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.

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.

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			48	3		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	3	0

Variants in NPTX2

This is a list of pathogenic ClinVar variants found in the NPTX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-98617490-C-T		not specified	Likely benign (Feb 21, 2024)
7-98617521-C-G		not specified	Uncertain significance (Feb 19, 2025)
7-98617556-T-C		not specified	Uncertain significance (Jul 26, 2024)
7-98617559-C-G		not specified	Uncertain significance (Sep 03, 2024)
7-98617599-G-T		not specified	Uncertain significance (Mar 07, 2025)
7-98617604-T-G		not specified	Uncertain significance (Jan 03, 2024)
7-98617649-T-C		not specified	Uncertain significance (Nov 13, 2023)
7-98617663-G-C		not specified	Uncertain significance (Nov 14, 2023)
7-98617688-C-T		not specified	Uncertain significance (Oct 05, 2023)
7-98617702-C-G		not specified	Uncertain significance (Jul 14, 2021)
7-98617703-G-T		not specified	Uncertain significance (Nov 08, 2024)
7-98617727-G-A		not specified	Uncertain significance (Aug 19, 2024)
7-98617745-A-C		not specified	Uncertain significance (Dec 14, 2023)
7-98617772-G-A		not specified	Uncertain significance (Feb 05, 2025)
7-98617783-A-G		not specified	Uncertain significance (Jan 04, 2022)
7-98617798-A-G		not specified	Uncertain significance (Jul 20, 2021)
7-98617805-A-C		not specified	Uncertain significance (Dec 04, 2024)
7-98617867-G-A		not specified	Uncertain significance (Aug 11, 2022)
7-98617871-G-A		not specified	Uncertain significance (Apr 05, 2023)
7-98617873-C-A		not specified	Uncertain significance (Jan 21, 2025)
7-98619649-C-T		not specified	Uncertain significance (Aug 13, 2021)
7-98619661-G-A		not specified	Uncertain significance (Nov 16, 2021)
7-98619661-G-T		not specified	Uncertain significance (Apr 06, 2024)
7-98619668-A-G		not specified	Uncertain significance (Dec 21, 2022)
7-98619682-G-A		not specified	Likely benign (Jun 30, 2022)

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