FKBP1A
FKBP prolyl isomerase 1A, the group of FKBP prolyl isomerases|MicroRNA protein coding host genes
Basic information
Region (hg38): 20:1368977-1393164
Previous symbols: [ "FKBP1" ]
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 FKBP1A 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 2 | 2 | 1 |
Variants in FKBP1A
This is a list of pathogenic ClinVar variants found in the FKBP1A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-1370028-T-C | Benign (Aug 22, 2019) | |||
| 20-1372136-A-G | not specified | Likely benign (Oct 05, 2023) | ||
| 20-1372136-A-T | not specified | Uncertain significance (May 13, 2024) | ||
| 20-1372139-G-A | not specified | Likely benign (Aug 26, 2024) | ||
| 20-1372151-G-A | not specified | Likely benign (Jun 01, 2023) | ||
| 20-1372153-C-T | not specified | Uncertain significance (Oct 06, 2024) | ||
| 20-1372159-G-C | not specified | Uncertain significance (Feb 23, 2023) | ||
| 20-1392971-G-A | not specified | Uncertain significance (Dec 17, 2021) | ||
| 20-1392986-C-T | Uncertain significance (-) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FKBP1A | protein_coding | protein_coding | ENST00000400137 | 4 | 24185 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.815 | 0.181 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.66 | 20 | 54.6 | 0.366 | 0.00000266 | 695 |
| Missense in Polyphen | 2 | 14.142 | 0.14143 | 176 | ||
| Synonymous | 0.895 | 15 | 20.1 | 0.746 | 0.00000101 | 214 |
| Loss of Function | 2.19 | 0 | 5.57 | 0.00 | 3.22e-7 | 70 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Keeps in an inactive conformation TGFBR1, the TGF-beta type I serine/threonine kinase receptor, preventing TGF-beta receptor activation in absence of ligand. Recruits SMAD7 to ACVR1B which prevents the association of SMAD2 and SMAD3 with the activin receptor complex, thereby blocking the activin signal. May modulate the RYR1 calcium channel activity. PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. {ECO:0000269|PubMed:16720724, ECO:0000269|PubMed:1696686, ECO:0000269|PubMed:1701173, ECO:0000269|PubMed:9233797}.;
- Pathway
- Tacrolimus/Cyclosporine Pathway, Pharmacodynamics;Target Of Rapamycin (TOR) Signaling;Spinal Cord Injury;Calcium Regulation in the Cardiac Cell;TGF-beta Receptor Signaling;Disease;Signal Transduction;mtor signaling pathway;insulin Mam;TGF_beta_Receptor;TGFBR2 Kinase Domain Mutants in Cancer;Loss of Function of TGFBR2 in Cancer;TGFBR1 KD Mutants in Cancer;Loss of Function of TGFBR1 in Cancer;Signaling by TGF-beta Receptor Complex in Cancer;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;TGF-beta receptor signaling activates SMADs;ALK1 signaling events;Diseases of signal transduction;Alpha-synuclein signaling;Role of Calcineurin-dependent NFAT signaling in lymphocytes;ALK2 signaling events;TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition);TGF-beta receptor signaling;Calcium signaling in the CD4+ TCR pathway;insulin
(Consensus)
Recessive Scores
- pRec
- 0.338
Intolerance Scores
- loftool
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 60.96
Haploinsufficiency Scores
- pHI
- 0.420
- hipred
- N
- hipred_score
- 0.345
- ghis
- 0.647
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.977
Mouse Genome Informatics
- Gene name
- Fkbp1a
- Phenotype
- muscle phenotype; cellular phenotype; homeostasis/metabolism 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); normal 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); 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); growth/size/body region 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); liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype;
Gene ontology
- Biological process
- protein peptidyl-prolyl isomerization;heart morphogenesis;protein folding;'de novo' protein folding;SMAD protein complex assembly;protein maturation by protein folding;positive regulation of protein ubiquitination;positive regulation of protein binding;negative regulation of phosphoprotein phosphatase activity;regulation of protein localization;regulation of activin receptor signaling pathway;protein refolding;T cell activation;positive regulation of I-kappaB kinase/NF-kappaB signaling;regulation of immune response;negative regulation of release of sequestered calcium ion into cytosol;ventricular cardiac muscle tissue morphogenesis;regulation of ryanodine-sensitive calcium-release channel activity;negative regulation of ryanodine-sensitive calcium-release channel activity;heart trabecula formation;chaperone-mediated protein folding;calcium ion transmembrane transport;supramolecular fiber organization;regulation of amyloid precursor protein catabolic process;amyloid fibril formation
- Cellular component
- cytoplasm;cytosol;terminal cisterna;membrane;sarcoplasmic reticulum;Z disc;extrinsic component of organelle membrane;cytoplasmic side of membrane;ryanodine receptor complex
- Molecular function
- peptidyl-prolyl cis-trans isomerase activity;transforming growth factor beta receptor binding;protein binding;macrolide binding;FK506 binding;calcium channel inhibitor activity;type I transforming growth factor beta receptor binding;ion channel binding;SMAD binding;activin binding