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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 19.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000303155.9	ENSP00000306726.5	9	-	-
ENST00000562435.6	ENSP00000455169.1	9	yes	-
ENST00000562559.5	ENSP00000454213.1	5	-	-
ENST00000563078.1	ENSP00000456818.1	4	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NETO2 gene.

• not_specified (69 variants)
• not_provided (1 variants)
• Prostate_cancer (1 variants)

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. These statistics are base on transcript: NM_000018092.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2			2
missense			70		1	71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	74	0	1

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
		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

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

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