PTX3

pentraxin 3, the group of Long pentraxins

Basic information

Region (hg38): 3:157436849-157443633

Previous symbols: [ "TNFAIP5" ]

Links

ENSG00000163661 ∙ NCBI:5806 ∙ OMIM:602492 ∙ HGNC:9692 ∙ Uniprot:P26022 ∙ 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 PTX3 gene.

• Inborn genetic diseases (13 variants)
• not provided (6 variants)
• PTX3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTX3 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			15		3	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	5

Variants in PTX3

This is a list of pathogenic ClinVar variants found in the PTX3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-157436979-T-C			Benign (Jul 19, 2018)
3-157437041-T-C			Uncertain significance (-)
3-157437050-T-G			Benign (May 31, 2018)
3-157437633-A-T		not specified	Uncertain significance (Dec 14, 2021)
3-157437653-G-A		not specified	Uncertain significance (Feb 10, 2023)
3-157437662-C-T		not specified	Uncertain significance (Jun 02, 2023)
3-157437684-G-A		not specified	Uncertain significance (May 18, 2023)
3-157437737-G-C		PTX3-related disorder • not specified	Conflicting classifications of pathogenicity (Dec 20, 2022)
3-157437741-T-C		not specified	Uncertain significance (Dec 18, 2023)
3-157437758-G-C		not specified	Uncertain significance (Dec 17, 2023)
3-157437762-C-A		not specified	Uncertain significance (Jan 02, 2024)
3-157437795-A-C		not specified	Uncertain significance (Sep 16, 2021)
3-157437796-G-T		PTX3-related disorder	Uncertain significance (Jun 08, 2023)
3-157437804-G-T		not specified	Uncertain significance (Oct 24, 2023)
3-157437822-G-A		not specified	Uncertain significance (May 23, 2023)
3-157437846-A-G		not specified	Uncertain significance (Oct 17, 2023)
3-157437866-G-C		not specified	Uncertain significance (Aug 02, 2022)
3-157437874-C-G		not specified	Uncertain significance (Aug 10, 2021)
3-157437882-A-G			Benign (Jul 11, 2018)
3-157437912-C-A		not specified	Uncertain significance (Mar 01, 2024)
3-157442480-C-G		PTX3-related disorder	Uncertain significance (Feb 06, 2024)
3-157442525-G-A		not specified	Uncertain significance (Sep 29, 2023)
3-157442549-A-G		PTX3-related disorder	Uncertain significance (Feb 06, 2024)
3-157442626-G-C		not specified	Uncertain significance (Apr 22, 2022)
3-157442628-A-T		PTX3-related disorder	Benign/Likely benign (Oct 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTX3	protein_coding	protein_coding	ENST00000295927	3	6840

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000698	0.752	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0494	190	188	1.01	0.00000911	2424
Missense in Polyphen		58	63.304	0.91622		819
Synonymous	0.525	72	77.9	0.924	0.00000393	785
Loss of Function	1.07	8	12.0	0.667	5.90e-7	141

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000879	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000249	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of innate resistance to pathogens, inflammatory reactions, possibly clearance of self- components and female fertility. {ECO:0000250}.
• Pathway: Human Complement System;Lung fibrosis;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.612
• rvis_EVS: 1.04
• rvis_percentile_EVS: 91.21

Haploinsufficiency Scores

• pHI: 0.516
• hipred: N
• hipred_score: 0.277
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptx3
• Phenotype: cellular phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype; immune system phenotype; respiratory system phenotype; reproductive system phenotype

Gene ontology

• Biological process: ovarian cumulus expansion;response to yeast;inflammatory response;opsonization;extracellular matrix organization;neutrophil degranulation;negative regulation by host of viral exo-alpha-sialidase activity;negative regulation by host of viral glycoprotein metabolic process;innate immune response;positive regulation of nitric oxide biosynthetic process;negative regulation of viral entry into host cell;positive regulation of phagocytosis;negative regulation of exo-alpha-sialidase activity;negative regulation of glycoprotein metabolic process
• Cellular component: extracellular region;extracellular space;extracellular matrix;specific granule lumen;tertiary granule lumen
• Molecular function: complement component C1q binding;(1->3)-beta-D-glucan binding;protein binding;identical protein binding;virion binding