NPTXR

neuronal pentraxin receptor

Basic information

Region (hg38): 22:38818452-38844028

Links

ENSG00000221890 ∙ NCBI:23467 ∙ OMIM:609474 ∙ HGNC:7954 ∙ Uniprot:O95502 ∙ 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 NPTXR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPTXR 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			35	3		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	3	0

Variants in NPTXR

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

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

Position	Type	Phenotype	Significance	ClinVar
22-38822620-C-T		not specified	Uncertain significance (Sep 03, 2024)
22-38822638-C-T		not specified	Uncertain significance (Mar 15, 2024)
22-38822656-C-T		not specified	Uncertain significance (Jan 02, 2024)
22-38822670-T-A		not specified	Uncertain significance (Feb 12, 2024)
22-38822674-C-T		not specified	Uncertain significance (Dec 27, 2023)
22-38822695-G-C		not specified	Uncertain significance (Feb 23, 2023)
22-38822701-T-C		not specified	Uncertain significance (Aug 02, 2021)
22-38822715-G-A		not specified	Uncertain significance (Jun 17, 2024)
22-38822799-G-T		not specified	Uncertain significance (Sep 03, 2024)
22-38822806-T-C		not specified	Uncertain significance (Dec 08, 2023)
22-38822809-C-A		not specified	Uncertain significance (Aug 17, 2022)
22-38822829-G-T		not specified	Uncertain significance (Apr 25, 2022)
22-38823166-C-T		not specified	Uncertain significance (Sep 04, 2024)
22-38823222-T-C		not specified	Uncertain significance (Aug 02, 2022)
22-38826537-G-A		not specified	Uncertain significance (Apr 23, 2024)
22-38826588-G-T		not specified	Uncertain significance (Aug 05, 2024)
22-38826595-C-T		not specified	Uncertain significance (Oct 20, 2023)
22-38826601-C-T		not specified	Uncertain significance (Aug 21, 2023)
22-38826621-C-T		not specified	Uncertain significance (May 15, 2024)
22-38826673-C-A		not specified	Uncertain significance (Dec 15, 2023)
22-38826697-G-A		not specified	Uncertain significance (Jul 09, 2021)
22-38826702-G-C		not specified	Uncertain significance (Apr 18, 2023)
22-38826733-T-C		not specified	Uncertain significance (May 29, 2024)
22-38828307-C-T		not specified	Uncertain significance (Jul 14, 2023)
22-38828352-C-T		not specified	Likely benign (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPTXR	protein_coding	protein_coding	ENST00000333039	5	25531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.716	0.283	125735	0	9	125744	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	159	210	0.755	0.0000124	3119
Missense in Polyphen		69	94.318	0.73156		1264
Synonymous	0.900	83	94.1	0.882	0.00000575	1133
Loss of Function	2.80	2	12.8	0.156	5.53e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000632	0.0000615
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000182	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in mediating uptake of synaptic material during synapse remodeling or in mediating the synaptic clustering of AMPA glutamate receptors at a subset of excitatory synapses. {ECO:0000250}.

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0595

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nptxr
• 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: neuron projection development;regulation of postsynaptic neurotransmitter receptor activity
• Cellular component: plasma membrane;cytoplasmic side of plasma membrane;integral component of membrane;filopodium;dendrite;growth cone;neuronal cell body;glutamatergic synapse
• Molecular function: metal ion binding