NFATC2IP

nuclear factor of activated T cells 2 interacting protein, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 16:28950807-28967092

Links

ENSG00000176953 ∙ NCBI:84901 ∙ OMIM:614525 ∙ HGNC:25906 ∙ Uniprot:Q8NCF5 ∙ 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 NFATC2IP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFATC2IP 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						0
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in NFATC2IP

This is a list of pathogenic ClinVar variants found in the NFATC2IP region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28951022-C-T		not specified	Uncertain significance (Nov 17, 2022)
16-28951072-G-A		not specified	Uncertain significance (Jan 21, 2025)
16-28951091-G-C		not specified	Uncertain significance (Sep 22, 2022)
16-28951117-C-G		not specified	Uncertain significance (Dec 09, 2024)
16-28951127-C-T		not specified	Uncertain significance (Oct 03, 2022)
16-28951136-C-T		not specified	Uncertain significance (Jun 07, 2024)
16-28951151-C-G		not specified	Uncertain significance (Sep 30, 2024)
16-28951153-G-A		not specified	Uncertain significance (Oct 20, 2023)
16-28951184-T-G		not specified	Uncertain significance (Aug 15, 2023)
16-28951218-C-A		not specified	Uncertain significance (Aug 26, 2024)
16-28951235-C-G		not specified	Uncertain significance (Dec 26, 2023)
16-28951238-C-G		not specified	Uncertain significance (Jun 28, 2024)
16-28951253-C-T		not specified	Uncertain significance (Aug 12, 2021)
16-28951268-A-C		not specified	Uncertain significance (Feb 27, 2025)
16-28951282-G-A		not specified	Uncertain significance (Jan 26, 2025)
16-28951340-G-T		not specified	Uncertain significance (Aug 17, 2022)
16-28951367-A-T		not specified	Uncertain significance (Aug 11, 2024)
16-28951394-G-A		not specified	Likely benign (Jul 20, 2021)
16-28952199-A-C		not specified	Uncertain significance (May 17, 2023)
16-28954583-C-T		not specified	Uncertain significance (Dec 14, 2023)
16-28954607-C-T		not specified	Uncertain significance (Jul 27, 2024)
16-28956031-C-T		not specified	Uncertain significance (Jul 20, 2021)
16-28956039-C-T		not specified	Uncertain significance (Jun 01, 2023)
16-28956165-G-A		not specified	Uncertain significance (Mar 08, 2025)
16-28956254-G-A		not specified	Uncertain significance (Jan 25, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFATC2IP	protein_coding	protein_coding	ENST00000320805	8	16291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000174	0.888	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.640	190	217	0.878	0.0000115	2633
Missense in Polyphen		52	70.586	0.73669		834
Synonymous	1.42	72	89.0	0.809	0.00000430	932
Loss of Function	1.51	10	16.7	0.600	8.61e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.000218	0.000217
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In T-helper 2 (Th2) cells, regulates the magnitude of NFAT-driven transcription of a specific subset of cytokine genes, including IL3, IL4, IL5 and IL13, but not IL2. Recruits PRMT1 to the IL4 promoter; this leads to enhancement of histone H4 'Arg-3'- methylation and facilitates subsequent histone acetylation at the IL4 locus, thus promotes robust cytokine expression (By similarity). Down-regulates formation of poly-SUMO chains by UBE2I/UBC9 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0985

Haploinsufficiency Scores

• pHI: 0.0960
• hipred: N
• hipred_score: 0.274
• ghis: 0.583

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.773

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfatc2ip
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cytokine production;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;cytoplasm