KCNQ3
Basic information
Region (hg38): 8:132120861-132481095
Previous symbols: [ "EBN2" ]
Links
Phenotypes
GenCC
Source:
- seizures, benign familial neonatal, 2 (Moderate), mode of inheritance: AD
- benign neonatal seizures (Supportive), mode of inheritance: AD
- benign familial infantile epilepsy (Supportive), mode of inheritance: AD
- seizures, benign familial neonatal, 2 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Seizures, benign familial neonatal, 2 | AD | General | 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 | Neurologic | 1859177; 8102508; 9425900; 20437616; 22612257 |
ClinVar
This is a list of variants' phenotypes submitted to
- Benign neonatal seizures (18 variants)
- Seizures, benign familial neonatal, 2 (2 variants)
- not provided (2 variants)
- Intellectual disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNQ3 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 | 10 | 233 | 248 | |||
missense | 20 | 431 | 17 | 475 | ||
nonsense | 13 | |||||
start loss | 1 | |||||
frameshift | 13 | 21 | ||||
inframe indel | 22 | 22 | ||||
splice donor/acceptor (+/-2bp) | 3 | |||||
splice region | 1 | 18 | 32 | 51 | ||
non coding | 103 | 151 | 121 | 375 | ||
Total | 20 | 23 | 587 | 401 | 127 |
Highest pathogenic variant AF is 0.00000658
Variants in KCNQ3
This is a list of pathogenic ClinVar variants found in the KCNQ3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
8-132121114-C-T | Seizures, benign familial neonatal, 2 • Benign Neonatal Epilepsy | Benign (Jan 13, 2018) | ||
8-132121160-C-T | Seizures, benign familial neonatal, 2 | Uncertain significance (Jan 12, 2018) | ||
8-132121281-G-GA | Benign neonatal seizures • Benign Neonatal Epilepsy | Uncertain significance (Jun 14, 2016) | ||
8-132121339-C-G | Seizures, benign familial neonatal, 2 | Uncertain significance (Jan 12, 2018) | ||
8-132121540-A-T | Seizures, benign familial neonatal, 2 • Benign neonatal seizures | Benign/Likely benign (Jan 13, 2018) | ||
8-132121573-T-C | Seizures, benign familial neonatal, 2 • Benign neonatal seizures | Benign/Likely benign (Jan 12, 2018) | ||
8-132121750-A-C | Benign Neonatal Epilepsy • Seizures, benign familial neonatal, 2 | Uncertain significance (Jan 12, 2018) | ||
8-132121756-G-A | Seizures, benign familial neonatal, 2 • Benign neonatal seizures | Benign (Jan 13, 2018) | ||
8-132121758-G-C | Benign neonatal seizures • Seizures, benign familial neonatal, 2 | Benign/Likely benign (Jan 13, 2018) | ||
8-132121798-G-T | Seizures, benign familial neonatal, 2 • Benign Neonatal Epilepsy | Benign/Likely benign (Jan 13, 2018) | ||
8-132121801-C-T | Seizures, benign familial neonatal, 2 | Benign (Mar 06, 2018) | ||
8-132121849-C-G | Benign neonatal seizures • Seizures, benign familial neonatal, 2 | Benign/Likely benign (Jan 13, 2018) | ||
8-132121854-C-A | Seizures, benign familial neonatal, 2 | Uncertain significance (Jan 13, 2018) | ||
8-132121891-A-C | Benign neonatal seizures • Seizures, benign familial neonatal, 2 | Benign (Jan 13, 2018) | ||
8-132121931-T-C | Seizures, benign familial neonatal, 2 • Benign Neonatal Epilepsy | Conflicting classifications of pathogenicity (Jan 12, 2018) | ||
8-132122019-G-C | Seizures, benign familial neonatal, 2 • Benign neonatal seizures | Uncertain significance (Jan 13, 2018) | ||
8-132122041-G-A | Seizures, benign familial neonatal, 2 • Benign neonatal seizures | Benign (Jan 13, 2018) | ||
8-132122048-C-T | Seizures, benign familial neonatal, 2 • Benign Neonatal Epilepsy | Benign/Likely benign (Jan 12, 2018) | ||
8-132122058-C-T | Seizures, benign familial neonatal, 2 | Uncertain significance (Jan 13, 2018) | ||
8-132122102-G-C | Seizures, benign familial neonatal, 2 | Uncertain significance (Jan 12, 2018) | ||
8-132122119-T-C | Benign neonatal seizures • Seizures, benign familial neonatal, 2 | Benign (Jan 13, 2018) | ||
8-132122131-C-T | Benign neonatal seizures • Seizures, benign familial neonatal, 2 | Benign (Jan 13, 2018) | ||
8-132122132-G-A | Seizures, benign familial neonatal, 2 | Benign (Jan 12, 2018) | ||
8-132122143-G-A | Benign neonatal seizures • Seizures, benign familial neonatal, 2 | Benign (Jan 13, 2018) | ||
8-132122167-A-C | Seizures, benign familial neonatal, 2 • Benign neonatal seizures | Benign (Jan 12, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KCNQ3 | protein_coding | protein_coding | ENST00000388996 | 15 | 360093 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.801 | 0.199 | 125737 | 0 | 11 | 125748 | 0.0000437 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.07 | 350 | 477 | 0.734 | 0.0000291 | 5604 |
Missense in Polyphen | 109 | 209.28 | 0.52083 | 2433 | ||
Synonymous | 0.409 | 193 | 200 | 0.963 | 0.0000129 | 1796 |
Loss of Function | 4.74 | 8 | 40.5 | 0.197 | 0.00000251 | 451 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000181 | 0.000181 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.0000463 | 0.0000462 |
European (Non-Finnish) | 0.0000272 | 0.0000264 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Associates with KCNQ2 or KCNQ5 to form a potassium channel with essentially identical properties to the channel underlying the native M-current, a slowly activating and deactivating potassium conductance which plays a critical role in determining the subthreshold electrical excitability of neurons as well as the responsiveness to synaptic inputs. Therefore, it is important in the regulation of neuronal excitability. {ECO:0000269|PubMed:11159685, ECO:0000269|PubMed:14534157, ECO:0000269|PubMed:16319223, ECO:0000269|PubMed:9872318}.;
- Disease
- DISEASE: Seizures, benign familial neonatal 2 (BFNS2) [MIM:121201]: A disorder characterized by clusters of seizures occurring in the first days of life. Most patients have spontaneous remission by 12 months of age and show normal psychomotor development. The disorder is distinguished from benign familial infantile seizures by an earlier age at onset. {ECO:0000269|PubMed:10852552, ECO:0000269|PubMed:14534157, ECO:0000269|PubMed:25982755, ECO:0000269|PubMed:9425900, ECO:0000269|PubMed:9872318}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in KCNQ3 may be involved in epileptic disorders. These are characterized by paroxysmal transient disturbances of the electrical activity of the brain that may be manifested as episodic impairment or loss of consciousness, abnormal motor phenomena, psychic or sensory disturbances, or perturbation of the autonomic nervous system. {ECO:0000269|PubMed:22612257}.;
- Pathway
- Cholinergic synapse - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Developmental Biology;ion channels and their functional role in vascular endothelium;Neuronal System;Interaction between L1 and Ankyrins;L1CAM interactions;Axon guidance;Voltage gated Potassium channels;Potassium Channels
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.0830
- rvis_EVS
- -0.33
- rvis_percentile_EVS
- 30.82
Haploinsufficiency Scores
- pHI
- 0.771
- hipred
- Y
- hipred_score
- 0.850
- ghis
- 0.570
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.806
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kcnq3
- Phenotype
- growth/size/body region phenotype; homeostasis/metabolism phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);
Zebrafish Information Network
- Gene name
- kcnq3
- Affected structure
- transmission of nerve impulse
- Phenotype tag
- abnormal
- Phenotype quality
- process quality
Gene ontology
- Biological process
- chemical synaptic transmission;regulation of ion transmembrane transport;membrane hyperpolarization;potassium ion transmembrane transport
- Cellular component
- plasma membrane;integral component of plasma membrane;voltage-gated potassium channel complex;cell surface;integral component of membrane;node of Ranvier;axon initial segment
- Molecular function
- voltage-gated potassium channel activity;delayed rectifier potassium channel activity;protein binding;calmodulin binding