SELENOP
Basic information
Region (hg38): 5:42799879-42887392
Previous symbols: [ "SEPP1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 2 | |||||
missense | 14 | 16 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 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) | ||
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) | ||
5-42808242-C-G | not specified | Uncertain significance (Apr 23, 2024) | ||
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:
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:
- 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