SELENOT

selenoprotein T, the group of Selenoproteins

Basic information

Region (hg38): 3:150602875-150630436

Links

ENSG00000198843 ∙ NCBI:51714 ∙ OMIM:607912 ∙ HGNC:18136 ∙ Uniprot:P62341 ∙ 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 SELENOT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SELENOT 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in SELENOT

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

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

Position	Type	Phenotype	Significance	ClinVar
3-150603387-G-C		not specified	Uncertain significance (Jan 22, 2025)
3-150603394-C-G		not specified	Uncertain significance (Jun 29, 2022)
3-150603408-C-T		not specified	Uncertain significance (Apr 09, 2024)
3-150603438-G-T		not specified	Uncertain significance (Feb 23, 2023)
3-150603442-C-A		not specified	Uncertain significance (Oct 06, 2024)
3-150622420-A-G		not specified	Uncertain significance (Feb 07, 2025)
3-150622467-G-C		not specified	Uncertain significance (Aug 07, 2024)
3-150623095-A-G		not specified	Uncertain significance (Aug 12, 2021)
3-150624824-A-G		not specified	Uncertain significance (Jan 29, 2025)
3-150624830-G-A		not specified	Uncertain significance (Sep 25, 2023)
3-150624838-C-A		not specified	Uncertain significance (Jan 02, 2025)
3-150627045-C-A		not specified	Uncertain significance (Dec 15, 2023)
3-150627054-A-G		not specified	Uncertain significance (Apr 04, 2024)
3-150627097-A-G		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SELENOT	protein_coding	protein_coding	ENST00000471696	5	27561

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.115	0.860	124601	0	7	124608	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	65	92.4	0.703	0.00000429	1259
Missense in Polyphen		6	21.794	0.27531		327
Synonymous	-0.643	39	34.2	1.14	0.00000152	364
Loss of Function	1.94	3	9.41	0.319	4.66e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000313	0.0000313
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000443
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Selenoprotein with thioredoxin reductase-like oxidoreductase activity (By similarity). Protects dopaminergic neurons against oxidative stress ans cell death (PubMed:26866473). Involved in ADCYAP1/PACAP-induced calcium mobilization and neuroendocrine secretion (By similarity). Plays a role in fibroblast anchorage and redox regulation (By similarity). In gastric smooth muscle, modulates the contraction processes through the regulation of calcium release and MYLK activation (By similarity). In pancreatic islets, involved in the control of glucose homeostasis, contributes to prolonged ADCYAP1/PACAP- induced insulin secretion (By similarity). {ECO:0000250|UniProtKB:P62342, ECO:0000250|UniProtKB:Q1H5H1, ECO:0000269|PubMed:26866473}.
• Disease: DISEASE: Note=mRNA levels are increased more than 200-folds in the caudate putamen from Parkinson disease (PD) patients compared to control subjects. In conditional brain knockout mice, treatment with PD-inducing neurotoxins provoke rapid and severe parkinsonian-like motor defects. {ECO:0000269|PubMed:26866473}.
• Pathway: Selenium Micronutrient Network;Selenium Metabolism and Selenoproteins (Consensus)

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.288
• ghis: 0.572

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Selenot
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: selenocysteine incorporation;positive regulation of cytosolic calcium ion concentration;response to glucose;pancreas development;insulin secretion involved in cellular response to glucose stimulus;glucose homeostasis;cell redox homeostasis;oxidation-reduction process;positive regulation of growth hormone secretion;cellular oxidant detoxification
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: thioredoxin-disulfide reductase activity;selenium binding