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.

• not_specified (69 variants)
• not_provided (5 variants)

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. These statistics are base on transcript: NM_001322799.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			63	6	3	72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	6	4

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