NETO2

neuropilin and tolloid like 2

Basic information

Region (hg38): 16:47077703-47143945

Links

ENSG00000171208 ∙ NCBI:81831 ∙ OMIM:607974 ∙ HGNC:14644 ∙ Uniprot:Q8NC67 ∙ 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 NETO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NETO2 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			27		1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	1

Variants in NETO2

This is a list of pathogenic ClinVar variants found in the NETO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-47083267-C-G		Malignant tumor of prostate	Uncertain significance (-)
16-47083296-C-T		not specified	Uncertain significance (Apr 17, 2023)
16-47083303-C-T		not specified	Uncertain significance (Jul 15, 2021)
16-47083307-C-T		not specified	Uncertain significance (Apr 15, 2024)
16-47083433-A-T			Benign (May 21, 2018)
16-47083450-C-T		not specified	Uncertain significance (Jan 18, 2023)
16-47083462-C-T		not specified	Uncertain significance (Jan 04, 2022)
16-47083483-T-C		not specified	Uncertain significance (Aug 08, 2023)
16-47083520-G-A		not specified	Uncertain significance (Nov 09, 2021)
16-47083549-T-C		not specified	Uncertain significance (Jul 20, 2021)
16-47083597-A-G		not specified	Uncertain significance (Sep 27, 2022)
16-47083642-T-C		not specified	Uncertain significance (Sep 26, 2022)
16-47083652-C-T		not specified	Uncertain significance (Oct 13, 2023)
16-47083664-C-T		not specified	Uncertain significance (Oct 28, 2023)
16-47083696-A-G		not specified	Uncertain significance (Mar 07, 2024)
16-47083746-A-C		not specified	Uncertain significance (Feb 16, 2023)
16-47086238-T-A		not specified	Uncertain significance (Oct 04, 2022)
16-47086309-T-A		not specified	Uncertain significance (Jul 06, 2021)
16-47109506-A-G		not specified	Uncertain significance (Jan 08, 2024)
16-47109509-C-T		not specified	Uncertain significance (Feb 14, 2023)
16-47109524-C-T		not specified	Uncertain significance (Mar 20, 2023)
16-47109620-T-C		not specified	Uncertain significance (Jul 12, 2022)
16-47109671-T-C		not specified	Uncertain significance (Nov 01, 2022)
16-47109672-T-C		not specified	Uncertain significance (Apr 17, 2023)
16-47122664-T-A		not specified	Uncertain significance (May 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NETO2	protein_coding	protein_coding	ENST00000562435	9	66295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0627	0.937	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.988	239	286	0.836	0.0000156	3479
Missense in Polyphen		57	89.144	0.63941		1152
Synonymous	0.551	92	99.0	0.930	0.00000555	981
Loss of Function	3.68	8	29.6	0.270	0.00000193	311

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000278	0.000277
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Accessory subunit of neuronal kainate-sensitive glutamate receptors, GRIK2 and GRIK3. Increases kainate-receptor channel activity, slowing the decay kinetics of the receptors, without affecting their expression at the cell surface, and increasing the open probability of the receptor channels. Modulates the agonist sensitivity of kainate receptors. Slows the decay of kainate receptor-mediated excitatory postsynaptic currents (EPSCs), thus directly influencing synaptic transmission (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.603
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.172
• hipred: Y
• hipred_score: 0.550
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.464

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Neto2
• 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: regulation of kainate selective glutamate receptor activity
• Cellular component: postsynaptic density;integral component of membrane
• Molecular function: ionotropic glutamate receptor binding