KCNIP1

potassium voltage-gated channel interacting protein 1, the group of EF-hand domain containing|Potassium voltage-gated channel regulatory subunits

Basic information

Region (hg38): 5:170353486-170736632

Links

ENSG00000182132 ∙ NCBI:30820 ∙ OMIM:604660 ∙ HGNC:15521 ∙ Uniprot:Q9NZI2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCNIP1 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNIP1 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						0
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			13		1	14
Total	0	0	17	0	1

Variants in KCNIP1

This is a list of pathogenic ClinVar variants found in the KCNIP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-170378753-G-T		not specified	Uncertain significance (Apr 07, 2023)
5-170378801-G-C		not specified	Uncertain significance (Jan 03, 2022)
5-170378844-C-T		not specified	Uncertain significance (Sep 01, 2021)
5-170378846-C-T		not specified	Uncertain significance (Apr 25, 2022)
5-170378862-G-A		KCNMB1-related disorder	Benign (Jul 30, 2019)
5-170378867-G-A		not specified	Uncertain significance (Nov 30, 2022)
5-170378901-A-T		not specified	Uncertain significance (Nov 12, 2021)
5-170378943-A-C		not specified	Uncertain significance (Dec 06, 2021)
5-170378960-G-A		not specified	Uncertain significance (Oct 12, 2021)
5-170383686-T-C		not specified	Uncertain significance (Feb 22, 2023)
5-170383695-C-T		not specified	Uncertain significance (May 11, 2022)
5-170383707-G-A		not specified	Uncertain significance (Apr 12, 2022)
5-170383744-C-G		not specified	Uncertain significance (Sep 27, 2021)
5-170383745-G-A		KCNMB1-related disorder	Likely benign (Jun 26, 2019)
5-170383792-C-T		Hypertension, diastolic, resistance to • KCNMB1-related disorder	Benign (Nov 26, 2019)
5-170385354-A-G		not specified	Uncertain significance (Jun 06, 2023)
5-170385394-G-A			Benign (Dec 08, 2017)
5-170385435-G-T		not specified	Uncertain significance (Aug 22, 2023)
5-170718787-A-G		not specified	Uncertain significance (Sep 22, 2023)
5-170721887-G-C		not specified	Uncertain significance (Oct 29, 2021)
5-170722713-G-A		Idiopathic generalized epilepsy	Pathogenic (-)
5-170722735-T-G		not specified	Uncertain significance (Mar 21, 2023)
5-170732809-G-T		not specified	Uncertain significance (Jan 05, 2022)
5-170732837-T-C		not specified	Uncertain significance (Jan 26, 2022)
5-170732890-G-A		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNIP1	protein_coding	protein_coding	ENST00000411494	9	383146

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00421	0.989	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	79	133	0.595	0.00000723	1525
Missense in Polyphen		25	65.188	0.38351		754
Synonymous	0.862	45	53.0	0.849	0.00000356	382
Loss of Function	2.37	7	17.8	0.393	9.06e-7	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000466	0.000466
Ashkenazi Jewish	0.00	0.00
East Asian	0.00223	0.00223
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.00223	0.00223
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of Kv4/D (Shal)-type voltage-gated rapidly inactivating A-type potassium channels. Regulates channel density, inactivation kinetics and rate of recovery from inactivation in a calcium-dependent and isoform-specific manner. In vitro, modulates KCND1/Kv4.1 and KCND2/Kv4.2 currents. Increases the presence of KCND2 at the cell surface. {ECO:0000269|PubMed:10676964, ECO:0000269|PubMed:11423117, ECO:0000269|PubMed:12829703, ECO:0000269|PubMed:17187064}.
• Pathway: Phase 1 - inactivation of fast Na+ channels;Cardiac conduction;Muscle contraction (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.440
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.451
• hipred: N
• hipred_score: 0.425
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Kcnip1
• Phenotype: 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); 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)

Zebrafish Information Network

• Gene name: kcnip1a
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: potassium ion transmembrane transport;regulation of potassium ion transmembrane transport
• Cellular component: cytoplasm;plasma membrane;voltage-gated potassium channel complex;dendrite;extrinsic component of cytoplasmic side of plasma membrane
• Molecular function: voltage-gated ion channel activity;potassium channel activity;calcium ion binding;protein binding;potassium channel regulator activity