KCNN3

potassium calcium-activated channel subfamily N member 3, the group of Potassium calcium-activated channels

Basic information

Region (hg38): 1:154697455-154870281

Links

ENSG00000143603

∙ NCBI:3782 ∙ OMIM:602983 ∙ HGNC:6292 ∙ Uniprot:Q9UGI6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

schizophrenia (Limited), mode of inheritance: Unknown
Zimmermann-Laband syndrome 3 (Moderate), mode of inheritance: AD
Zimmermann-Laband syndrome (Supportive), mode of inheritance: AR
Zimmermann-Laband syndrome 3 (Strong), mode of inheritance: AD
Zimmermann-Laband syndrome 3 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Zimmermann-Laband syndrome 3	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dental; Dermatologic; Musculoskeletal; Neurologic	31155282

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCNN3 gene.

not_provided (55 variants)
Inborn_genetic_diseases (52 variants)
Zimmermann-Laband_syndrome_3 (19 variants)
not_specified (18 variants)
KCNN3-related_disorder (2 variants)
Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002249.6. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				9 clinvar		9
missense	4 clinvar	1 clinvar	78 clinvar	17 clinvar		100
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	4	1	84	26	0

Highest pathogenic variant AF is 0.00021241316

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCNN3	protein_coding	protein_coding	ENST00000271915	8	172826

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.972	0.0277	125703	32	13	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.33	245	442	0.555	0.0000265	4808
Missense in Polyphen		66	152.56	0.43262		1753
Synonymous	0.221	190	194	0.980	0.0000127	1494
Loss of Function	4.27	4	28.7	0.139	0.00000152	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000979	0.000979
Ashkenazi Jewish	0.000878	0.000198
East Asian	0.000911	0.000272
Finnish	0.000348	0.000185
European (Non-Finnish)	0.000375	0.000123
Middle Eastern	0.000911	0.000272
South Asian	0.00132	0.000294
Other	0.00227	0.000489

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.;
Pathway: Insulin secretion - Homo sapiens (human);Neuronal System;Ca2+ activated K+ channels;Potassium Channels (Consensus)

Recessive Scores

pRec: 0.156

Intolerance Scores

loftool: 0.0697
rvis_EVS: -0.56
rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

pHI: 0.200
hipred: Y
hipred_score: 0.658
ghis: 0.564

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.329

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Kcnn3
Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; respiratory system phenotype;

Gene ontology

Biological process: potassium ion transmembrane transport
Cellular component: plasma membrane;integral component of membrane;neuron projection;neuronal cell body
Molecular function: calmodulin binding;small conductance calcium-activated potassium channel activity