KCNS1

potassium voltage-gated channel modifier subfamily S member 1, the group of Potassium voltage-gated channels

Basic information

Region (hg38): 20:45091214-45101127

Links

ENSG00000124134 ∙ NCBI:3787 ∙ OMIM:602905 ∙ HGNC:6300 ∙ Uniprot:Q96KK3 ∙ 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 KCNS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNS1 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			27	2	3	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	4

Variants in KCNS1

This is a list of pathogenic ClinVar variants found in the KCNS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45094880-T-G			Benign (Dec 28, 2017)
20-45094928-T-C			Benign (Aug 21, 2018)
20-45094932-C-T		not specified	Uncertain significance (Jul 09, 2021)
20-45095027-C-T		not specified	Uncertain significance (Aug 23, 2021)
20-45095047-C-A		not specified	Uncertain significance (Jan 24, 2024)
20-45095055-G-A			Benign (Dec 31, 2019)
20-45095057-C-T		not specified	Uncertain significance (Dec 05, 2022)
20-45095117-C-A		not specified	Uncertain significance (Mar 30, 2024)
20-45095187-C-A		not specified	Uncertain significance (Feb 22, 2023)
20-45095212-C-A		not specified	Uncertain significance (Mar 29, 2022)
20-45095330-C-T		not specified	Uncertain significance (Mar 30, 2022)
20-45097691-C-T		not specified	Uncertain significance (May 14, 2024)
20-45097791-G-A			Benign (Jul 31, 2018)
20-45097799-C-G		not specified	Uncertain significance (Dec 17, 2023)
20-45097814-G-C		not specified	Uncertain significance (Nov 08, 2022)
20-45097928-A-G		not specified	Uncertain significance (Feb 16, 2023)
20-45097976-C-T		not specified	Uncertain significance (Dec 02, 2021)
20-45097985-G-C		not specified	Likely benign (Apr 07, 2023)
20-45097988-T-C		not specified	Uncertain significance (Apr 07, 2023)
20-45097988-T-G		not specified	Uncertain significance (Aug 06, 2021)
20-45098002-A-C		not specified	Uncertain significance (Dec 03, 2021)
20-45098078-C-T		not specified	Uncertain significance (Oct 02, 2023)
20-45098092-A-T		not specified	Uncertain significance (Jan 08, 2024)
20-45098177-A-G		not specified	Uncertain significance (Dec 20, 2023)
20-45098231-G-A		not specified	Uncertain significance (Nov 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNS1	protein_coding	protein_coding	ENST00000306117	3	8803

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.112	0.883	125735	0	9	125744	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	237	321	0.739	0.0000213	3295
Missense in Polyphen		108	154.79	0.69773		1608
Synonymous	2.42	107	144	0.743	0.00000984	1131
Loss of Function	2.42	4	13.7	0.293	6.75e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000127
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.0000544	0.0000544
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 (PubMed:10484328). {ECO:0000269|PubMed:10484328}.
• Pathway: Neuronal System;Voltage gated Potassium channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.110

Haploinsufficiency Scores

• pHI: 0.0800
• hipred: Y
• hipred_score: 0.669
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0306

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcns1

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;delayed rectifier potassium channel activity;protein binding;potassium channel regulator activity