NPTX2

neuronal pentraxin 2, the group of Long pentraxins

Basic information

Region (hg38): 7:98617285-98629869

Links

ENSG00000106236

∙ NCBI:4885 ∙ OMIM:600750 ∙ HGNC:7953 ∙ Uniprot:P47972 ∙ 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 NPTX2 gene.

not_specified (73 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPTX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002523.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			71 clinvar	3 clinvar		74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	71	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPTX2	protein_coding	protein_coding	ENST00000265634	5	12572

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0305	0.961	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.679	194	223	0.872	0.0000136	2734
Missense in Polyphen		71	86.564	0.8202		981
Synonymous	-0.454	114	108	1.06	0.00000759	921
Loss of Function	2.29	5	14.4	0.348	6.63e-7	158

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)	0.0000356	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Likely to play role in the modification of cellular properties that underlie long-term plasticity. Binds to agar matrix in a calcium-dependent manner (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.288

Haploinsufficiency Scores

pHI: 0.469
hipred: Y
hipred_score: 0.662
ghis: 0.567

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.393

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nptx2
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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: nptx2a
Affected structure: motor neuron
Phenotype tag: abnormal
Phenotype quality: decreased process quality

Gene ontology

Biological process: chemical synaptic transmission;associative learning;neuron projection development;regulation of postsynaptic neurotransmitter receptor activity
Cellular component: cellular_component;extracellular region;plasma membrane;cytoplasmic side of plasma membrane;filopodium;dendrite;growth cone;neuronal cell body;glutamatergic synapse
Molecular function: molecular_function;carbohydrate binding;metal ion binding