KIAA0586

protein-coding

KIAA0586

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

NM_001329943.3

Inheritance

AR

ClinVar variants

P:169U:674B:358

Top phenotype

Joubert syndrome 23; Short rib thoracic dysplasia 14 with polydactyly

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr14:58,427,385-58,551,297

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~123.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Joubert syndrome 23STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014664

Submitter: Ambry Genetics

Joubert syndrome 23STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014664

Submitter: Labcorp Genetics (formerly Invitae)

short-rib thoracic dysplasia 14 with polydactylySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014688

Submitter: Genomics England PanelApp

Joubert syndrome with Jeune asphyxiating thoracic dystrophySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0018342

Submitter: Orphanet

short-rib thoracic dysplasia 14 with polydactylySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014688

Submitter: PanelApp Australia

Joubert syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0018772

Submitter: Orphanet

short-rib thoracic dysplasia 14 with polydactylySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014688

Submitter: Labcorp Genetics (formerly Invitae)

Joubert syndrome 23STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014664

Submitter: PanelApp Australia

short-rib thoracic dysplasia 14 with polydactylyMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0014688

Submitter: Ambry Genetics

Joubert syndrome 23DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014664

Submitter: G2P

Clinical Genomic Database (CGD)

Joubert syndrome 23; Short rib thoracic dysplasia 14 with polydactylyAR

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

Refs: 26096313; 26166481; 26386044Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KIAA0586 variants in ClinVar

19 Conditions Cataloged
Joubert syndrome 23Total: 1298
Short-rib thoracic dysplasia 14 with polydactylyTotal: 1276
not providedTotal: 297
Inborn genetic diseasesTotal: 259
not specifiedTotal: 169
KIAA0586-related disorderTotal: 103
Joubert syndrome and related disordersTotal: 9
Neurodevelopmental disorderTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
15
clinvar
291
clinvar
1
clinvar
310
missense
4
clinvar
640
clinvar
63
clinvar
3
clinvar
710
nonsense
32
clinvar
18
clinvar
3
clinvar
53
start loss
2
clinvar
2
frameshift
39
clinvar
33
clinvar
5
clinvar
77
splice donor/acceptor (+/-2bp)
4
clinvar
36
clinvar
9
clinvar
49
Total779267435441201

Highest pathogenic variant AF is 0.003834522

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001329943.3RefSeqNP_001316872.131MANE Select
ENST00000652326.2EnsemblENSP00000498929.131MANE Select
NM_001244189.2RefSeqNP_001231118.134Standard
NM_001244190.2RefSeqNP_001231119.131Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
si:ch211-185a18.2Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3717357640.9620.000036210687
Missense (PolyPhen)246233.531.05343362
Synonymous-0.02832672661.000.00001353085
Loss of Function3.443666.20.5440.000002971006

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00160.0015notable
Latino/Admixed American0.00270.0021notable
Ashkenazi Jewish0.00840.0075notable
East Asian0.000430.00039rare
Finnish0.000810.00079rare
European (Non-Finnish)0.00500.0046notable
South Asian0.000890.00078rare
Other0.00270.0023notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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