KCNIP4

potassium voltage-gated channel interacting protein 4, the group of MicroRNA protein coding host genes|EF-hand domain containing|Potassium voltage-gated channel regulatory subunits

Basic information

Region (hg38): 4:20728605-21948772

Links

ENSG00000185774 ∙ NCBI:80333 ∙ OMIM:608182 ∙ HGNC:30083 ∙ Uniprot:Q6PIL6 ∙ 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 KCNIP4 gene.

• Inborn genetic diseases (3 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNIP4 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			2			2
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	4	0	0

Variants in KCNIP4

This is a list of pathogenic ClinVar variants found in the KCNIP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-20749655-A-G		KCNIP4-related disorder	Benign (Oct 16, 2019)
4-20749681-T-C		not specified	Uncertain significance (Dec 15, 2022)
4-20758859-G-T		not specified	Uncertain significance (Dec 26, 2023)
4-20758897-A-G			Benign (Dec 31, 2019)
4-20850543-A-G		KCNIP4-related disorder	Benign (Oct 18, 2019)
4-20850621-A-G		KCNIP4-related disorder	Benign (Oct 18, 2019)
4-20850662-C-T		not specified	Uncertain significance (Nov 17, 2022)
4-20850664-C-T		not specified	Uncertain significance (Mar 08, 2024)
4-20882649-A-G		not specified	Uncertain significance (Feb 26, 2024)
4-21697422-T-A			Uncertain significance (Feb 01, 2019)
4-21948616-C-T		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNIP4	protein_coding	protein_coding	ENST00000382152	9	1220184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.821	0.179	125704	0	3	125707	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	94	140	0.669	0.00000754	1688
Missense in Polyphen		24	50.672	0.47364		635
Synonymous	0.0220	49	49.2	0.996	0.00000288	429
Loss of Function	3.03	2	14.4	0.139	6.10e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000628	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000628	0.0000544
South Asian	0.00	0.00
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. Modulates KCND2 channel density, inactivation kinetics and rate of recovery from inactivation in a calcium-dependent and isoform-specific manner (PubMed:11847232, PubMed:18957440, PubMed:23576435). Modulates KCND3/Kv4.3 currents (PubMed:23576435). Isoform 4 does not increase KCND2 expression at the cell membrane (PubMed:18957440). Isoform 4 retains KCND3 in the endoplasmic reticulum and negatively regulates its expression at the cell membrane. {ECO:0000250|UniProtKB:Q6PHZ8, ECO:0000269|PubMed:11847232, ECO:0000269|PubMed:18957440, ECO:0000269|PubMed:23576435}.
• Pathway: Phase 1 - inactivation of fast Na+ channels;Cardiac conduction;Muscle contraction;Regulation of nuclear beta catenin signaling and target gene transcription (Consensus)

Intolerance Scores

• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.371
• hipred: Y
• hipred_score: 0.641
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnip4

Gene ontology

• Biological process: potassium ion transmembrane transport;protein localization to plasma membrane;regulation of potassium ion transmembrane transport
• Cellular component: cytoplasm;endoplasmic reticulum;cytosol;plasma membrane;voltage-gated potassium channel complex
• Molecular function: voltage-gated ion channel activity;potassium channel activity;calcium ion binding;protein binding;potassium channel regulator activity