THY1
Thy-1 cell surface antigen, the group of CD molecules|Ig-like cell adhesion molecule family|Immunoglobulin like domain containing
Basic information
Region (hg38): 11:119415476-119424985
Links
Phenotypes
GenCC
Source:
No genCC data.
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 THY1 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 | 0 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in THY1
This is a list of pathogenic ClinVar variants found in the THY1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-119419461-G-C | not specified | Uncertain significance (Jul 30, 2023) | ||
| 11-119419481-T-C | not specified | Uncertain significance (Dec 12, 2023) | ||
| 11-119420066-C-T | not specified | Likely benign (Mar 16, 2024) | ||
| 11-119420081-T-C | not specified | Uncertain significance (Jun 21, 2022) | ||
| 11-119420116-G-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 11-119420147-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 11-119420159-G-A | not specified | Uncertain significance (May 27, 2022) | ||
| 11-119420200-C-T | not specified | Uncertain significance (Dec 08, 2023) | ||
| 11-119420253-C-G | not specified | Uncertain significance (May 06, 2024) | ||
| 11-119420308-C-T | not specified | Uncertain significance (May 28, 2024) | ||
| 11-119420318-G-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 11-119420371-C-T | not specified | Uncertain significance (Feb 10, 2022) | ||
| 11-119420881-G-A | not specified | Uncertain significance (Jan 08, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| THY1 | protein_coding | protein_coding | ENST00000284240 | 3 | 7606 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0499 | 0.867 | 125736 | 0 | 12 | 125748 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.908 | 70 | 94.9 | 0.738 | 0.00000562 | 1033 |
| Missense in Polyphen | 21 | 36.879 | 0.56943 | 371 | ||
| Synonymous | 0.953 | 37 | 45.1 | 0.820 | 0.00000289 | 349 |
| Loss of Function | 1.44 | 3 | 7.14 | 0.420 | 4.76e-7 | 68 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000116 | 0.000116 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000925 | 0.0000924 |
| European (Non-Finnish) | 0.00000888 | 0.00000879 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000329 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role in cell-cell or cell-ligand interactions during synaptogenesis and other events in the brain.;
- Pathway
- Leukocyte transendothelial migration - Homo sapiens (human);Cardiac Progenitor Differentiation;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;Beta3 integrin cell surface interactions;amb2 Integrin signaling;IL4-mediated signaling events;Beta2 integrin cell surface interactions
(Consensus)
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- loftool
- 0.518
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.762
- hipred
- N
- hipred_score
- 0.416
- ghis
- 0.649
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Thy1
- Phenotype
- normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); respiratory system phenotype;
Gene ontology
- Biological process
- angiogenesis;regulation of cell-matrix adhesion;positive regulation of cellular extravasation;negative regulation of protein kinase activity;cytoskeleton organization;integrin-mediated signaling pathway;cell-cell signaling;negative regulation of cell migration;positive regulation of heterotypic cell-cell adhesion;receptor clustering;positive regulation of GTPase activity;retinal cone cell development;protein autophosphorylation;focal adhesion assembly;negative regulation of axonogenesis;T cell receptor signaling pathway;negative regulation of T cell receptor signaling pathway;positive regulation of T cell activation;positive regulation of release of sequestered calcium ion into cytosol;positive regulation of focal adhesion assembly;negative regulation of protein tyrosine kinase activity;negative regulation of neuron projection regeneration;cell-cell adhesion;regulation of Rho-dependent protein serine/threonine kinase activity
- Cellular component
- extracellular region;endoplasmic reticulum;cytosol;plasma membrane;integral component of plasma membrane;focal adhesion;external side of plasma membrane;cell surface;apical plasma membrane;dendrite;growth cone;axolemma;anchored component of external side of plasma membrane;dendrite membrane;neuronal cell body membrane;myelin sheath;membrane raft;extracellular exosome
- Molecular function
- GTPase activator activity;integrin binding;protein binding;protein kinase binding;GPI anchor binding