KCNK18

protein-coding

potassium 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

NM_181840.1

Inheritance

AD

ClinVar variants

P:3U:64B:34

Top phenotype

Migraine, with or without aura, susceptibility to, 13

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr10:117,197,489-117,210,299

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~12.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

migraine, with or without aura, susceptibility to, 13LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0013344

Submitter: Ambry Genetics

migraine, with or without aura, susceptibility to, 13LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0013344

Submitter: Labcorp Genetics (formerly Invitae)

migraine, with or without aura, susceptibility to, 13STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013344

Submitter: PanelApp Australia

migraine, with or without aura, susceptibility to, 13LIMITED

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)

Migraine, with or without aura, susceptibility to, 13AD

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

Refs: 20871611Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KCNK18 variants in ClinVar

8 Conditions Cataloged
not specifiedTotal: 60
not providedTotal: 45
KCNK18-related disorderTotal: 12
Migraine, with or without aura, susceptibility to, 13Total: 6
KCNK18-related neurodevelopmental disorderTotal: 1
Parkinson diseaseTotal: 1
Parkinsonian disorderTotal: 1
Vascular parkinsonismTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
22
clinvar
23
missense
1
clinvar
1
clinvar
57
clinvar
7
clinvar
5
clinvar
71
nonsense
1
clinvar
1
start loss
0
frameshift
6
clinvar
6
splice donor/acceptor (+/-2bp)
0
Total2164295101

Highest pathogenic variant AF is 0.000119564465

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_181840.1RefSeqNP_862823.13MANE Select
ENST00000334549.1EnsemblENSP00000334650.13MANE Select
ENST00000850990.1EnsemblENSP00000521071.13Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.2682091981.050.00001102523
Missense (PolyPhen)5452.7311.0241724
Synonymous-1.2810185.91.180.00000539759
Loss of Function1.33610.70.5604.71e-7138

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00031rare
Latino/Admixed American0.000840.00084rare
Ashkenazi Jewish00.0absent
East Asian0.00260.0026notable
Finnish0.000280.00028rare
European (Non-Finnish)0.00100.0010notable
South Asian0.0190.019notable
Other0.00110.0011notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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