KCNIP3

potassium voltage-gated channel interacting protein 3, the group of EF-hand domain containing|Potassium voltage-gated channel regulatory subunits

Basic information

Region (hg38): 2:95297327-95386077

Previous symbols: [ "CSEN" ]

Links

ENSG00000115041 ∙ NCBI:30818 ∙ OMIM:604662 ∙ HGNC:15523 ∙ Uniprot:Q9Y2W7 ∙ 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 KCNIP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNIP3 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in KCNIP3

This is a list of pathogenic ClinVar variants found in the KCNIP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-95310368-C-T		not specified	Likely benign (Dec 21, 2023)
2-95310371-C-T		not specified	Uncertain significance (May 17, 2023)
2-95310425-G-A		not specified	Uncertain significance (Sep 04, 2024)
2-95310425-G-T		not specified	Uncertain significance (Oct 08, 2024)
2-95310454-C-T		not specified	Uncertain significance (Mar 04, 2024)
2-95374355-C-A		not specified	Uncertain significance (Jan 04, 2024)
2-95374874-A-C		not specified	Uncertain significance (Dec 13, 2023)
2-95374896-G-A		not specified	Uncertain significance (Jan 18, 2023)
2-95375156-A-G		not specified	Uncertain significance (Dec 20, 2023)
2-95375158-T-G		not specified	Uncertain significance (Dec 04, 2023)
2-95375177-A-G		not specified	Uncertain significance (Sep 14, 2023)
2-95375180-C-T		not specified	Uncertain significance (Oct 06, 2024)
2-95381600-T-C		not specified	Uncertain significance (Oct 30, 2023)
2-95381605-G-T		not specified	Uncertain significance (Oct 21, 2024)
2-95381645-A-C		not specified	Uncertain significance (Mar 25, 2024)
2-95381665-C-T		not specified	Uncertain significance (Jul 27, 2024)
2-95381690-A-C		not specified	Uncertain significance (Jan 26, 2023)
2-95382389-A-G		not specified	Uncertain significance (Jan 26, 2022)
2-95382410-A-G		not specified	Uncertain significance (Jan 17, 2023)
2-95382419-C-T		not specified	Uncertain significance (Mar 06, 2023)
2-95382449-G-C		not specified	Uncertain significance (Nov 03, 2023)
2-95382450-C-T		not specified	Uncertain significance (Jun 21, 2023)
2-95383252-T-G		not specified	Uncertain significance (Sep 30, 2021)
2-95383262-A-C		not specified	Uncertain significance (Feb 15, 2023)
2-95383283-G-T		not specified	Uncertain significance (Aug 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNIP3	protein_coding	protein_coding	ENST00000295225	9	88774

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0376	0.956	125722	0	10	125732	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.888	126	157	0.801	0.00000943	1708
Missense in Polyphen		49	58.641	0.8356		688
Synonymous	-0.538	75	69.3	1.08	0.00000499	470
Loss of Function	2.38	5	14.9	0.335	6.35e-7	176

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000311	0.000308
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent transcriptional repressor that binds to the DRE element of genes including PDYN and FOS. Affinity for DNA is reduced upon binding to calcium and enhanced by binding to magnesium. Seems to be involved in nociception (By similarity). {ECO:0000250|UniProtKB:Q9QXT8}.; FUNCTION: May play a role in the regulation of PSEN2 proteolytic processing and apoptosis. Together with PSEN2 involved in modulation of amyloid-beta formation. {ECO:0000269|PubMed:11259376, ECO:0000269|PubMed:11988022, ECO:0000269|PubMed:9771752}.
• Pathway: Human Thyroid Stimulating Hormone (TSH) signaling pathway;repression of pain sensation by the transcriptional regulator dream;Phase 1 - inactivation of fast Na+ channels;Cardiac conduction;Muscle contraction;IL3 (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.206
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.152
• hipred: Y
• hipred_score: 0.809
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnip3
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism 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)

Zebrafish Information Network

• Gene name: kcnip3b
• Affected structure: endocrine pancreas
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;intracellular protein transport;apoptotic process;signal transduction;potassium ion transmembrane transport;protein localization to plasma membrane;regulation of potassium ion transmembrane transport
• Cellular component: nucleus;endoplasmic reticulum;Golgi apparatus;cytosol;plasma membrane;voltage-gated potassium channel complex;dendrite;protein-DNA complex;axon terminus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;transcription corepressor activity;voltage-gated ion channel activity;potassium channel activity;calcium ion binding;protein binding;potassium channel regulator activity;ion channel binding