NFATC3

nuclear factor of activated T cells 3, the group of Nuclear factors of activated T-cells |IPT domain containing

Basic information

Region (hg38): 16:68084751-68229259

Links

ENSG00000072736 ∙ NCBI:4775 ∙ OMIM:602698 ∙ HGNC:7777 ∙ Uniprot:Q12968 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NFATC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFATC3 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				2	1	3
missense			56	5	1	62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	56	7	2

Variants in NFATC3

This is a list of pathogenic ClinVar variants found in the NFATC3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-68085739-G-A		not specified	Uncertain significance (Nov 17, 2023)
16-68085770-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-68122059-C-T		not specified	Uncertain significance (Apr 27, 2024)
16-68122065-G-A		not specified	Uncertain significance (Aug 08, 2022)
16-68122076-C-T		not specified	Uncertain significance (Mar 11, 2024)
16-68122086-C-T		not specified	Uncertain significance (Dec 20, 2023)
16-68122130-C-T		not specified	Uncertain significance (Sep 26, 2022)
16-68122190-C-T		not specified	Uncertain significance (Aug 14, 2024)
16-68122295-C-T			Benign (Jan 30, 2018)
16-68122307-G-C		not specified	Uncertain significance (Sep 25, 2023)
16-68122313-C-T		not specified	Uncertain significance (May 29, 2024)
16-68122320-G-C		not specified	Uncertain significance (Sep 14, 2022)
16-68122355-C-T		not specified	Uncertain significance (Jul 26, 2022)
16-68122449-A-G		not specified	Uncertain significance (Feb 28, 2024)
16-68122469-T-A		not specified	Uncertain significance (Oct 20, 2024)
16-68122469-T-G		not specified	Uncertain significance (Jul 25, 2024)
16-68122488-G-A		not specified	Uncertain significance (Dec 10, 2024)
16-68122494-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-68122559-C-T		not specified	Uncertain significance (Jul 27, 2022)
16-68122572-G-T		not specified	Uncertain significance (Mar 16, 2024)
16-68122620-G-A		not specified	Uncertain significance (Jan 29, 2024)
16-68122664-T-C		not specified	Uncertain significance (Jul 15, 2021)
16-68122699-G-A			Benign/Likely benign (Nov 01, 2022)
16-68122760-C-A		not specified	Uncertain significance (Mar 02, 2023)
16-68122772-C-T		not specified	Uncertain significance (Jul 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFATC3	protein_coding	protein_coding	ENST00000346183	10	144509

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00187	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.494	524	557	0.941	0.0000276	6886
Missense in Polyphen		170	212.42	0.8003		2608
Synonymous	0.424	196	204	0.962	0.0000102	2269
Loss of Function	5.37	6	44.8	0.134	0.00000266	524

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000110	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a regulator of transcriptional activation. Plays a role in the inducible expression of cytokine genes in T-cells, especially in the induction of the IL-2. {ECO:0000269|PubMed:18815128}.
• Pathway: Oxytocin signaling pathway - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);B cell receptor signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Axon guidance - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Heart Development;B Cell Receptor Signaling Pathway;Initiation of transcription and translation elongation at the HIV-1 LTR;MAPK Signaling Pathway;Wnt Signaling Pathway;Calcineurin activates NFAT;Signaling by the B Cell Receptor (BCR);CLEC7A (Dectin-1) induces NFAT activation;CLEC7A (Dectin-1) signaling;C-type lectin receptors (CLRs);FCERI mediated Ca+2 mobilization;Fc epsilon receptor (FCERI) signaling;Innate Immune System;Immune System;Adaptive Immune System;Downstream signaling events of B Cell Receptor (BCR);BCR;Downstream signaling in naïve CD8+ T cells;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;AP-1 transcription factor network;FOXM1 transcription factor network;Role of Calcineurin-dependent NFAT signaling in lymphocytes;Validated transcriptional targets of AP1 family members Fra1 and Fra2;Calcium signaling in the CD4+ TCR pathway (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.512
• rvis_EVS: 0.16
• rvis_percentile_EVS: 64.96

Haploinsufficiency Scores

• pHI: 0.709
• hipred: Y
• hipred_score: 0.825
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nfatc3
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism 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); digestive/alimentary phenotype; muscle phenotype; 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); reproductive 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); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; immune system phenotype; vision/eye phenotype

Gene ontology

• Biological process: cytokine production;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;inflammatory response;calcineurin-NFAT signaling cascade;Fc-epsilon receptor signaling pathway;positive regulation of transcription by RNA polymerase II;negative regulation of pri-miRNA transcription by RNA polymerase II;negative regulation of vascular smooth muscle cell differentiation
• Cellular component: nucleus;nucleoplasm;transcription factor complex;cytoplasm;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 repressor 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