KCNN1

potassium calcium-activated channel subfamily N member 1, the group of Potassium calcium-activated channels

Basic information

Region (hg38): 19:17951293-18000085

Links

ENSG00000105642 ∙ NCBI:3780 ∙ OMIM:602982 ∙ HGNC:6290 ∙ Uniprot:Q92952 ∙ 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 KCNN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNN1 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	2
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	25	2	1

Variants in KCNN1

This is a list of pathogenic ClinVar variants found in the KCNN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17973952-G-A		not specified	Uncertain significance (May 11, 2022)
19-17973978-C-T			Benign (Feb 26, 2018)
19-17973989-C-T		not specified	Uncertain significance (Dec 03, 2024)
19-17973998-C-T		not specified	Uncertain significance (Sep 26, 2023)
19-17974007-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-17974028-C-G		not specified	Uncertain significance (Aug 02, 2021)
19-17974046-G-A		not specified	Likely benign (Jul 13, 2022)
19-17974057-G-A		not specified	Uncertain significance (Nov 29, 2021)
19-17974067-G-A		not specified	Uncertain significance (Jan 04, 2024)
19-17974243-G-A		not specified	Uncertain significance (Aug 10, 2021)
19-17974243-G-T		not specified	Uncertain significance (May 08, 2023)
19-17975137-A-G		not specified	Uncertain significance (Sep 18, 2024)
19-17975168-A-G		not specified	Uncertain significance (Jul 10, 2024)
19-17975173-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-17981975-C-T			Likely benign (Dec 01, 2022)
19-17982114-C-T		not specified	Uncertain significance (May 02, 2023)
19-17982135-C-T			Benign (Feb 26, 2018)
19-17985428-G-T		not specified	Uncertain significance (Sep 06, 2022)
19-17988433-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-17988454-C-T		not specified	Uncertain significance (Mar 21, 2023)
19-17988487-G-A		not specified	Uncertain significance (Mar 27, 2023)
19-17988524-G-A		not specified	Uncertain significance (Jan 24, 2024)
19-17989768-A-T		not specified	Uncertain significance (Mar 21, 2023)
19-17989775-G-C		not specified	Uncertain significance (Mar 31, 2024)
19-17989797-G-T		not specified	Uncertain significance (Jun 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNN1	protein_coding	protein_coding	ENST00000222249	9	48788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.854	0.146	125663	0	8	125671	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.41	237	367	0.646	0.0000261	3471
Missense in Polyphen		38	96.105	0.3954		810
Synonymous	0.697	155	166	0.931	0.0000130	1142
Loss of Function	3.46	3	19.5	0.154	8.35e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000936	0.0000907
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.0000556	0.0000544
Finnish	0.0000931	0.0000924
European (Non-Finnish)	0.00000885	0.00000880
Middle Eastern	0.0000556	0.0000544
South Asian	0.0000378	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Forms a voltage-independent potassium channel activated by intracellular calcium. Activation is followed by membrane hyperpolarization. Thought to regulate neuronal excitability by contributing to the slow component of synaptic afterhyperpolarization. The channel is blocked by apamin (By similarity). {ECO:0000250}.
• Pathway: Insulin secretion - Homo sapiens (human);Neuronal System;Ca2+ activated K+ channels;Potassium Channels (Consensus)

Recessive Scores

• pRec: 0.122

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.715

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.737

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kcnn1

Gene ontology

• Biological process: potassium ion transport;chemical synaptic transmission;potassium ion transmembrane transport
• Cellular component: plasma membrane;voltage-gated potassium channel complex;neuron projection;neuronal cell body
• Molecular function: calmodulin binding;calcium-activated potassium channel activity;small conductance calcium-activated potassium channel activity;protein heterodimerization activity