NGFR

nerve growth factor receptor, the group of CD molecules|Tumor necrosis factor receptor superfamily|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:49495292-49515008

Links

ENSG00000064300 ∙ NCBI:4804 ∙ OMIM:162010 ∙ HGNC:7809 ∙ Uniprot:P08138 ∙ 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 NGFR gene.

• Inborn genetic diseases (23 variants)
• not provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NGFR 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				4	3	7
missense			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	1	2
Total	0	0	23	5	5

Variants in NGFR

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

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

Position	Type	Phenotype	Significance	ClinVar
17-49502059-C-T			Benign (Jul 31, 2018)
17-49502075-G-T		not specified	Uncertain significance (Jan 10, 2023)
17-49502175-A-G		not specified	Uncertain significance (Dec 28, 2022)
17-49506408-G-A			Likely benign (Mar 30, 2018)
17-49506418-G-T		not specified	Uncertain significance (Nov 10, 2022)
17-49506423-C-T			Benign (Mar 29, 2018)
17-49506438-T-A		not specified	Uncertain significance (Apr 01, 2022)
17-49506475-G-A		not specified	Uncertain significance (Aug 16, 2021)
17-49506485-C-T			Benign (Jul 10, 2018)
17-49506500-C-G		not specified	Uncertain significance (Oct 12, 2021)
17-49506604-G-C		not specified	Uncertain significance (Jun 24, 2022)
17-49506623-G-T		not specified	Uncertain significance (Dec 15, 2022)
17-49506634-C-T		not specified	Uncertain significance (Oct 26, 2022)
17-49506643-G-A		not specified	Uncertain significance (Feb 22, 2023)
17-49506655-G-C		not specified	Uncertain significance (Oct 26, 2022)
17-49506667-G-A			Likely benign (Apr 24, 2018)
17-49510435-C-T		not specified	Uncertain significance (May 23, 2023)
17-49510444-C-G		not specified	Uncertain significance (Jul 12, 2022)
17-49510471-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-49510473-C-T			Likely benign (Apr 10, 2018)
17-49510478-C-A		not specified	Uncertain significance (Jul 20, 2022)
17-49510577-G-A		not specified	Uncertain significance (Nov 08, 2022)
17-49510595-T-C		not specified	Uncertain significance (May 24, 2023)
17-49511882-C-G			Benign (Dec 28, 2017)
17-49511932-C-T		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NGFR	protein_coding	protein_coding	ENST00000172229	6	19725

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0979	0.901	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	217	282	0.771	0.0000195	2723
Missense in Polyphen		59	94.796	0.62239		935
Synonymous	1.01	117	132	0.888	0.0000109	883
Loss of Function	2.79	5	17.7	0.283	8.43e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000565	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.0000565	0.0000544
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of the translocation of GLUT4 to the cell surface in adipocytes and skeletal muscle cells in response to insulin, probably by regulating RAB31 activity, and thereby contributes to the regulation of insulin-dependent glucose uptake (By similarity). Low affinity receptor which can bind to NGF, BDNF, NT-3, and NT-4. Can mediate cell survival as well as cell death of neural cells. Necessary for the circadian oscillation of the clock genes ARNTL/BMAL1, PER1, PER2 and NR1D1 in the suprachiasmatic nucleus (SCN) of the brain and in liver and of the genes involved in glucose and lipid metabolism in the liver. {ECO:0000250, ECO:0000269|PubMed:14966521, ECO:0000269|PubMed:23785138}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Neurotrophin signaling pathway - Homo sapiens (human);Apoptosis - multiple species - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Spinal Cord Injury;nerve growth factor pathway (ngf);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Ras Signaling;Signal Transduction;p75NTR signals via NF-kB;phosphorylation of mek1 by cdk5/p35 down regulates the map kinase pathway;erk1/erk2 mapk signaling pathway;IL-7 signaling;BDNF;NRIF signals cell death from the nucleus;NFG and proNGF binds to p75NTR;NRAGE signals death through JNK;JAK STAT pathway and regulation;NADE modulates death signalling;p75NTR recruits signalling complexes;EPO signaling;NF-kB is activated and signals survival;Death Receptor Signalling;Ceramide signalling;Axonal growth stimulation;Axonal growth inhibition (RHOA activation);p75NTR regulates axonogenesis;Regulated proteolysis of p75NTR;p75 NTR receptor-mediated signalling;VEGF;Neurotrophic factor-mediated Trk receptor signaling;p75(NTR)-mediated signaling;Cell death signalling via NRAGE, NRIF and NADE;p75NTR negatively regulates cell cycle via SC1 (Consensus)

Recessive Scores

• pRec: 0.744

Intolerance Scores

• loftool: 0.120
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.458
• hipred: Y
• hipred_score: 0.857
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.610

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ngfr
• Phenotype: vision/eye phenotype; limbs/digits/tail phenotype; hearing/vestibular/ear 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; skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); 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); growth/size/body region 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; craniofacial phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); taste/olfaction phenotype

Zebrafish Information Network

• Gene name: ngfrb
• Affected structure: anterior lateral line neuromast
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: cellular glucose homeostasis;intracellular protein transport;activation of cysteine-type endopeptidase activity involved in apoptotic process;Rho protein signal transduction;membrane protein intracellular domain proteolysis;circadian regulation of gene expression;glucose homeostasis;positive regulation of apoptotic process;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;regulation of cysteine-type endopeptidase activity involved in apoptotic process;neurotrophin TRK receptor signaling pathway;negative regulation of axonogenesis;positive regulation of axonogenesis;neuron apoptotic process;positive regulation of protein localization to nucleus;positive regulation of pri-miRNA transcription by RNA polymerase II;negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis;cellular response to amyloid-beta
• Cellular component: extracellular region;nucleoplasm;endosome;cytosol;plasma membrane;integral component of plasma membrane;cell surface;integral component of membrane
• Molecular function: amyloid-beta binding;transmembrane signaling receptor activity;death receptor activity;protein binding;calmodulin binding;coreceptor activity;Rab GTPase binding;ubiquitin protein ligase binding;signaling receptor activity;neurotrophin binding;nerve growth factor binding