KIAA0586
protein-codingKIAA0586
Gene summary
This gene encodes a conserved centrosomal protein that functions in ciliogenesis and responds to hedgehog signaling. Mutations in this gene causes Joubert syndrome 23. Alternative splicing results in multiple transcript variants and protein isoforms. [provided by RefSeq, Aug 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~123.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014664
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014664
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014688
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0018342
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014688
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0018772
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014688
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014664
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014688
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014664
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KIAA0586 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001329943.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 15 | 291 | 1 | 310 |
| missense | 4 | 640 | 63 | 3 | 710 | |
| nonsense | 32 | 18 | 3 | 53 | ||
| start loss | 2 | 2 | ||||
| frameshift | 39 | 33 | 5 | 77 | ||
| splice donor/acceptor (+/-2bp) | 4 | 36 | 9 | 49 | ||
| Total | 77 | 92 | 674 | 354 | 4 | 1201 |
Highest pathogenic variant AF is 0.003834522
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001316872.1 | 31 | MANE Select | |
| Ensembl | ENSP00000498929.1 | 31 | MANE Select | |
| RefSeq | NP_001231118.1 | 34 | Standard | |
| RefSeq | NP_001231119.1 | 31 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| si:ch211-185a18.2 | Danio rerio | Structure: eye photoreceptor cell Quality: mislocalised abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- smoothened signaling pathway
- cilium assembly
- regulation of establishment of protein localization
Cellular Component
- photoreceptor inner segment
- centrosome
- centriole
- ciliary basal body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000354386
- Coding exons
- 34
- Length
- 121114
- Individuals with no LoFs
- 123905
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 747
- Defined
- 124653
- p
- 0.00300
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.371 | 735 | 764 | 0.962 | 0.0000362 | 10687 |
| Missense (PolyPhen) | 246 | 233.53 | 1.0534 | 3362 | ||
| Synonymous | -0.0283 | 267 | 266 | 1.00 | 0.0000135 | 3085 |
| Loss of Function | 3.44 | 36 | 66.2 | 0.544 | 0.00000297 | 1006 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0016 | 0.0015 | notable |
| Latino/Admixed American | 0.0027 | 0.0021 | notable |
| Ashkenazi Jewish | 0.0084 | 0.0075 | notable |
| East Asian | 0.00043 | 0.00039 | rare |
| Finnish | 0.00081 | 0.00079 | rare |
| European (Non-Finnish) | 0.0050 | 0.0046 | notable |
| South Asian | 0.00089 | 0.00078 | rare |
| Other | 0.0027 | 0.0023 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required for ciliogenesis and sonic hedgehog/SHH signaling. Required for the centrosomal recruitment of RAB8A and for the targeting of centriole satellite proteins to centrosomes such as of PCM1. May play a role in early ciliogenesis in the disappearance of centriolar satellites that preceeds ciliary vesicle formation (PubMed:24421332). Involved in regulation of cell intracellular organization. Involved in regulation of cell polarity (By similarity). Required for asymmetrical localization of CEP120 to daughter centrioles (By similarity). {ECO:0000250|UniProtKB:E9PV87, ECO:0000250|UniProtKB:Q1G7G9, ECO:0000269|PubMed:24421332}.;
- Disease
- DISEASE: Joubert syndrome 23 (JBTS23) [MIM:616490]: A mild form of Joubert syndrome, a disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly. {ECO:0000269|PubMed:26026149, ECO:0000269|PubMed:26096313, ECO:0000269|PubMed:26386044, ECO:0000269|PubMed:26386247, ECO:0000269|PubMed:26429889}. Note=The disease is caused by mutations affecting the gene represented in this entry. Some patients with biallelic KIAA0586 mutations manifest a disease phenotype with features of Joubert syndrome and additional findings of a small thorax and respiratory problems consistent with Jeune syndrome (Joubert-Jeune ciliopathy). {ECO:0000269|PubMed:26386044}.; DISEASE: Short-rib thoracic dysplasia 14 with polydactyly (SRTD14) [MIM:616546]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269|PubMed:26166481}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.0940
Intolerance Scores
- LoFtool
- 0.978
- RVIS EVS
- 0.61
- RVIS percentile EVS
- 82.97
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.365
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |