KCNC1 potassium voltage-gated channel subfamily C member 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: KCNC1provided by HGNC
Official Full Name: potassium voltage-gated channel subfamily C member 1provided by HGNC
Primary source: HGNC:HGNC:6233
See related: Ensembl:ENSG00000129159 MIM:176258; AllianceGenome:HGNC:6233
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: KV4; EPM7; NGK2; KV3.1
Summary: This gene encodes a member of a family of integral membrane proteins that mediate the voltage-dependent potassium ion permeability of excitable membranes. Alternative splicing is thought to result in two transcript variants encoding isoforms that differ at their C-termini. These isoforms have had conflicting names in the literature: the longer isoform has been called both "b" and "alpha", while the shorter isoform has been called both "a" and "beta" (PMIDs 1432046, 12091563). [provided by RefSeq, Oct 2014]
Expression: Biased expression in brain (RPKM 5.1) and testis (RPKM 0.7) See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 11p15.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (17734781..17783057)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (17832488..17880755)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (17756328..17804604)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A KCNC1-related neurological disorder due to gain of Kv3.1 function.
Title: A KCNC1-related neurological disorder due to gain of Kv3.1 function.
Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain.
Title: Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain.
A KCNC1 mutation in epilepsy of infancy with focal migrating seizures produces functional channels that fail to be regulated by PKC phosphorylation.
Title: A KCNC1 mutation in epilepsy of infancy with focal migrating seizures produces functional channels that fail to be regulated by PKC phosphorylation.
Methylation gene KCNC1 is associated with overall survival in patients with seminoma.
Title: Methylation gene KCNC1 is associated with overall survival in patients with seminoma.
Genetic diagnosis of infantile-onset epilepsy in the clinic: Application of whole-exome sequencing following epilepsy gene panel testing.
Title: Genetic diagnosis of infantile-onset epilepsy in the clinic: Application of whole-exome sequencing following epilepsy gene panel testing.
Cross Pharmacological, Biochemical and Computational Studies of a Human Kv3.1b Inhibitor from Androctonus australis Venom.
Title: Cross Pharmacological, Biochemical and Computational Studies of a Human Kv3.1b Inhibitor from Androctonus australis Venom.
Progressive myoclonus epilepsy KCNC1 variant causes a developmental dendritopathy.
Title: Progressive myoclonus epilepsy KCNC1 variant causes a developmental dendritopathy.
First Evidence of Kv3.1b Potassium Channel Subtype Expression during Neuronal Serotonergic 1C11 Cell Line Development.
Title: First Evidence of Kv3.1b Potassium Channel Subtype Expression during Neuronal Serotonergic 1C11 Cell Line Development.
Mechanisms Underlying the Hyperexcitability of CA3 and Dentate Gyrus Hippocampal Neurons Derived From Patients With Bipolar Disorder.
Title: Mechanisms Underlying the Hyperexcitability of CA3 and Dentate Gyrus Hippocampal Neurons Derived From Patients With Bipolar Disorder.
Authors identified three new de novo missense variants in KCNC1 in five unrelated individuals causing different phenotypes featuring either isolated nonprogressive myoclonus (p.Cys208Tyr), intellectual disability (p.Thr399Met), or epilepsy with myoclonic, absence and generalized tonic-clonic seizures, ataxia, and developmental delay (p.Ala421Val, three patients).
Title: KCNC1-related disorders: new de novo variants expand the phenotypic spectrum.

Submit: New GeneRIF Correction See all GeneRIFs (27)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Progressive myoclonic epilepsy type 7 MedGen: C4015420 OMIM: 616187 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genome-wide association study of opioid dependence: multiple associations mapped to calcium and potassium pathways. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

D11S4138 (e-PCR)
- UniSTS:58142

D11S4130 (e-PCR), detects polymorphism
- UniSTS:13902

RH15955 (e-PCR)
- UniSTS:13164

NoName (e-PCR)
- UniSTS:481418

D11S1888 (e-PCR), detects polymorphism
- UniSTS:31626

KCNC1_879 (e-PCR)
- UniSTS:277411

KCNC1_V172 (e-PCR)
- UniSTS:277411

RH27338 (e-PCR)
- UniSTS:85691

D11S2313E (e-PCR)
- UniSTS:52464

UniSTS:531455 (e-PCR)
- UniSTS:531455

Kcnc1 (e-PCR), detects polymorphism
- UniSTS:531455

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables delayed rectifier potassium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables delayed rectifier potassium channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables kinesin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane transporter binding	IEA Inferred from Electronic Annotation more info
enables voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IEA Inferred from Electronic Annotation more info
enables voltage-gated potassium channel activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
involved_in cerebellum development	IEA Inferred from Electronic Annotation more info
involved_in corpus callosum development	IEA Inferred from Electronic Annotation more info
involved_in globus pallidus development	IEA Inferred from Electronic Annotation more info
involved_in optic nerve development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of potassium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in potassium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in potassium ion transmembrane transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in potassium ion transport	TAS Traceable Author Statement more info	PubMed
involved_in protein homooligomerization	IEA Inferred from Electronic Annotation more info
involved_in protein tetramerization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of presynaptic membrane potential	IEA Inferred from Electronic Annotation more info
involved_in response to amine	IEA Inferred from Electronic Annotation more info
involved_in response to auditory stimulus	IEA Inferred from Electronic Annotation more info
involved_in response to fibroblast growth factor	IEA Inferred from Electronic Annotation more info
involved_in response to light intensity	IEA Inferred from Electronic Annotation more info
involved_in response to nerve growth factor	IEA Inferred from Electronic Annotation more info
involved_in response to potassium ion	IEA Inferred from Electronic Annotation more info
involved_in response to toxic substance	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in axolemma	IEA Inferred from Electronic Annotation more info
is_active_in axon terminus	IBA Inferred from Biological aspect of Ancestor more info
located_in calyx of Held	IEA Inferred from Electronic Annotation more info
located_in cell surface	IEA Inferred from Electronic Annotation more info
is_active_in dendrite membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in neuronal cell body membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in neuronal cell body membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info
is_active_in postsynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in presynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
part_of voltage-gated potassium channel complex	IBA Inferred from Biological aspect of Ancestor more info
part_of voltage-gated potassium channel complex	IDA Inferred from Direct Assay more info	PubMed
part_of voltage-gated potassium channel complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

Go to the top of the page Help

Preferred Names: voltage-gated potassium channel KCNC1

Names: potassium channel, voltage gated Shaw related subfamily C, member 1; voltage-gated potassium channel protein KV3.1; voltage-gated potassium channel subunit Kv4

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_041827.1 RefSeqGene

Range

3834..52110

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001112741.2 → NP_001106212.1 voltage-gated potassium channel KCNC1 isoform 1

See identical proteins and their annotated locations for NP_001106212.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1).

Source sequence(s)

AC124056, AC124078, AC124301

Consensus CDS

CCDS44547.1

UniProtKB/TrEMBL

A0A6Q8PHL6

Related

ENSP00000265969.7, ENST00000265969.8

Conserved Domains (2) summary

cd18414
Location:6 → 122

BTB_KCNC1_3; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily C members KCNC1 and KCNC3

pfam00520
Location:189 → 447

Ion_trans; Ion transport protein
NM_004976.4 → NP_004967.1 voltage-gated potassium channel KCNC1 isoform 2

See identical proteins and their annotated locations for NP_004967.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two exons and its 3' exon extends past a splice site used in variant 1, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AC124056, AK125480, AW452561, BC107129, DN993192

Consensus CDS

CCDS7827.1

UniProtKB/Swiss-Prot

K4DI87, P48547, Q3KNS8

UniProtKB/TrEMBL

A0A6Q8PHL6

Related

ENSP00000368785.3, ENST00000379472.4

Conserved Domains (2) summary

pfam00520
Location:189 → 447

Ion_trans; Ion transport protein

pfam02214
Location:10 → 104

BTB_2; BTB/POZ domain