KCNS2

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

Basic information

Region (hg38): 8:98426957-98432853

Links

ENSG00000156486 ∙ NCBI:3788 ∙ OMIM:602906 ∙ HGNC:6301 ∙ Uniprot:Q9ULS6 ∙ 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 KCNS2 gene.

• Inborn genetic diseases (11 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNS2 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					1	1
missense			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	2

Variants in KCNS2

This is a list of pathogenic ClinVar variants found in the KCNS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-98427998-T-C		not specified	Uncertain significance (Jan 10, 2023)
8-98428037-C-T		not specified	Uncertain significance (Jun 30, 2022)
8-98428101-C-T		not specified	Uncertain significance (Dec 01, 2022)
8-98428362-T-C		not specified	Uncertain significance (Feb 24, 2022)
8-98428466-G-A		not specified	Uncertain significance (Mar 06, 2023)
8-98428520-G-A		not specified	Uncertain significance (Apr 13, 2022)
8-98428590-T-C		not specified	Uncertain significance (Jul 28, 2021)
8-98428640-C-T		not specified	Uncertain significance (Dec 19, 2022)
8-98428650-A-G		not specified	Uncertain significance (Jan 08, 2024)
8-98428736-C-G		not specified	Uncertain significance (Jan 26, 2023)
8-98428784-G-A			Benign (Jul 13, 2018)
8-98428832-C-A		not specified	Uncertain significance (Feb 13, 2024)
8-98428880-C-A			Benign (Jul 13, 2018)
8-98428925-C-T		not specified	Uncertain significance (Nov 06, 2023)
8-98429067-C-T		not specified	Uncertain significance (Dec 17, 2023)
8-98429133-C-G		not specified	Uncertain significance (Dec 19, 2023)
8-98429216-T-C		not specified	Uncertain significance (May 31, 2023)
8-98429232-G-A		not specified	Uncertain significance (Oct 27, 2021)
8-98429261-C-T		not specified	Uncertain significance (Feb 11, 2022)
8-98429282-G-A		not specified	Uncertain significance (Nov 09, 2021)
8-98429317-C-G		not specified	Uncertain significance (Aug 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNS2	protein_coding	protein_coding	ENST00000287042	1	5827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0590	0.926	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	203	281	0.723	0.0000173	3141
Missense in Polyphen		100	163.18	0.61281		1813
Synonymous	0.549	118	126	0.938	0.00000850	968
Loss of Function	2.11	4	11.8	0.338	5.18e-7	141

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000326	0.000326
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potassium channel subunit that does not form functional channels by itself. Can form functional heterotetrameric channels with KCNB1 and KCNB2; modulates the delayed rectifier voltage- gated potassium channel activation and deactivation rates of KCNB1 and KCNB2. {ECO:0000250|UniProtKB:O35174}.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.0659
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.311
• hipred: Y
• hipred_score: 0.627
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.459

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcns2
• Phenotype: normal phenotype

Gene ontology

• Biological process: potassium ion transport;protein homooligomerization;potassium ion transmembrane transport;regulation of delayed rectifier potassium channel activity
• Cellular component: plasma membrane;voltage-gated potassium channel complex;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: voltage-gated potassium channel activity;protein binding