DZIP1L

DAZ interacting zinc finger protein 1 like

Basic information

Region (hg38): 3:138061989-138115818

Links

ENSG00000158163 ∙ NCBI:199221 ∙ OMIM:617570 ∙ HGNC:26551 ∙ Uniprot:Q8IYY4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive polycystic kidney disease (Supportive), mode of inheritance: AR
• polycystic kidney disease 5 (Moderate), mode of inheritance: AR
• autosomal recessive polycystic kidney disease (Definitive), mode of inheritance: AR
• polycystic kidney disease 5 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Polycyctic kidney disease 5	AR	Renal	Individuals have been described with early-onset renal disease and failure, and awareness may allow early diagnosis and interventions; Renal transplant has been described	Renal	28530676

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DZIP1L gene.

• not provided (125 variants)
• Inborn genetic diseases (36 variants)
• Polycystic kidney disease 5 (10 variants)
• DZIP1L-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DZIP1L 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				14	4	18
missense			63	6	15	84
nonsense	1	1	3			5
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			5	7	1	13
non coding				13	20	33
Total	1	1	67	33	39

Variants in DZIP1L

This is a list of pathogenic ClinVar variants found in the DZIP1L region.

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

Position	Type	Phenotype	Significance	ClinVar
3-138062820-C-T			Uncertain significance (May 23, 2022)
3-138062832-C-G		DZIP1L-related disorder	Benign/Likely benign (Jan 15, 2024)
3-138062836-G-A		DZIP1L-related disorder	Benign/Likely benign (Nov 27, 2023)
3-138062846-G-A			Likely benign (Sep 24, 2022)
3-138062847-C-T		Inborn genetic diseases	Uncertain significance (Dec 06, 2023)
3-138062865-A-C			Uncertain significance (Jul 15, 2022)
3-138062874-G-T			Uncertain significance (Mar 19, 2021)
3-138062881-T-C		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
3-138062886-C-T		Inborn genetic diseases	Uncertain significance (Apr 28, 2022)
3-138062887-G-A		DZIP1L-related disorder	Benign/Likely benign (Jan 09, 2024)
3-138062906-C-T		DZIP1L-related disorder	Likely benign (Jan 07, 2023)
3-138062916-T-C		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
3-138062926-G-A		DZIP1L-related disorder	Likely benign (Jan 14, 2023)
3-138062984-G-C			Likely benign (Aug 06, 2022)
3-138062987-G-A			Likely benign (Feb 09, 2022)
3-138062988-TA-T			Likely benign (Aug 29, 2023)
3-138062995-G-A			Likely benign (May 09, 2022)
3-138063081-A-C			Benign (May 11, 2021)
3-138064653-G-T		Inborn genetic diseases	Uncertain significance (Aug 08, 2022)
3-138064673-G-A		DZIP1L-related disorder	Likely benign (Aug 30, 2023)
3-138064681-A-C			Uncertain significance (Jul 27, 2022)
3-138064723-C-A		not specified	Uncertain significance (Jun 13, 2022)
3-138064725-A-G			Uncertain significance (Aug 06, 2022)
3-138064730-C-T		DZIP1L-related disorder	Likely benign (Nov 16, 2019)
3-138064756-G-A		Polycystic kidney disease 5	Likely pathogenic (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DZIP1L	protein_coding	protein_coding	ENST00000327532	15	53829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.39e-25	0.000405	125641	0	107	125748	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.101	430	436	0.986	0.0000256	4966
Missense in Polyphen		108	113.64	0.95036		1291
Synonymous	0.387	164	170	0.962	0.00000919	1520
Loss of Function	0.0611	38	38.4	0.989	0.00000173	441

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00161	0.00160
Ashkenazi Jewish	0.00	0.00
East Asian	0.000283	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000473	0.000457
Middle Eastern	0.000283	0.000272
South Asian	0.000381	0.000359
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in primary cilium formation (PubMed:19852954, PubMed:28530676). Probably acts as a transition zone protein required for localization of PKD1/PC1 and PKD2/PC2 to the ciliary membrane (PubMed:28530676). {ECO:0000269|PubMed:19852954, ECO:0000269|PubMed:28530676}.
• Disease: DISEASE: Polycystic kidney disease 5 (PKD5) [MIM:617610]: A form of polycystic kidney disease, a disorder characterized by progressive formation and enlargement of cysts in both kidneys, typically leading to end-stage renal disease in adult life. Cysts may also occur in other organs, particularly the liver. PKD5 inheritance is autosomal recessive. {ECO:0000269|PubMed:28530676}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0883

Intolerance Scores

• loftool: 0.993
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.12

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.170
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.242

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dzip1l
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; vision/eye 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); liver/biliary system phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype

Zebrafish Information Network

• Gene name: dzip1l
• Affected structure: multi-ciliated epithelial cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: regulation of protein localization;cilium assembly
• Cellular component: cytoplasm;centriole;ciliary basal body
• Molecular function: nucleic acid binding;protein binding;metal ion binding