KCNIP1 potassium voltage-gated channel interacting protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: KCNIP1provided by HGNC
Official Full Name: potassium voltage-gated channel interacting protein 1provided by HGNC
Primary source: HGNC:HGNC:15521
See related: Ensembl:ENSG00000182132 MIM:604660; AllianceGenome:HGNC:15521
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: VABP; KCHIP1
Summary: This gene encodes a member of the family of cytosolic voltage-gated potassium (Kv) channel-interacting proteins (KCNIPs), which belong to the neuronal calcium sensor (NCS) family of the calcium binding EF-hand proteins. They associate with Kv4 alpha subunits to form native Kv4 channel complexes. The encoded protein may regulate rapidly inactivating (A-type) currents, and hence neuronal membrane excitability, in response to changes in the concentration of intracellular calcium. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2013]
Expression: Biased expression in brain (RPKM 5.5), testis (RPKM 1.0) and 6 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q35.1

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (170353487..170736632)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (170892193..171275276)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (169780491..170163636)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

This is the first copy number variation association study of the KCNIP1 gene in Chinese population, and these data indicated that KCNIP1 might function as a type 2 diabetes-susceptibility gene whose dysregulation alters insulin production.
Title: Divergent patterns of genic copy number variation in KCNIP1 gene reveal risk locus of type 2 diabetes in Chinese population.
Study shows that the VAPB-PTPIP51 tethers regulate autophagy and demonstrates that overexpression of VAPB or PTPIP51 to tighten endoplasmic reticulum-mitochondria contacts impairs, whereas small interfering RNA-mediated loss of VAPB or PTPIP51 to loosen contacts stimulates, autophagosome formation.
Title: The ER-Mitochondria Tethering Complex VAPB-PTPIP51 Regulates Autophagy.
the current study provides evidence that genetic variants of Kv accessory proteins may contribute to the susceptibility of Attention-deficit/hyperactivity disorder.
Title: Attention-deficit/hyperactivity disorder associated with KChIP1 rs1541665 in Kv channels accessory proteins.
These studies showed that a common copy number variation in KCNIP1 gene is a genetic predictor of atrial fibrillation risk possibly pointing to a functional pathway.
Title: Genome-wide screening identifies a KCNIP1 copy number variant as a genetic predictor for atrial fibrillation.
KCNIP1 from copy number variations study might function as a type 2 diabetes susceptibility gene whose dysregulation alters insulin production.
Title: Genome-wide copy number variation study reveals KCNIP1 as a modulator of insulin secretion.
Protein aggregation due to nsSNP resulting in P56S VABP protein is associated with amyotrophic lateral sclerosis
Title: Protein aggregation due to nsSNP resulting in P56S VABP protein is associated with amyotrophic lateral sclerosis.
V234I-VAPB induces ubiquitin aggregation followed by cell death; proposed that V234I-VAPB exhibits the characteristics of amyotrophic lateral sclerosis in spite of not having the typical aggregation property of different mutations in various neurodegenerative diseases
Title: First evidence of pathogenicity of V234I mutation of hVAPB found in Amyotrophic Lateral Sclerosis.
our findings suggest that KChIP1 interacts with Kv4.3 in interneurons at the stratum lacunosum-moleculare/radiatum junction
Title: KChIP1 modulation of Kv4.3-mediated A-type K(+) currents and repetitive firing in hippocampal interneurons.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

bac51805S (e-PCR)
- UniSTS:181509

SHGC-143803 (e-PCR)
- UniSTS:172053

RH120081 (e-PCR)
- UniSTS:132902

D5S1402 (e-PCR)
- UniSTS:149297

RH79077 (e-PCR)
- UniSTS:15206

bac51040T (e-PCR)
- UniSTS:181413

SHGC-146954 (e-PCR)
- UniSTS:175526

REN31472 (e-PCR)
- UniSTS:356272

KCNMB1_3183 (e-PCR)
- UniSTS:462291

SHGC-142398 (e-PCR)
- UniSTS:174036

SHGC-147924 (e-PCR)
- UniSTS:176098

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables potassium channel activity	IEA Inferred from Electronic Annotation more info
enables potassium channel regulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables potassium channel regulator activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane transporter binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in chemical synaptic transmission	NAS Non-traceable Author Statement more info	PubMed
involved_in membrane repolarization	NAS Non-traceable Author Statement more info	PubMed
involved_in muscle contraction	NAS Non-traceable Author Statement more info	PubMed
involved_in potassium ion export across plasma membrane	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of heart contraction	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of potassium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of potassium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of signal transduction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of Kv4.3-KChIP1 channel complex	IPI Inferred from Physical Interaction more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in synapse	IEA Inferred from Electronic Annotation 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

General protein information

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Preferred Names: A-type potassium channel modulatory protein KCNIP1

Names: A-type potassium channel modulatory protein 1; Kv channel interacting protein 1; potassium channel interacting protein 1; vesicle APC-binding protein

NCBI Reference Sequences (RefSeq)

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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_011538.2 RefSeqGene

Range

155144..387756

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001034837.3 → NP_001030009.1 A-type potassium channel modulatory protein KCNIP1 isoform 1

See identical proteins and their annotated locations for NP_001030009.1

Status: REVIEWED

Description

Transcript Variant: This variant (1, also known as KCNP1-Ib) contains an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 5. It encodes isoform 1 which is shorter than isoform 5.

Source sequence(s)

AC008619, AI884645, AY170821, BC035032, BF514334, DQ148478

Consensus CDS

CCDS34286.1

UniProtKB/Swiss-Prot

A0A0C4DFQ7, B7Z7B4, Q3YAD0, Q3YAD1, Q3YAD2, Q3YAD3, Q5U822, Q9NZI2

Related

ENSP00000395323.1, ENST00000411494.5

Conserved Domains (1) summary

COG5126
Location:50 → 216

FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
NM_001034838.3 → NP_001030010.1 A-type potassium channel modulatory protein KCNIP1 isoform 3

See identical proteins and their annotated locations for NP_001030010.1

Status: REVIEWED

Description

Transcript Variant: This variant (3, also known as KCNIP1-Ia deltaII) contains an alternate 5' terminal exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 5. It encodes isoform 3 which has a distinct N-terminus and is shorter than isoform 5.

Source sequence(s)

AK301775, AY780424, BC035032, DC420716

Consensus CDS

CCDS34285.1

Related

ENSP00000366577.4, ENST00000377360.8

Conserved Domains (1) summary

COG5126
Location:48 → 214

FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
NM_001278339.2 → NP_001265268.1 A-type potassium channel modulatory protein KCNIP1 isoform 5

See identical proteins and their annotated locations for NP_001265268.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) encodes the longest isoform (5).

Source sequence(s)

AC008619, AI884645, AY170821, BC035032, BF514334, DQ148479

Consensus CDS

CCDS64312.1

Related

ENSP00000414886.1, ENST00000434108.5

Conserved Domains (1) summary

COG5126
Location:39 → 230

FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
NM_001278340.2 → NP_001265269.1 A-type potassium channel modulatory protein KCNIP1 isoform 4

See identical proteins and their annotated locations for NP_001265269.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, uses an alternate in-frame splice site in the 5' coding region and initiates translation at a downstream start codon, compared to variant 5. It encodes isoform 4 which is shorter than isoform 5.

Source sequence(s)

AC008619, AY170821, AY780424, BC035032, BF514334

Consensus CDS

CCDS64313.1

Related

ENSP00000431102.1, ENST00000520740.5

Conserved Domains (1) summary

COG5126
Location:11 → 177

FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
NM_014592.4 → NP_055407.1 A-type potassium channel modulatory protein KCNIP1 isoform 2

See identical proteins and their annotated locations for NP_055407.1

Status: REVIEWED

Description

Transcript Variant: This variant (2, also known as KCNP1-Ib deltaII) uses an alternate in-frame splice site in the 5' coding region compared to variant 5. It encodes isoform 2 which is shorter than isoform 5.

Source sequence(s)

AC008619, AF199597, AI884645, AY170821, BC035032, BF514334

Consensus CDS

CCDS4374.1

Related

ENSP00000329686.4, ENST00000328939.9

Conserved Domains (1) summary

COG5126
Location:39 → 205

FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

170353487..170736632

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017009407.2 → XP_016864896.1 A-type potassium channel modulatory protein KCNIP1 isoform X1

Conserved Domains (1) summary

COG5126
Location:48 → 214

FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
XM_017009408.2 → XP_016864897.1 A-type potassium channel modulatory protein KCNIP1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

170892193..171275276

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054352477.1 → XP_054208452.1 A-type potassium channel modulatory protein KCNIP1 isoform X1
XM_054352478.1 → XP_054208453.1 A-type potassium channel modulatory protein KCNIP1 isoform X2