SELENOP

selenoprotein P, the group of Selenoproteins

Basic information

Region (hg38): 5:42799879-42887392

Previous symbols: [ "SEPP1" ]

Links

ENSG00000250722NCBI:6414OMIM:601484HGNC:10751Uniprot:P49908AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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
clinvar
1
clinvar
2
missense
14
clinvar
2
clinvar
16
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
Total 0 0 14 4 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-G not specified Uncertain significance (Mar 18, 2024)3317251
5-42800763-C-T not specified Uncertain significance (Sep 20, 2023)3159606
5-42800785-T-C not specified Uncertain significance (Dec 13, 2023)3159605
5-42800806-T-G not specified Uncertain significance (May 25, 2022)3159604
5-42800976-G-C not specified Uncertain significance (Apr 07, 2022)3159615
5-42800982-A-G not specified Likely benign (Sep 16, 2021)3159614
5-42801176-T-C Benign (May 31, 2018)783435
5-42801259-G-A not specified Uncertain significance (Nov 22, 2021)3159613
5-42801261-G-A not specified Uncertain significance (May 31, 2023)2527084
5-42801304-G-A not specified Uncertain significance (Jun 06, 2023)2511083
5-42804675-C-T not specified Uncertain significance (May 24, 2023)2553607
5-42804759-A-G not specified Uncertain significance (Dec 28, 2022)3159612
5-42806886-A-G Benign (Mar 30, 2018)787815
5-42806930-T-G not specified Uncertain significance (May 30, 2022)3159611
5-42806944-A-G not specified Uncertain significance (Oct 26, 2022)3159610
5-42807008-G-C not specified Uncertain significance (Mar 17, 2023)2526256
5-42807022-C-T not specified Likely benign (Jun 03, 2022)3159608
5-42807092-C-T not specified Uncertain significance (Apr 13, 2022)3159607
5-42808242-C-G not specified Uncertain significance (Apr 23, 2024)3317250
5-42808299-T-TC Likely benign (Aug 15, 2018)747158
5-42808307-G-A not specified Uncertain significance (Jun 06, 2023)2569209
5-42808309-T-C Likely benign (Sep 01, 2023)2655451

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SELENOPprotein_codingprotein_codingENST00000514985 487513
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.29e-70.7551247010981247990.000393
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.01241971970.9980.000009622497
Missense in Polyphen4744.341.06569
Synonymous0.1766364.80.9720.00000290701
Loss of Function1.271217.80.6750.00000112199

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001620.00162
Ashkenazi Jewish0.0001990.000199
East Asian0.0005770.000556
Finnish0.000.00
European (Non-Finnish)0.0002650.000256
Middle Eastern0.0005770.000556
South Asian0.0002050.000196
Other0.0001650.000165

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

loftool
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