DZIP1L
Basic information
Region (hg38): 3:138061990-138115818
Links
Phenotypes
GenCC
Source:
- autosomal recessive polycystic kidney disease (Supportive), mode of inheritance: AR
- polycystic kidney disease 5 (Strong), mode of inheritance: AR
- polycystic kidney disease 5 (Moderate), mode of inheritance: AR
- autosomal recessive polycystic kidney disease (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
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
- not provided (2 variants)
- Polycystic kidney disease 5 (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 | 26 | 29 | ||||
missense | 78 | 11 | 10 | 99 | ||
nonsense | 7 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 5 | 8 | 1 | 14 | ||
non coding | 22 | 19 | 41 | |||
Total | 3 | 3 | 81 | 59 | 32 |
Highest pathogenic variant AF is 0.00000657
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 | DZIP1L-related disorder | Uncertain significance (May 23, 2022) | ||
3-138062832-C-G | DZIP1L-related disorder • Inborn genetic diseases | Benign/Likely benign (Oct 29, 2024) | ||
3-138062836-G-A | DZIP1L-related disorder | 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 (Jun 03, 2024) | ||
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 | Inborn genetic diseases | Uncertain significance (Nov 28, 2024) | ||
3-138064702-C-T | Inborn genetic diseases | Uncertain significance (Oct 01, 2024) | ||
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) |
GnomAD
Source:
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:
- 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