NFAT5
protein-codingnuclear factor of activated T cells 5, the group of Nuclear factors of activated T-cells |IPT domain containing
Gene summary
The product of this gene is a member of the nuclear factors of activated T cells family of transcription factors. Proteins belonging to this family play a central role in inducible gene transcription during the immune response. This protein regulates gene expression induced by osmotic stress in mammalian cells. Unlike monomeric members of this protein family, this protein exists as a homodimer and forms stable dimers with DNA elements. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~139.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0003778
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0021094
Submitter: ClinGen
*NFAT5* was first reported in relation to autosomal dominant immunodeficiency disease in 2022 (PMID: 36238298). This condition is characterized by impaired adaptive and innate immune responses, including lymphopenia, abnormal B‑ and T‑cell function, poor antigen‑specific responses, and susceptibility to infections, particularly from Epstein-Barr virus. Two missense variants that have been reported in 2 probands in 1 publication (PMID: 36238298) are included in this curation. The mechanism of pathogenicity is presumed to involve haploinsufficiency of *NFAT5,* consistent with impaired osmoprotective gene induction and reduced lymphocyte survival under stress conditions (PMID: 10051678). This gene–disease relationship is also supported by experimental evidence, including biochemical function studies showing that *NFAT5* is required for tonicity‑responsive gene expression in lymphocytes (PMID: 10051678) and multiple mouse models demonstrating reduced thymic cellularity, peripheral lymphopenia, impaired lymphocyte proliferation, and diminished antigen‑specific immune responses in NFAT5‑deficient mice (PMIDs: 12421923, 15247420). These model systems together support a biological role for *NFAT5* in immune homeostasis, although they cannot model human‑specific phenotypes such as EBV susceptibility. In summary, there is limited evidence to support this gene‑disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene‑disease relationship. This classification was approved by the ClinGen Primary Immune Regulatory Disorders Gene Curation Expert Panel on the meeting date March 19, 2024 (SOP Version 9).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NFAT5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_138713.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 249 | 8 | 260 | ||
| missense | 523 | 9 | 2 | 534 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 1 | 4 | |||
| Total | 0 | 0 | 533 | 259 | 10 | 802 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_619727.2 | 14 | MANE Select | |
| Ensembl | ENSP00000338806.3 | 14 | MANE Select | |
| RefSeq | NP_001106649.1 | 14 | Standard | |
| RefSeq | NP_001354638.1 | 11 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| nfat5a | Danio rerio | Structure: pericardium Quality: edematous abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cytokine production
- transcription by RNA polymerase II
- signal transduction
- excretion
- calcineurin-NFAT signaling cascade
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
Cellular Component
- nucleus
- nucleoplasm
- transcription factor complex
- cytosol
- nuclear transcription factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000432919
- Coding exons
- 14
- Length
- 139573
- Individuals with no LoFs
- 125718
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 30
- Defined
- 125748
- p
- 0.000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.13 | 537 | 784 | 0.685 | 0.0000379 | 10215 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00089 | 0.00087 | rare |
| Finnish | 0.000096 | 0.000092 | rare |
| European (Non-Finnish) | 0.000085 | 0.000079 | rare |
| South Asian | 0.000037 | 0.000033 | rare |
| Other | 0.00019 | 0.00016 | rare |
dbNSFP Gene Annotations
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
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.514
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |