NPTX1

neuronal pentraxin 1, the group of Long pentraxins

Basic information

Region (hg38): 17:80466834-80477843

Links

ENSG00000171246 ∙ NCBI:4884 ∙ OMIM:602367 ∙ HGNC:7952 ∙ Uniprot:Q15818 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia 50 (Moderate), mode of inheritance: AD
• spinocerebellar ataxia 50 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia 50	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	34788392; 35285082; 35288776; 35560436

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NPTX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPTX1 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					2	2
missense		2	29	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	2	29	4	2

Variants in NPTX1

This is a list of pathogenic ClinVar variants found in the NPTX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-80470824-GGCGACAGGCCTCGAAGGTCCACTTGGT-G		Spinocerebellar ataxia 50	Likely pathogenic (Sep 25, 2024)
17-80470826-C-T		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
17-80470869-C-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
17-80470890-C-T		Inborn genetic diseases	Uncertain significance (May 28, 2024)
17-80470947-C-T		Spinocerebellar ataxia 50 • Inborn genetic diseases	Pathogenic/Likely pathogenic (Apr 01, 2025)
17-80470961-C-T		Inborn genetic diseases	Uncertain significance (Apr 20, 2023)
17-80471003-T-C		Spinocerebellar ataxia 50	Likely pathogenic (Dec 07, 2023)
17-80471755-C-T		Inborn genetic diseases	Uncertain significance (Sep 04, 2024)
17-80471768-G-A			Benign (Dec 31, 2019)
17-80471829-T-C		Spinocerebellar ataxia 50	Pathogenic (Dec 20, 2022)
17-80473250-C-G		Inborn genetic diseases	Uncertain significance (May 16, 2024)
17-80473411-T-C		Inborn genetic diseases	Uncertain significance (Apr 06, 2023)
17-80473419-G-T		Inborn genetic diseases	Uncertain significance (Sep 14, 2023)
17-80473429-C-T		Inborn genetic diseases	Uncertain significance (Jul 16, 2024)
17-80475526-T-C		Inborn genetic diseases	Uncertain significance (Dec 07, 2024)
17-80475555-G-T		Inborn genetic diseases	Uncertain significance (Oct 06, 2022)
17-80475556-T-A		Inborn genetic diseases	Likely benign (Aug 05, 2023)
17-80475594-C-A		Inborn genetic diseases	Uncertain significance (Feb 22, 2025)
17-80475624-C-A		Spinocerebellar ataxia 50	Likely pathogenic (Jan 22, 2024)
17-80475652-C-T		Inborn genetic diseases	Uncertain significance (Jul 26, 2024)
17-80475708-C-A		Inborn genetic diseases	Uncertain significance (Feb 01, 2025)
17-80476005-C-T		Inborn genetic diseases	Uncertain significance (Aug 05, 2024)
17-80476019-C-A		Spinocerebellar ataxia 50	Pathogenic (Dec 20, 2022)
17-80476022-G-C		Inborn genetic diseases	Uncertain significance (May 23, 2023)
17-80476051-T-G		Spinocerebellar ataxia 50	Uncertain significance (Apr 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPTX1	protein_coding	protein_coding	ENST00000306773	5	10696

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.625	0.375	125684	0	4	125688	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	168	252	0.668	0.0000134	2783
Missense in Polyphen		35	86.559	0.40435		931
Synonymous	-0.0986	116	115	1.01	0.00000677	891
Loss of Function	3.03	3	16.1	0.186	6.93e-7	174

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	0.0000465	0.0000462
European (Non-Finnish)	0.0000280	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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: 0.185

Intolerance Scores

• loftool: 0.240
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.373
• hipred: Y
• hipred_score: 0.755
• ghis: 0.585

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.838

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nptx1
• 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); vision/eye phenotype

Gene ontology

• Biological process: chemical synaptic transmission;central nervous system development;axonogenesis involved in innervation;regulation of postsynaptic neurotransmitter receptor activity
• Cellular component: plasma membrane;transport vesicle;neuron projection;glutamatergic synapse
• Molecular function: metal ion binding