FKBP4
FKBP prolyl isomerase 4, the group of FKBP prolyl isomerases|Tetratricopeptide repeat domain containing
Basic information
Region (hg38): 12:2794970-2805423
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (38 variants)
- not_provided (6 variants)
- FKBP4-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FKBP4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002014.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 38 | 43 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 38 | 3 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FKBP4 | protein_coding | protein_coding | ENST00000001008 | 10 | 10458 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.155 | 0.844 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.21 | 197 | 251 | 0.785 | 0.0000140 | 3001 |
| Missense in Polyphen | 67 | 98.929 | 0.67725 | 1147 | ||
| Synonymous | -1.06 | 109 | 95.8 | 1.14 | 0.00000522 | 853 |
| Loss of Function | 3.34 | 6 | 23.5 | 0.256 | 0.00000124 | 280 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000881 | 0.0000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Immunophilin protein with PPIase and co-chaperone activities. Component of steroid receptors heterocomplexes through interaction with heat-shock protein 90 (HSP90). May play a role in the intracellular trafficking of heterooligomeric forms of steroid hormone receptors between cytoplasm and nuclear compartments. The isomerase activity controls neuronal growth cones via regulation of TRPC1 channel opening. Acts also as a regulator of microtubule dynamics by inhibiting MAPT/TAU ability to promote microtubule assembly. May have a protective role against oxidative stress in mitochondria. {ECO:0000269|PubMed:1279700, ECO:0000269|PubMed:1376003, ECO:0000269|PubMed:19945390, ECO:0000269|PubMed:21730050, ECO:0000269|PubMed:2378870}.;
- Pathway
- Estrogen signaling pathway - Homo sapiens (human);Glucocorticoid Pathway (Peripheral Tissue), Pharmacodynamics;Androgen receptor signaling pathway;Cellular response to heat stress;Signal Transduction;HSF1 activation;Attenuation phase;HSF1-dependent transactivation;Regulation of HSF1-mediated heat shock response;HSP90 chaperone cycle for steroid hormone receptors (SHR);Cellular responses to stress;Cellular responses to external stimuli;Glucocorticoid receptor regulatory network;Coregulation of Androgen receptor activity;Cellular response to heat stress;Signaling by Nuclear Receptors;ESR-mediated signaling
(Consensus)
Recessive Scores
- pRec
- 0.187
Intolerance Scores
- loftool
- 0.191
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 57.15
Haploinsufficiency Scores
- pHI
- 0.218
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.408
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.858
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fkbp4
- Phenotype
- embryo 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); digestive/alimentary phenotype; renal/urinary system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region 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);
Zebrafish Information Network
- Gene name
- fkbp4
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased length
Gene ontology
- Biological process
- protein peptidyl-prolyl isomerization;protein folding;steroid hormone receptor complex assembly;copper ion transport;embryo implantation;negative regulation of neuron projection development;androgen receptor signaling pathway;prostate gland development;negative regulation of microtubule polymerization or depolymerization;negative regulation of microtubule polymerization;protein-containing complex localization;male sex differentiation;chaperone-mediated protein folding;regulation of cellular response to heat
- Cellular component
- nucleoplasm;cytoplasm;mitochondrion;cytosol;microtubule;protein-containing complex;neuronal cell body;axonal growth cone;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- RNA binding;peptidyl-prolyl cis-trans isomerase activity;protein binding;ATP binding;GTP binding;FK506 binding;protein binding, bridging;heat shock protein binding;copper-dependent protein binding;glucocorticoid receptor binding;tau protein binding;phosphoprotein binding