Mitral_valve_prolapse,_myxomatous_3 (1 variants)
• Intellectual_developmental_disorder_61 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DZIP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000198968.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1		1	2
missense	1		115	4	2	122
nonsense	1		1			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4			4
Total	2	0	121	4	3

Highest pathogenic variant AF is 0.0000013790859

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DZIP1	protein_coding	protein_coding	ENST00000347108	20	66501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125653	0	95	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.954	421	480	0.877	0.0000270	5740
Missense in Polyphen		79	103.8	0.76105		1320
Synonymous	0.525	181	190	0.952	0.0000121	1550
Loss of Function	1.39	36	46.2	0.780	0.00000226	575

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000752	0.000752
Ashkenazi Jewish	0.000301	0.000298
East Asian	0.000599	0.000598
Finnish	0.000236	0.000231
European (Non-Finnish)	0.000360	0.000334
Middle Eastern	0.000599	0.000598
South Asian	0.000457	0.000457
Other	0.000920	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in spermatogenesis via its interaction with DAZ (PubMed:15081113). Has a role in primary cilium formation (PubMed:19852954). {ECO:0000269|PubMed:15081113, ECO:0000269|PubMed:19852954}.
• Pathway: Signal Transduction;Hedgehog ,on, state;Signaling by Hedgehog (Consensus)

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• loftool: 0.980
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.32

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: dzip1
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: misrouted

Gene ontology

• Biological process: smoothened signaling pathway;multicellular organism development;germ cell development;spermatogenesis;regulation of protein binding;establishment of protein localization;positive regulation of cilium assembly;cytoplasmic sequestering of protein;cilium assembly;protein localization to cilium
• Cellular component: nucleus;nucleoplasm;cytoplasm;centriole;microtubule organizing center;cytosol;ciliary basal body;ciliary transition fiber
• Molecular function: nucleic acid binding;protein binding;metal ion binding