NTF3

neurotrophin 3, the group of Neurotrophins

Basic information

Region (hg38): 12:5432107-5521536

Links

ENSG00000185652 ∙ NCBI:4908 ∙ OMIM:162660 ∙ HGNC:8023 ∙ Uniprot:P20783 ∙ 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 NTF3 gene.

• Inborn genetic diseases (9 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTF3 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				1	4	5
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	4

Variants in NTF3

This is a list of pathogenic ClinVar variants found in the NTF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-5494276-T-C		not specified	Uncertain significance (Jan 12, 2024)
12-5494407-A-G		not specified	Uncertain significance (Oct 26, 2022)
12-5494423-G-A		not specified	Uncertain significance (May 31, 2022)
12-5494432-A-T		not specified	Uncertain significance (Feb 12, 2024)
12-5494440-G-A		Hirschsprung disease, susceptibility to, 1	Uncertain significance (Apr 01, 2015)
12-5494441-G-A		Aganglionic megacolon	Likely benign (-)
12-5494476-A-G		not specified	Uncertain significance (Dec 02, 2021)
12-5494484-C-T			Benign (Sep 14, 2018)
12-5494540-G-A		not specified	Uncertain significance (Aug 14, 2023)
12-5494564-T-C		not specified	Uncertain significance (Jun 06, 2023)
12-5494572-A-C		not specified	Uncertain significance (Aug 11, 2021)
12-5494620-C-G		not specified	Uncertain significance (Jan 10, 2023)
12-5494621-G-A		not specified	Uncertain significance (Jul 20, 2021)
12-5494651-G-T		not specified	Uncertain significance (Sep 29, 2023)
12-5494760-C-T			Benign (May 24, 2018)
12-5494803-G-A		not specified	Uncertain significance (Aug 22, 2023)
12-5494823-C-T			Benign (Aug 20, 2018)
12-5494832-G-A			Likely benign (Jul 01, 2022)
12-5494901-A-G			Benign (Jul 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTF3	protein_coding	protein_coding	ENST00000423158	2	89425

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.932	0.0679	125744	0	3	125747	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	108	172	0.628	0.0000123	1736
Missense in Polyphen		40	86.146	0.46433		829
Synonymous	0.423	69	73.6	0.937	0.00000554	540
Loss of Function	3.08	1	13.0	0.0771	9.99e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to promote the survival of visceral and proprioceptive sensory neurons.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Neurotrophin signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;MAPK Signaling Pathway;PI3K-Akt Signaling Pathway;Signal Transduction;role of erk5 in neuronal survival pathway;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;NTF3 activates NTRK2 (TRKB) signaling;Signaling by NTRK2 (TRKB);Signaling by NTRKs;BDNF;SHP2 signaling;GPCR signaling-G alpha i;Signaling by Receptor Tyrosine Kinases;Neurotrophic factor-mediated Trk receptor signaling;p75(NTR)-mediated signaling;Trk receptor signaling mediated by the MAPK pathway (Consensus)

Recessive Scores

• pRec: 0.530

Intolerance Scores

• loftool: 0.448
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.352
• hipred: Y
• hipred_score: 0.786
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.619

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntf3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); vision/eye 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); homeostasis/metabolism phenotype; growth/size/body region phenotype; muscle phenotype

Gene ontology

• Biological process: activation of MAPK activity;positive regulation of receptor internalization;signal transduction;transmembrane receptor protein tyrosine kinase signaling pathway;cell-cell signaling;nervous system development;peripheral nervous system development;memory;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of phospholipase C activity;positive regulation of phosphatidylinositol 3-kinase signaling;nerve development;positive regulation of cell migration;activation of protein kinase B activity;positive regulation of peptidyl-serine phosphorylation;nerve growth factor signaling pathway;regulation of apoptotic process;negative regulation of neuron apoptotic process;regulation of neuron differentiation;neuron projection morphogenesis;positive regulation of peptidyl-tyrosine phosphorylation;negative regulation of peptidyl-tyrosine phosphorylation;modulation of chemical synaptic transmission;positive chemotaxis;induction of positive chemotaxis;activation of GTPase activity;positive regulation of actin cytoskeleton reorganization
• Cellular component: extracellular region;extracellular space;synaptic vesicle;axon;dendrite;cytoplasmic vesicle
• Molecular function: signaling receptor binding;neurotrophin receptor binding;protein binding;growth factor activity;chemoattractant activity