NFAT5

protein-coding

nuclear 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

NM_138713.4

Inheritance

AD

ClinVar variants

U:533B:269

Top phenotype

Immunodeficiency

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr16:69,565,094-69,704,666

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~139.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

inborn error of immunityMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0003778

Submitter: PanelApp Australia

immunodeficiency diseaseLIMITED

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

7 Conditions Cataloged
ImmunodeficiencyTotal: 808
not specifiedTotal: 186
NFAT5-related disorderTotal: 36
not providedTotal: 27
Primary ciliary dyskinesiaTotal: 1
Inflammatory bowel disease-recurrent sinopulmonary infections syndromeTotal: 1
Immunodeficiency and Autoimmune EnterocolopathyTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
249
clinvar
8
clinvar
260
missense
523
clinvar
9
clinvar
2
clinvar
534
nonsense
2
clinvar
2
start loss
0
frameshift
2
clinvar
2
splice donor/acceptor (+/-2bp)
3
clinvar
1
clinvar
4
Total0053325910802
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_138713.4RefSeqNP_619727.214MANE Select
ENST00000349945.7EnsemblENSP00000338806.314MANE Select
NM_001113178.3RefSeqNP_001106649.114Standard
NM_001367709.1RefSeqNP_001354638.111Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
nfat5aDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.135377840.6850.000037910215
Missense (PolyPhen)171324.280.527324316
Synonymous1.132632870.9150.00001492991
Loss of Function7.15976.40.1180.00000417804

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian0.000890.00087rare
Finnish0.0000960.000092rare
European (Non-Finnish)0.0000850.000079rare
South Asian0.0000370.000033rare
Other0.000190.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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