KCNB2

potassium voltage-gated channel subfamily B member 2, the group of Potassium voltage-gated channels

Basic information

Region (hg38): 8:72537224-72938349

Links

ENSG00000182674 ∙ NCBI:9312 ∙ OMIM:607738 ∙ HGNC:6232 ∙ Uniprot:Q92953 ∙ 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 KCNB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNB2 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				2	5	7
missense			33	3	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	33	5	8

Variants in KCNB2

This is a list of pathogenic ClinVar variants found in the KCNB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-72567488-A-G			Benign (Sep 04, 2018)
8-72567778-G-A		not specified	Uncertain significance (Jan 12, 2024)
8-72567815-T-C		KCNB2-related disorder	Likely benign (Aug 13, 2019)
8-72567816-A-T		not specified	Uncertain significance (Apr 18, 2023)
8-72567833-C-G		not specified	Uncertain significance (Feb 28, 2023)
8-72567890-G-T		KCNB2-related disorder	Benign (May 04, 2021)
8-72567905-C-G		KCNB2-related disorder	Benign (Dec 01, 2020)
8-72567943-A-G		not specified	Uncertain significance (Feb 15, 2023)
8-72568050-G-A		not specified	Uncertain significance (May 29, 2024)
8-72568306-C-T		not specified	Uncertain significance (Mar 11, 2022)
8-72827017-G-A		Colorectal cancer	risk factor (Mar 01, 2022)
8-72935904-A-T			Benign (Sep 04, 2018)
8-72936215-A-G		not specified	Uncertain significance (Dec 30, 2023)
8-72936222-C-A		not specified	Uncertain significance (Jan 23, 2024)
8-72936274-C-T		not specified	Uncertain significance (May 26, 2023)
8-72936439-G-A		not specified	Uncertain significance (Jun 24, 2022)
8-72936560-G-A			Uncertain significance (Jun 01, 2023)
8-72936656-T-A		not specified	Uncertain significance (Apr 15, 2024)
8-72936727-T-C		not specified	Uncertain significance (May 21, 2024)
8-72936799-G-A		not specified	Likely benign (May 08, 2023)
8-72937006-C-G		not specified	Uncertain significance (Jun 29, 2023)
8-72937015-T-C		not specified	Uncertain significance (May 27, 2022)
8-72937097-G-A		not specified	Uncertain significance (Oct 12, 2021)
8-72937230-C-T			Benign (Jul 16, 2018)
8-72937261-G-T		not specified	Uncertain significance (Sep 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNB2	protein_coding	protein_coding	ENST00000523207	2	400959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00387	125706	0	8	125714	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.25	368	511	0.720	0.0000299	6010
Missense in Polyphen		52	168.21	0.30914		1993
Synonymous	-1.33	244	219	1.11	0.0000150	1816
Loss of Function	4.53	3	29.6	0.101	0.00000184	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Voltage-gated potassium channel that mediates transmembrane potassium transport in excitable membranes, primarily in the brain and smooth muscle cells. Channels open or close in response to the voltage difference across the membrane, letting potassium ions pass in accordance with their electrochemical gradient. Homotetrameric channels mediate a delayed-rectifier voltage-dependent outward potassium current that display rapid activation and slow inactivation in response to membrane depolarization. Can form functional homotetrameric and heterotetrameric channels that contain variable proportions of KCNB1; channel properties depend on the type of alpha subunits that are part of the channel. Can also form functional heterotetrameric channels with other alpha subunits that are non- conducting when expressed alone, such as KCNS1 and KCNS2, creating a functionally diverse range of channel complexes. In vivo, membranes probably contain a mixture of heteromeric potassium channel complexes, making it difficult to assign currents observed in intact tissues to any particular potassium channel family member. Contributes to the delayed-rectifier voltage-gated potassium current in cortical pyramidal neurons and smooth muscle cells. {ECO:0000250|UniProtKB:A6H8H5, ECO:0000250|UniProtKB:Q63099}.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.0810
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.83

Haploinsufficiency Scores

• pHI: 0.266
• hipred: Y
• hipred_score: 0.755
• ghis: 0.456

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.292

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnb2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: potassium ion transport;regulation of smooth muscle contraction;regulation of ion transmembrane transport;protein homooligomerization;potassium ion transmembrane transport;protein localization to plasma membrane
• Cellular component: plasma membrane;voltage-gated potassium channel complex;integral component of membrane;dendrite;neuronal cell body membrane;neuronal cell body;perikaryon
• Molecular function: voltage-gated potassium channel activity;delayed rectifier potassium channel activity;protein heterodimerization activity