PTX4

pentraxin 4, the group of Long pentraxins

Basic information

Region (hg38): 16:1485885-1488981

Previous symbols: [ "C16orf38" ]

Links

ENSG00000251692 ∙ NCBI:390667 ∙ OMIM:613442 ∙ HGNC:14171 ∙ Uniprot:Q96A99 ∙ 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 PTX4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTX4 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			39	8		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	8	0

Variants in PTX4

This is a list of pathogenic ClinVar variants found in the PTX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1485949-C-A		not specified	Likely benign (Mar 20, 2024)
16-1485949-C-T		not specified	Likely benign (Nov 29, 2023)
16-1485989-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-1486003-T-C		not specified	Uncertain significance (Jan 10, 2022)
16-1486012-G-A		not specified	Uncertain significance (Oct 16, 2023)
16-1486017-G-C		not specified	Uncertain significance (Apr 04, 2023)
16-1486043-C-T		not specified	Uncertain significance (Mar 07, 2024)
16-1486079-C-A		not specified	Uncertain significance (May 25, 2022)
16-1486081-C-T		not specified	Uncertain significance (Jun 18, 2024)
16-1486084-T-C		not specified	Uncertain significance (Dec 01, 2022)
16-1486108-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-1486124-C-G		not specified	Uncertain significance (May 15, 2024)
16-1486237-C-T		not specified	Uncertain significance (Jun 11, 2021)
16-1486270-G-A		not specified	Uncertain significance (Oct 05, 2023)
16-1486342-G-A		not specified	Uncertain significance (Oct 04, 2022)
16-1486402-A-G		not specified	Uncertain significance (Dec 09, 2023)
16-1486421-C-T		not specified	Uncertain significance (May 27, 2022)
16-1486451-G-A		not specified	Uncertain significance (Aug 10, 2021)
16-1486529-C-T		not specified	Uncertain significance (Sep 23, 2023)
16-1486549-G-C		not specified	Uncertain significance (Jun 29, 2023)
16-1486556-C-T		not specified	Likely benign (Jun 11, 2021)
16-1486571-C-T		not specified	Uncertain significance (Aug 01, 2022)
16-1487445-G-C		not specified	Uncertain significance (Jul 13, 2021)
16-1487448-G-A		not specified	Uncertain significance (Sep 25, 2023)
16-1487453-C-A		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTX4	protein_coding	protein_coding	ENST00000293922	3	3096

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.76e-13	0.0125	125672	0	67	125739	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.609	334	304	1.10	0.0000214	2941
Missense in Polyphen		70	72.551	0.96484		858
Synonymous	0.0527	142	143	0.994	0.0000101	1083
Loss of Function	-0.429	18	16.1	1.12	0.00000102	133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00114	0.00112
Ashkenazi Jewish	0.00	0.00
East Asian	0.000331	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000331	0.000326
South Asian	0.000649	0.000621
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 2.65
• rvis_percentile_EVS: 98.84

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ptx4

Gene ontology

• Cellular component: extracellular region
• Molecular function: metal ion binding