KCNK2
potassium two pore domain channel subfamily K member 2, the group of Potassium two pore domain channel subfamily K
Basic information
Region (hg38): 1:215005775-215237090
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNK2 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 | 1 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 0 |
Variants in KCNK2
This is a list of pathogenic ClinVar variants found in the KCNK2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-215083401-T-C | not specified | Uncertain significance (Dec 09, 2023) | ||
| 1-215086371-C-T | not specified | Uncertain significance (Sep 19, 2022) | ||
| 1-215086403-G-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 1-215086419-C-T | not specified | Uncertain significance (Mar 26, 2024) | ||
| 1-215086455-C-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 1-215086482-T-C | not specified | Uncertain significance (Feb 15, 2023) | ||
| 1-215169219-C-T | not specified | Uncertain significance (Feb 17, 2024) | ||
| 1-215169328-A-G | not specified | Uncertain significance (Aug 08, 2022) | ||
| 1-215194960-C-T | Likely benign (Dec 31, 2019) | |||
| 1-215194961-G-A | not specified | Uncertain significance (May 01, 2024) | ||
| 1-215195099-A-C | Likely benign (Dec 31, 2019) | |||
| 1-215234970-T-C | not specified | Uncertain significance (Nov 19, 2022) | ||
| 1-215235053-C-T | not specified | Uncertain significance (May 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| KCNK2 | protein_coding | protein_coding | ENST00000444842 | 7 | 231319 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0191 | 0.977 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.31 | 147 | 250 | 0.589 | 0.0000139 | 2752 |
| Missense in Polyphen | 46 | 103.82 | 0.44307 | 1150 | ||
| Synonymous | 0.758 | 92 | 102 | 0.904 | 0.00000646 | 882 |
| Loss of Function | 2.54 | 6 | 17.5 | 0.343 | 8.24e-7 | 209 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ion channel that contributes to passive transmembrane potassium transport (PubMed:23169818). Reversibly converts between a voltage-insensitive potassium leak channel and a voltage- dependent outward rectifying potassium channel in a phosphorylation-dependent manner (PubMed:11319556). In astrocytes, forms mostly heterodimeric potassium channels with KCNK1, with only a minor proportion of functional channels containing homodimeric KCNK2. In astrocytes, the heterodimer formed by KCNK1 and KCNK2 is required for rapid glutamate release in response to activation of G-protein coupled receptors, such as F2R and CNR1 (By similarity). {ECO:0000250|UniProtKB:P97438, ECO:0000269|PubMed:10784345, ECO:0000269|PubMed:11319556, ECO:0000269|PubMed:23169818}.;
- Pathway
- Cortisol synthesis and secretion - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Gastric acid secretion - Homo sapiens (human);Neuronal System;Phase 4 - resting membrane potential;Cardiac conduction;Muscle contraction;TWIK related potassium channel (TREK);Tandem pore domain potassium channels;Potassium Channels
(Consensus)
Intolerance Scores
- loftool
- 0.480
- rvis_EVS
- -0.45
- rvis_percentile_EVS
- 24
Haploinsufficiency Scores
- pHI
- 0.128
- hipred
- Y
- hipred_score
- 0.837
- ghis
- 0.521
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kcnk2
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- cardiac ventricle development;G protein-coupled receptor signaling pathway;memory;response to mechanical stimulus;positive regulation of cell death;stabilization of membrane potential;regulation of membrane potential;response to axon injury;negative regulation of cardiac muscle cell proliferation;cellular response to hypoxia;potassium ion transmembrane transport;cochlea development;positive regulation of cellular response to hypoxia;negative regulation of DNA biosynthetic process
- Cellular component
- nucleus;endoplasmic reticulum membrane;plasma membrane;integral component of plasma membrane;voltage-gated potassium channel complex;cell surface;apical plasma membrane;neuronal cell body;calyx of Held;astrocyte projection
- Molecular function
- outward rectifier potassium channel activity;potassium ion leak channel activity