SELENOP

selenoprotein P, the group of Selenoproteins

Basic information

Region (hg38): 5:42799879-42887392

Previous symbols: [ "SEPP1" ]

Links

ENSG00000250722 ∙ NCBI:6414 ∙ OMIM:601484 ∙ HGNC:10751 ∙ Uniprot:P49908 ∙ 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 SELENOP gene.

• Inborn genetic diseases (5 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SELENOP 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			5			5
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	5	2	2

Variants in SELENOP

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

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

Position	Type	Phenotype	Significance	ClinVar
5-42800763-C-T		not specified	Uncertain significance (Sep 20, 2023)
5-42800785-T-C		not specified	Uncertain significance (Dec 13, 2023)
5-42800806-T-G		not specified	Uncertain significance (May 25, 2022)
5-42800976-G-C		not specified	Uncertain significance (Apr 07, 2022)
5-42800982-A-G		not specified	Likely benign (Sep 16, 2021)
5-42801176-T-C			Benign (May 31, 2018)
5-42801259-G-A		not specified	Uncertain significance (Nov 22, 2021)
5-42801261-G-A		not specified	Uncertain significance (May 31, 2023)
5-42801304-G-A		not specified	Uncertain significance (Jun 06, 2023)
5-42804675-C-T		not specified	Uncertain significance (May 24, 2023)
5-42804759-A-G		not specified	Uncertain significance (Dec 28, 2022)
5-42806886-A-G			Benign (Mar 30, 2018)
5-42806930-T-G		not specified	Uncertain significance (May 30, 2022)
5-42806944-A-G		not specified	Uncertain significance (Oct 26, 2022)
5-42807008-G-C		not specified	Uncertain significance (Mar 17, 2023)
5-42807022-C-T		not specified	Likely benign (Jun 03, 2022)
5-42807092-C-T		not specified	Uncertain significance (Apr 13, 2022)
5-42808299-T-TC			Likely benign (Aug 15, 2018)
5-42808307-G-A		not specified	Uncertain significance (Jun 06, 2023)
5-42808309-T-C			Likely benign (Sep 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SELENOP	protein_coding	protein_coding	ENST00000514985	4	87513

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.29e-7	0.755	124701	0	98	124799	0.000393

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0124	197	197	0.998	0.00000962	2497
Missense in Polyphen		47	44.34	1.06		569
Synonymous	0.176	63	64.8	0.972	0.00000290	701
Loss of Function	1.27	12	17.8	0.675	0.00000112	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00162	0.00162
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000577	0.000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000265	0.000256
Middle Eastern	0.000577	0.000556
South Asian	0.000205	0.000196
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Might be responsible for some of the extracellular antioxidant defense properties of selenium or might be involved in the transport of selenium. May supply selenium to tissues such as brain and testis.
• Pathway: Selenium Micronutrient Network;Integrin-mediated Cell Adhesion;Selenium Metabolism and Selenoproteins;ESC Pluripotency Pathways;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.530

Intolerance Scores

• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• pHI: 0.220
• hipred: N
• hipred_score: 0.146
• ghis: 0.457

Mouse Genome Informatics

• Gene name: Selenop
• Phenotype: limbs/digits/tail phenotype; renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; reproductive system 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); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: selenium compound metabolic process;platelet degranulation;response to oxidative stress;brain development;locomotory behavior;post-embryonic development;response to selenium ion;sexual reproduction;regulation of growth
• Cellular component: extracellular region;extracellular space;platelet dense granule lumen;extracellular exosome
• Molecular function: selenium binding