SELENOK

selenoprotein K, the group of Selenoproteins

Basic information

Region (hg38): 3:53884417-53891885

Links

ENSG00000113811

∙ NCBI:58515 ∙ OMIM:607916 ∙ HGNC:30394 ∙ Uniprot:Q9Y6D0 ∙ 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 SELENOK gene.

not_specified (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SELENOK gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021237.5. 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						0
missense			13 clinvar	1 clinvar		14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SELENOK	protein_coding	protein_coding	ENST00000495461	5	7579

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000111	0.386	125047	0	14	125061	0.0000560

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.339	37	43.3	0.855	0.00000214	587
Missense in Polyphen		8	14.664	0.54556		214
Synonymous	-0.244	14	12.9	1.09	5.54e-7	167
Loss of Function	0.0775	6	6.21	0.966	2.62e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000147	0.000147
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000164
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000353
Middle Eastern	0.000164	0.000164
South Asian	0.00	0.00
Other	0.000332	0.000329

dbNSFP

Source: dbNSFP

Function: FUNCTION: Required for Ca(2+) flux in immune cells and plays a role in T-cell proliferation and in T-cell and neutrophil migration (By similarity). Involved in endoplasmic reticulum- associated degradation (ERAD) of soluble glycosylated proteins (PubMed:22016385). Required for palmitoylation and cell surface expression of CD36 and involved in macrophage uptake of low- density lipoprotein and in foam cell formation (By similarity). Together with ZDHHC6, required for palmitoylation of ITPR1 in immune cells, leading to regulate ITPR1 stability and function (PubMed:25368151). Plays a role in protection of cells from ER stress-induced apoptosis (PubMed:20692228). Protects cells from oxidative stress when overexpressed in cardiomyocytes (PubMed:16962588). {ECO:0000250|UniProtKB:Q9JLJ1, ECO:0000269|PubMed:16962588, ECO:0000269|PubMed:20692228, ECO:0000269|PubMed:22016385, ECO:0000269|PubMed:25368151}.;
Pathway: Selenium Micronutrient Network;Selenium Metabolism and Selenoproteins (Consensus)

Intolerance Scores

loftool
rvis_EVS: 0.19
rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

pHI
hipred: N
hipred_score: 0.292
ghis: 0.499

Mouse Genome Informatics

Gene name: Selenok
Phenotype: cellular phenotype; homeostasis/metabolism phenotype; 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); growth/size/body region phenotype; hematopoietic system phenotype; skeleton phenotype; immune system phenotype;

Gene ontology

Biological process: positive regulation of defense response to virus by host;calcium ion transport;response to oxidative stress;macrophage derived foam cell differentiation;protein palmitoylation;endoplasmic reticulum calcium ion homeostasis;positive regulation of tumor necrosis factor production;positive regulation of T cell proliferation;respiratory burst after phagocytosis;regulation of calcium-mediated signaling;intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress;positive regulation of monocyte chemotactic protein-1 production;positive regulation of chemokine secretion;positive regulation of T cell migration;positive regulation of interleukin-6 secretion
Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;plasma membrane;integral component of membrane
Molecular function: protein binding;identical protein binding