SELENOS

selenoprotein S, the group of Selenoproteins

Basic information

Region (hg38): 15:101270816-101277500

Previous symbols: [ "VIMP" ]

Links

ENSG00000131871 ∙ NCBI:55829 ∙ OMIM:607918 ∙ HGNC:30396 ∙ Uniprot:Q9BQE4 ∙ 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 SELENOS gene.

• not provided (4 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SELENOS 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	2	3
missense			2		1	3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	1	3

Variants in SELENOS

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

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

Position	Type	Phenotype	Significance	ClinVar
15-101272816-G-A			Likely benign (Jun 15, 2018)
15-101272847-G-C		not specified	Uncertain significance (Jul 09, 2021)
15-101274445-C-T			Benign (May 24, 2018)
15-101274611-C-A			Benign (Aug 16, 2018)
15-101274640-G-A			Benign (Aug 14, 2018)
15-101274645-A-G		not specified	Uncertain significance (Oct 25, 2022)
15-101274659-T-C		not specified	Uncertain significance (Oct 21, 2021)
15-101275302-C-T		not specified	Uncertain significance (Jan 03, 2024)
15-101275344-T-C		not specified	Uncertain significance (Feb 28, 2024)
15-101276591-C-G		not specified	Uncertain significance (Dec 09, 2023)
15-101276592-G-C		not specified	Uncertain significance (Dec 03, 2021)
15-101276604-T-C		not specified	Uncertain significance (Aug 12, 2021)
15-101276643-T-C		not specified	Uncertain significance (Nov 07, 2022)
15-101276663-A-G		not specified	Uncertain significance (Nov 17, 2023)
15-101276672-C-T		not specified	Uncertain significance (Dec 05, 2022)
15-101277344-G-A		not specified	Uncertain significance (Feb 13, 2024)
15-101277365-C-T		not specified	Uncertain significance (Jan 26, 2023)
15-101277366-C-G		not specified	Uncertain significance (May 09, 2023)
15-101277369-C-T		not specified	Uncertain significance (Nov 08, 2022)
15-101277392-G-A		not specified	Uncertain significance (Jan 19, 2024)
15-101277403-C-G		not specified	Uncertain significance (Oct 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SELENOS	protein_coding	protein_coding	ENST00000398226	6	6684

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.43e-9	0.0595	124583	0	40	124623	0.000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.610	112	95.2	1.18	0.00000525	1163
Missense in Polyphen		37	35.352	1.0466		478
Synonymous	-0.296	41	38.7	1.06	0.00000221	369
Loss of Function	-0.277	13	12.0	1.09	6.10e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000686	0.000670
Ashkenazi Jewish	0.00	0.00
East Asian	0.000120	0.000111
Finnish	0.0000515	0.0000464
European (Non-Finnish)	0.000160	0.000142
Middle Eastern	0.000120	0.000111
South Asian	0.0000671	0.0000654
Other	0.000544	0.000496

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins. Participates in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner. Probably acts by serving as a linker between DERL1, which mediates the retrotranslocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination. {ECO:0000269|PubMed:15215856}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Selenium Micronutrient Network;Selenium Metabolism and Selenoproteins;Post-translational protein modification;Metabolism of proteins;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.354
• ghis: 0.557

Mouse Genome Informatics

• Gene name: Selenos

Gene ontology

• Biological process: negative regulation of acute inflammatory response to antigenic stimulus;regulation of gluconeogenesis;ER overload response;response to glucose;protein ubiquitination;ubiquitin-dependent ERAD pathway;endoplasmic reticulum unfolded protein response;retrograde protein transport, ER to cytosol;negative regulation of interleukin-6 production;negative regulation of tumor necrosis factor production;cellular response to insulin stimulus;cellular response to oxidative stress;establishment of protein localization;cell redox homeostasis;negative regulation of glycogen biosynthetic process;negative regulation of glucose import;negative regulation of inflammatory response;negative regulation of nitric-oxide synthase biosynthetic process;response to redox state;cellular response to lipopolysaccharide;regulation of nitric oxide metabolic process;cellular oxidant detoxification;negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway;negative regulation of macrophage apoptotic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;cytoplasmic microtubule;plasma membrane;integral component of endoplasmic reticulum membrane;very-low-density lipoprotein particle;low-density lipoprotein particle;Derlin-1-VIMP complex;Derlin-1 retrotranslocation complex
• Molecular function: protein binding;antioxidant activity;enzyme binding;signaling receptor activity;ATPase binding;ubiquitin-specific protease binding