NFAT5
nuclear factor of activated T cells 5, the group of Nuclear factors of activated T-cells |IPT domain containing
Basic information
Region (hg38): 16:69565094-69704666
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Immunodeficiency (716 variants)
- not_specified (126 variants)
- NFAT5-related_disorder (29 variants)
- not_provided (24 variants)
- Immunodeficiency_and_Autoimmune_Enterocolopathy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFAT5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138713.4. 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 | 221 | 11 | 235 | |||
| missense | 448 | 458 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 3 | |||||
| Total | 0 | 0 | 456 | 228 | 14 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NFAT5 | protein_coding | protein_coding | ENST00000432919 | 14 | 139573 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000192 | 125718 | 0 | 30 | 125748 | 0.000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.13 | 537 | 784 | 0.685 | 0.0000379 | 10215 |
| Missense in Polyphen | 171 | 324.28 | 0.52732 | 4316 | ||
| Synonymous | 1.13 | 263 | 287 | 0.915 | 0.0000149 | 2991 |
| Loss of Function | 7.15 | 9 | 76.4 | 0.118 | 0.00000417 | 804 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000294 | 0.0000294 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000894 | 0.000870 |
| Finnish | 0.0000959 | 0.0000924 |
| European (Non-Finnish) | 0.0000849 | 0.0000791 |
| Middle Eastern | 0.000894 | 0.000870 |
| South Asian | 0.0000368 | 0.0000327 |
| Other | 0.000190 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor involved, among others, in the transcriptional regulation of osmoprotective and inflammatory genes. Mediates the transcriptional response to hypertonicity (PubMed:10051678). Positively regulates the transcription of LCN2 and S100A4 genes; optimal transactivation of these genes requires the presence of DDX5/DDX17 (PubMed:22266867). Binds the DNA consensus sequence 5'- [ACT][AG]TGGAAA[CAT]A[TA][ATC][CA][ATG][GT][GAC][CG][CT]-3' (PubMed:10377394). {ECO:0000269|PubMed:10051678, ECO:0000269|PubMed:10377394, ECO:0000269|PubMed:22266867}.;
Recessive Scores
- pRec
- 0.302
Intolerance Scores
- loftool
- 0.439
- rvis_EVS
- -1.37
- rvis_percentile_EVS
- 4.45
Haploinsufficiency Scores
- pHI
- 0.855
- hipred
- Y
- hipred_score
- 0.532
- ghis
- 0.638
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.514
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nfat5
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle 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); hematopoietic system phenotype; 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); immune system phenotype; renal/urinary system phenotype;
Zebrafish Information Network
- Gene name
- nfat5a
- Affected structure
- pericardium
- Phenotype tag
- abnormal
- Phenotype quality
- edematous
Gene ontology
- Biological process
- cytokine production;transcription by RNA polymerase II;signal transduction;excretion;calcineurin-NFAT signaling cascade;positive regulation of transcription by RNA polymerase II;regulation of calcineurin-NFAT signaling cascade;cellular response to cytokine stimulus;positive regulation of NIK/NF-kappaB signaling;positive regulation of leukocyte adhesion to vascular endothelial cell
- Cellular component
- nucleus;nucleoplasm;transcription factor complex;cytosol;nuclear transcription factor complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;protein binding;transcription factor binding