ARTN

artemin, the group of GDNF family ligands

Basic information

Region (hg38): 1:43933320-43937240

Links

ENSG00000117407 ∙ NCBI:9048 ∙ OMIM:603886 ∙ HGNC:727 ∙ Uniprot:Q5T4W7 ∙ 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 ARTN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARTN 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			15			15
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	0	0

Variants in ARTN

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

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

Position	Type	Phenotype	Significance	ClinVar
1-43935669-C-G		not specified	Uncertain significance (Nov 30, 2022)
1-43935685-C-A		not specified	Uncertain significance (Jun 04, 2024)
1-43935685-C-T		not specified	Uncertain significance (Mar 20, 2024)
1-43935699-C-T		not specified	Uncertain significance (May 24, 2024)
1-43936169-G-A		not specified	Uncertain significance (Jun 10, 2024)
1-43936317-G-A		not specified	Uncertain significance (Sep 29, 2022)
1-43936385-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-43936400-C-A		not specified	Uncertain significance (Jan 23, 2023)
1-43936430-G-A		not specified	Uncertain significance (Oct 24, 2023)
1-43936448-C-G		not specified	Uncertain significance (Jun 28, 2022)
1-43936521-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-43936531-G-C		not specified	Uncertain significance (Nov 08, 2022)
1-43936571-G-T		not specified	Uncertain significance (Sep 21, 2023)
1-43936574-C-T		not specified	Uncertain significance (Mar 29, 2024)
1-43936587-A-G		not specified	Uncertain significance (Jan 04, 2024)
1-43936662-G-A		not specified	Uncertain significance (Dec 14, 2021)
1-43936688-G-A		not specified	Uncertain significance (Sep 23, 2023)
1-43936704-T-A		not specified	Uncertain significance (Feb 12, 2024)
1-43936713-C-T		not specified	Uncertain significance (Jan 24, 2023)
1-43936719-G-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARTN	protein_coding	protein_coding	ENST00000414809	3	3922

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.358	0.595	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	54	85.7	0.630	0.00000418	1356
Missense in Polyphen		17	33.588	0.50613		514
Synonymous	0.437	37	40.5	0.913	0.00000216	556
Loss of Function	1.56	1	4.60	0.217	2.01e-7	58

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ligand for the GFR-alpha-3-RET receptor complex but can also activate the GFR-alpha-1-RET receptor complex. Supports the survival of sensory and sympathetic peripheral neurons in culture and also supports the survival of dopaminergic neurons of the ventral mid-brain. Strong attractant of gut hematopoietic cells thus promoting the formation Peyer's patch-like structures, a major component of the gut-associated lymphoid tissue. {ECO:0000269|PubMed:10583383, ECO:0000269|PubMed:9883723}.
• 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: 0.180

Haploinsufficiency Scores

• pHI: 0.0360
• hipred: N
• hipred_score: 0.285

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.590

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Artn
• 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); vision/eye phenotype

Zebrafish Information Network

• Gene name: artnb
• Affected structure: adductor hyohyoid
• Phenotype tag: abnormal
• Phenotype quality: has fewer parts of type

Gene ontology

• Biological process: MAPK cascade;signal transduction;neuroblast proliferation;axon guidance;peripheral nervous system development;regulation of signaling receptor activity;induction of positive chemotaxis;Peyer's patch morphogenesis;lymphocyte migration into lymphoid organs
• Cellular component: extracellular region;extracellular space
• Molecular function: Ras guanyl-nucleotide exchange factor activity;signaling receptor binding;protein binding;growth factor activity