NETO1

neuropilin and tolloid like 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 18:72742314-72868146

Links

ENSG00000166342 ∙ NCBI:81832 ∙ OMIM:607973 ∙ HGNC:13823 ∙ Uniprot:Q8TDF5 ∙ 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 NETO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NETO1 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	1	2	18
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	1	2

Variants in NETO1

This is a list of pathogenic ClinVar variants found in the NETO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-72749072-A-G		not specified	Uncertain significance (May 30, 2024)
18-72750107-G-A		not specified	Uncertain significance (Jan 08, 2024)
18-72750143-G-C			Benign (Feb 14, 2018)
18-72750279-C-T		not specified	Uncertain significance (Feb 21, 2024)
18-72750327-T-G		not specified	Uncertain significance (Dec 27, 2023)
18-72750435-G-T		not specified	Uncertain significance (Jan 03, 2024)
18-72756139-C-T		not specified	Uncertain significance (Aug 08, 2022)
18-72783743-C-T		not specified	Uncertain significance (Jun 13, 2023)
18-72783863-T-G		not specified	Uncertain significance (Feb 06, 2023)
18-72783870-A-T		not specified	Uncertain significance (Jan 03, 2022)
18-72794161-C-A		not specified	Uncertain significance (Sep 20, 2023)
18-72794244-G-A		not specified	Likely benign (Feb 28, 2023)
18-72858857-C-T		not specified	Uncertain significance (Apr 28, 2023)
18-72859008-C-T		not specified	Uncertain significance (Nov 29, 2023)
18-72859048-A-G		not specified	Uncertain significance (Sep 06, 2022)
18-72859068-G-A		not specified	Uncertain significance (Aug 15, 2023)
18-72864831-C-T		not specified	Uncertain significance (May 31, 2023)
18-72865236-C-T			Benign (Mar 29, 2018)
18-72867284-T-C		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NETO1	protein_coding	protein_coding	ENST00000327305	10	125833

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0526	0.947	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.80	213	301	0.708	0.0000162	3524
Missense in Polyphen		68	125.04	0.54383		1412
Synonymous	-0.303	110	106	1.04	0.00000574	984
Loss of Function	3.62	8	29.1	0.275	0.00000180	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000109	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the development and/or maintenance of neuronal circuitry. Accessory subunit of the neuronal N-methyl-D- aspartate receptor (NMDAR) critical for maintaining the abundance of GRIN2A-containing NMDARs in the postsynaptic density. Regulates long-term NMDA receptor-dependent synaptic plasticity and cognition, at least in the context of spatial learning and memory (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.393

Intolerance Scores

• loftool: 0.443
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.71

Haploinsufficiency Scores

• pHI: 0.301
• hipred: Y
• hipred_score: 0.837
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Neto1
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: memory;visual learning;regulation of long-term neuronal synaptic plasticity;receptor localization to synapse;regulation of kainate selective glutamate receptor activity;positive regulation of excitatory postsynaptic potential
• Cellular component: extracellular region;postsynaptic density;cell junction;excitatory synapse;postsynaptic density membrane;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: ionotropic glutamate receptor binding