NFAM1

NFAT activating protein with ITAM motif 1

Basic information

Region (hg38): 22:42380407-42432403

Links

ENSG00000235568 ∙ NCBI:150372 ∙ OMIM:608740 ∙ HGNC:29872 ∙ Uniprot:Q8NET5 ∙ 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 NFAM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFAM1 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	2
missense			15	5	3	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	5	5

Variants in NFAM1

This is a list of pathogenic ClinVar variants found in the NFAM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-42385181-G-A			Benign (Jul 19, 2018)
22-42385192-C-G			Benign (Oct 24, 2018)
22-42385213-G-A		not specified	Likely benign (Jun 23, 2021)
22-42387039-C-T		not specified	Uncertain significance (Aug 30, 2022)
22-42387057-C-T		not specified	Uncertain significance (Apr 12, 2024)
22-42387065-C-T		not specified	Uncertain significance (Feb 21, 2024)
22-42397899-C-A		not specified	Uncertain significance (Nov 27, 2023)
22-42397946-C-T		not specified	Likely benign (Feb 06, 2023)
22-42397947-G-A		not specified	Uncertain significance (May 30, 2024)
22-42397952-C-T		not specified	Likely benign (May 23, 2023)
22-42409438-G-C			Benign (Dec 31, 2019)
22-42409457-G-A		not specified	Uncertain significance (Jun 07, 2024)
22-42409525-C-T			Benign (Dec 31, 2019)
22-42409526-G-A		not specified	Uncertain significance (Aug 30, 2021)
22-42411442-G-A		not specified	Uncertain significance (Sep 29, 2023)
22-42411449-G-A			Benign (Dec 31, 2019)
22-42411457-T-C		not specified	Likely benign (Jan 24, 2024)
22-42411560-G-T		not specified	Uncertain significance (Jan 24, 2024)
22-42411583-C-T		not specified	Uncertain significance (Apr 05, 2023)
22-42411592-C-T		not specified	Uncertain significance (Jun 24, 2022)
22-42411607-T-A		not specified	Uncertain significance (Jul 13, 2022)
22-42411677-T-C		not specified	Likely benign (Apr 25, 2022)
22-42432255-C-T		not specified	Uncertain significance (Aug 30, 2021)
22-42432270-C-T		not specified	Uncertain significance (Jan 31, 2024)
22-42432308-G-A		not specified	Uncertain significance (Aug 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFAM1	protein_coding	protein_coding	ENST00000329021	6	51986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000629	0.731	125395	0	7	125402	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.266	140	149	0.939	0.00000859	1696
Missense in Polyphen		33	41.647	0.79236		539
Synonymous	-0.209	67	64.9	1.03	0.00000392	566
Loss of Function	1.02	8	11.8	0.678	6.13e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00000972	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in immune system as a receptor which activates via the calcineurin/NFAT-signaling pathway the downstream cytokine gene promoters. Activates the transcription of IL-13 and TNF-alpha promoters. May be involved in the regulation of B-cell, but not T-cell, development. Overexpression activates downstream effectors without ligand binding or antibody cross- linking. {ECO:0000269|PubMed:12615919, ECO:0000269|PubMed:15143214}.
• Pathway: Neutrophil degranulation;TCR;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0811

Intolerance Scores

• loftool: 0.436
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.0631
• hipred: N
• hipred_score: 0.257
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0901

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfam1

Gene ontology

• Biological process: positive regulation of cytokine production;inflammatory response;signal transduction;cell surface receptor signaling pathway;B cell differentiation;intracellular signal transduction;neutrophil degranulation;regulation of B cell differentiation;positive regulation of B cell receptor signaling pathway;positive regulation of DNA-binding transcription factor activity
• Cellular component: plasma membrane;integral component of membrane;azurophil granule membrane
• Molecular function: transmembrane signaling receptor activity