KCNK18
protein-codingpotassium two pore domain channel subfamily K member 18, the group of Potassium two pore domain channel subfamily K
Gene summary
Potassium channels play a role in many cellular processes including maintenance of the action potential, muscle contraction, hormone secretion, osmotic regulation, and ion flow. This gene encodes a member of the superfamily of potassium channel proteins containing two pore-forming P domains and the encoded protein functions as an outward rectifying potassium channel. A mutation in this gene has been found to be associated with migraine with aura.[provided by RefSeq, Jan 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0013344
Submitter: Ambry Genetics
Inheritance Pattern: Unknown
Disease ID:MONDO:0013344
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0013344
Submitter: PanelApp Australia
Inheritance Pattern: Unknown
Disease ID:MONDO:0013344
Submitter: Laboratory for Molecular Medicine
This gene-disease relationship has undergone rapid assessment. Classifications are based on preliminary review of gene-disease validity during analysis of genomic sequencing results.
Clinical Genomic Database (CGD)
Manifestation: Neurologic
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 KCNK18 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_181840.1. 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 | 1 | 22 | 23 | |||
| missense | 1 | 1 | 57 | 7 | 5 | 71 |
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 6 | 6 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 2 | 1 | 64 | 29 | 5 | 101 |
Highest pathogenic variant AF is 0.000119564465
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_862823.1 | 3 | MANE Select | |
| Ensembl | ENSP00000334650.1 | 3 | MANE Select | |
| Ensembl | ENSP00000521071.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neuronal System
- Phase 4 - resting membrane potential
- Cardiac conduction
- Muscle contraction
- TWIK-related spinal cord K+ channel (TRESK)
Biological Process
- potassium ion transport
- stabilization of membrane potential
- cellular response to pH
- potassium ion transmembrane transport
- potassium ion export across plasma membrane
Molecular Function
- potassium channel activity
- calcium-activated potassium channel activity
- outward rectifier potassium channel activity
- potassium ion leak channel activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000334549
- Coding exons
- 3
- Length
- 12811
- Individuals with no LoFs
- 124965
- Homozygous LoFs
- 12
- Heterozygous LoFs
- 771
- Defined
- 125748
- p
- 0.00312
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.268 | 209 | 198 | 1.05 | 0.0000110 | 2523 |
| Missense (PolyPhen) | 54 | 52.731 | 1.0241 | 724 | ||
| Synonymous | -1.28 | 101 | 85.9 | 1.18 | 0.00000539 | 759 |
| Loss of Function | 1.33 | 6 | 10.7 | 0.560 | 4.71e-7 | 138 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00084 | 0.00084 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0026 | 0.0026 | notable |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.0010 | 0.0010 | notable |
| South Asian | 0.019 | 0.019 | notable |
| Other | 0.0011 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Outward rectifying potassium channel. Produces rapidly activating outward rectifier K(+) currents. May function as background potassium channel that sets the resting membrane potential. Channel activity is directly activated by calcium signal. Activated by the G(q)-protein coupled receptor pathway. The calcium signal robustly activates the channel via calcineurin, whereas the anchoring of 14-3-3/YWHAH interferes with the return of the current to the resting state after activation. Inhibited also by arachidonic acid and other naturally occurring unsaturated free fatty acids. Channel activity is also enhanced by volatile anesthetics, such as isoflurane. Appears to be the primary target of hydroxy-alpha-sanshool, an ingredient of Schezuan pepper. May be involved in the somatosensory function with special respect to pain sensation (By similarity). {ECO:0000250, ECO:0000269|PubMed:12754259, ECO:0000269|PubMed:15562060}.;
- Disease
- DISEASE: Migraine with or without aura 13 (MGR13) [MIM:613656]: A form of migraine transmitted in an autosomal dominant pattern. Migraine is a disabling symptom complex of periodic headaches, usually temporal and unilateral. Headaches are often accompanied by irritability, nausea, vomiting and photophobia, preceded by constriction of the cranial arteries. The two major subtypes are common migraine (migraine without aura) and classic migraine (migraine with aura). Classic migraine is characterized by recurrent attacks of reversible neurological symptoms (aura) that precede or accompany the headache. Aura may include a combination of sensory disturbances, such as blurred vision, hallucinations, vertigo, numbness and difficulty in concentrating and speaking. {ECO:0000269|PubMed:20871611}. Note=The disease is caused by mutations affecting the gene represented in this entry. Susceptibility to migraine has been shown to be conferred by a frameshift mutation that segregates with the disorder in a large multigenerational family. Migraine was associated with sensitivity to lights, sounds, and smells, as well as nausea and occasional vomiting. Triggers included fatigue, alcohol and bright lights. Mutations in KCNK18 are a rare cause of migraine.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.617
- RVIS EVS
- 0.35
- RVIS percentile EVS
- 74.58
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |