SELL
Basic information
Region (hg38): 1:169690664-169711702
Previous symbols: [ "LYAM1", "LNHR" ]
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 SELL 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 | 13 | 16 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 13 | 1 | 4 |
Variants in SELL
This is a list of pathogenic ClinVar variants found in the SELL region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-169701571-C-A | not specified | Uncertain significance (Jun 30, 2022) | ||
1-169701668-T-C | not specified | Uncertain significance (Oct 14, 2023) | ||
1-169701681-G-T | not specified | Uncertain significance (Jan 03, 2022) | ||
1-169703321-T-G | not specified | Uncertain significance (Sep 07, 2022) | ||
1-169703422-A-G | not specified | Uncertain significance (Dec 21, 2023) | ||
1-169704603-A-G | not specified | Uncertain significance (Dec 16, 2023) | ||
1-169704637-A-T | not specified | Uncertain significance (Nov 03, 2022) | ||
1-169704686-G-C | not specified | Uncertain significance (Dec 28, 2023) | ||
1-169704733-C-G | Benign (Apr 24, 2018) | |||
1-169707344-A-T | not specified | Uncertain significance (Aug 16, 2021) | ||
1-169707357-G-A | not specified | Uncertain significance (Dec 03, 2021) | ||
1-169707371-A-G | not specified | Uncertain significance (Jan 12, 2024) | ||
1-169707414-C-G | not specified | Uncertain significance (Jul 12, 2023) | ||
1-169707428-C-T | not specified | Uncertain significance (May 12, 2024) | ||
1-169708538-A-G | Benign (Dec 31, 2019) | |||
1-169708606-C-T | not specified | Uncertain significance (Jan 18, 2022) | ||
1-169708639-G-A | not specified | Uncertain significance (Jun 17, 2024) | ||
1-169708716-C-T | not specified | Likely benign (Dec 01, 2022) | ||
1-169708782-G-C | Benign (May 13, 2018) | |||
1-169710455-C-A | Benign (Feb 16, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SELL | protein_coding | protein_coding | ENST00000236147 | 9 | 21032 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.96e-7 | 0.859 | 124602 | 0 | 17 | 124619 | 0.0000682 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.320 | 179 | 191 | 0.935 | 0.00000908 | 2514 |
Missense in Polyphen | 56 | 74.001 | 0.75675 | 959 | ||
Synonymous | 0.170 | 63 | 64.7 | 0.973 | 0.00000316 | 647 |
Loss of Function | 1.53 | 13 | 20.5 | 0.635 | 8.64e-7 | 278 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000649 | 0.0000646 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000559 | 0.0000557 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000851 | 0.0000797 |
Middle Eastern | 0.0000559 | 0.0000557 |
South Asian | 0.000230 | 0.000196 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-dependent lectin that mediates cell adhesion by binding to glycoproteins on neighboring cells (PubMed:12403782, PubMed:28489325, PubMed:28011641). Mediates the adherence of lymphocytes to endothelial cells of high endothelial venules in peripheral lymph nodes. Promotes initial tethering and rolling of leukocytes in endothelia (PubMed:12403782, PubMed:28011641). {ECO:0000269|PubMed:12403782, ECO:0000269|PubMed:28011641, ECO:0000305|PubMed:28489325}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Human Complement System;Neutrophil degranulation;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Cell surface interactions at the vascular wall;Hemostasis
(Consensus)
Recessive Scores
- pRec
- 0.564
Intolerance Scores
- loftool
- rvis_EVS
- 0.79
- rvis_percentile_EVS
- 87.4
Haploinsufficiency Scores
- pHI
- 0.258
- hipred
- N
- hipred_score
- 0.401
- ghis
- 0.396
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.871
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sell
- Phenotype
- endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; respiratory system phenotype; liver/biliary system phenotype; immune system phenotype;
Gene ontology
- Biological process
- cell adhesion;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;response to ATP;neutrophil degranulation;regulation of immune response;leukocyte migration;leukocyte tethering or rolling
- Cellular component
- plasma membrane;integral component of plasma membrane;external side of plasma membrane;secretory granule membrane
- Molecular function
- protease binding;calcium ion binding;protein binding;heparin binding;carbohydrate binding;glycosphingolipid binding;cell adhesion molecule binding;oligosaccharide binding