KCNS3

potassium voltage-gated channel modifier subfamily S member 3, the group of Potassium voltage-gated channels

Basic information

Region (hg38): 2:17877847-18361616

Links

ENSG00000170745 ∙ NCBI:3790 ∙ OMIM:603888 ∙ HGNC:6302 ∙ Uniprot:Q9BQ31 ∙ 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 KCNS3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNS3 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			26	2	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	1

Variants in KCNS3

This is a list of pathogenic ClinVar variants found in the KCNS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-17931043-A-C		not specified	Uncertain significance (Nov 20, 2024)
2-17931069-G-A		not specified	Uncertain significance (May 04, 2022)
2-17931228-T-G		not specified	Uncertain significance (Dec 07, 2024)
2-17931367-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-17931370-A-G		KCNS3-related disorder	Likely benign (Jun 06, 2022)
2-17931388-A-G		not specified	Uncertain significance (Nov 17, 2023)
2-17931402-G-C		not specified	Uncertain significance (Jul 19, 2023)
2-17931429-A-C		not specified	Uncertain significance (Dec 15, 2023)
2-17931439-C-G		not specified	Uncertain significance (Jan 18, 2023)
2-17931454-C-T		not specified	Uncertain significance (Sep 22, 2022)
2-17931558-G-A		not specified	Uncertain significance (Feb 22, 2023)
2-17931573-A-T		not specified	Uncertain significance (Jun 18, 2024)
2-17931606-G-T		not specified	Uncertain significance (Jan 17, 2024)
2-17931609-G-A		Autism spectrum disorder	association (-)
2-17931612-A-G		not specified	Uncertain significance (May 22, 2023)
2-17931618-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-17931631-C-T		not specified	Uncertain significance (Aug 30, 2022)
2-17931738-G-A		not specified	Uncertain significance (Jun 04, 2024)
2-17931888-C-T		not specified	Uncertain significance (Jan 10, 2022)
2-17931939-C-T		not specified	Uncertain significance (Jun 07, 2024)
2-17931940-G-A		not specified	Uncertain significance (Jun 06, 2023)
2-17932041-G-A		not specified	Uncertain significance (Jun 02, 2023)
2-17932075-G-A		not specified	Uncertain significance (Jan 07, 2022)
2-17932116-A-G		not specified	Uncertain significance (Sep 14, 2023)
2-17932116-A-T		not specified	Uncertain significance (Mar 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNS3	protein_coding	protein_coding	ENST00000403915	1	483769

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00119	0.961	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	234	282	0.829	0.0000165	3263
Missense in Polyphen		63	93.07	0.67691		1150
Synonymous	-0.702	128	118	1.08	0.00000765	952
Loss of Function	1.83	7	14.5	0.482	7.95e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000354	0.000354
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potassium channel subunit that does not form functional channels by itself. Can form functional heterotetrameric channels with KCNB1; modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1 (PubMed:10484328). Heterotetrameric channel activity formed with KCNB1 show increased current amplitude with the threshold for action potential activation shifted towards more negative values in hypoxic-treated pulmonary artery smooth muscle cells (By similarity). {ECO:0000250|UniProtKB:O88759, ECO:0000269|PubMed:10484328}.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.131
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.91

Haploinsufficiency Scores

• pHI: 0.654
• hipred: Y
• hipred_score: 0.521
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcns3

Gene ontology

• Biological process: potassium ion transport;regulation of ion transmembrane transport;regulation of insulin secretion;protein homooligomerization;potassium ion transmembrane transport
• Cellular component: Golgi apparatus;cytosol;plasma membrane;voltage-gated potassium channel complex;integral component of membrane
• Molecular function: voltage-gated potassium channel activity;delayed rectifier potassium channel activity;potassium channel regulator activity