NRTN

neurturin, the group of GDNF family ligands

Basic information

Region (hg38): 19:5805066-5828324

Links

ENSG00000171119 ∙ NCBI:4902 ∙ OMIM:602018 ∙ HGNC:8007 ∙ Uniprot:Q99748 ∙ 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 NRTN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRTN 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	2	3
missense			20	1	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	20	3	3

Variants in NRTN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-5824259-C-T		not specified	Uncertain significance (Dec 08, 2021)
19-5824260-G-A			Uncertain significance (Jun 26, 2020)
19-5824289-C-T		not specified	Uncertain significance (Apr 12, 2022)
19-5824309-C-T		not specified	Benign (-)
19-5824332-A-C		not specified	Uncertain significance (Oct 26, 2022)
19-5827731-C-T		not specified	Likely benign (-)
19-5827754-G-A		not specified	Benign (-)
19-5827793-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-5827803-C-G		not specified	Uncertain significance (Sep 13, 2023)
19-5827815-G-T		not specified	Uncertain significance (Oct 05, 2023)
19-5827869-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-5827880-C-T		not specified	Uncertain significance (Oct 26, 2021)
19-5827898-G-A		NRTN-related disorder • not specified	Uncertain significance (Jun 21, 2023)
19-5827953-T-C		not specified	Uncertain significance (Jan 10, 2023)
19-5827962-G-C		not specified	Uncertain significance (Apr 26, 2023)
19-5827997-G-C		not specified	Uncertain significance (Aug 17, 2021)
19-5828006-C-G		not specified	Uncertain significance (Dec 16, 2023)
19-5828006-C-T		not specified	Uncertain significance (Apr 19, 2024)
19-5828039-C-G		not specified	Likely benign (Apr 07, 2023)
19-5828040-T-G		not specified	Uncertain significance (Dec 06, 2021)
19-5828049-A-G		not specified	Uncertain significance (Dec 06, 2021)
19-5828053-G-C		not specified	Benign (-)
19-5828060-G-C		not specified	Uncertain significance (Aug 23, 2021)
19-5828093-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-5828095-C-G		not specified	Uncertain significance (Dec 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRTN	protein_coding	protein_coding	ENST00000303212	2	4523

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0302	0.821	123767	0	3	123770	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.679	68	85.7	0.794	0.00000536	1145
Missense in Polyphen		30	38.41	0.78104		578
Synonymous	0.833	34	40.8	0.834	0.00000232	477
Loss of Function	1.12	3	5.95	0.504	3.94e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000624	0.0000624
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000893	0.00000893
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Supports the survival of sympathetic neurons in culture. May regulate the development and maintenance of the CNS. Might control the size of non-neuronal cell population such as haemopoietic cells.
• Disease: DISEASE: Note=Genetic variations in NRTN may contribute to Hirschsprung disease, in association with mutations of RET gene, and possibly mutations in other loci. Hirschsprung disease is a disorder of neural crest development is characterized by the absence of intramural ganglion cells in the hindgut, often resulting in intestinal obstruction. {ECO:0000269|PubMed:9700200}.
• Pathway: Developmental Biology;Signal Transduction;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;NCAM signaling for neurite out-growth;NCAM1 interactions;RET signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.210

Haploinsufficiency Scores

• pHI: 0.151
• hipred: Y
• hipred_score: 0.506
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.607

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nrtn
• Phenotype: endocrine/exocrine gland phenotype; muscle phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; vision/eye phenotype; digestive/alimentary 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)

Gene ontology

• Biological process: MAPK cascade;neural crest cell migration;transmembrane receptor protein tyrosine kinase signaling pathway;nervous system development;axon guidance;regulation of signaling receptor activity;nerve development;neuron projection development
• Cellular component: extracellular region;axon
• Molecular function: Ras guanyl-nucleotide exchange factor activity;signaling receptor binding;growth factor activity