PTX4

protein-coding

pentraxin 4, the group of Long pentraxins

Gene summary

This gene belongs to the pentraxin superfamily, whose members encode highly conserved multifunctional proteins. The encoded protein, like other members of this family, contains a conserved pentraxin domain at the C-terminus. The highest levels of expression of the protein were observed in bone marrow, small intestine and testes. [provided by RefSeq, Jun 2016]

Previous symbols:

C16orf38

MANE transcript

NM_001328608.2

Inheritance

—

ClinVar variants

U:96B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.12

Max pathogenic AF

—

Genomic locus

chr16:1,485,886-1,488,981

External References & Databases

Ensembl (ENSG00000251692)

Transcript & Mutation Effects

hg38 • Region Span ~3.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PTX4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 122

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001328608.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			96 clinvar	12 clinvar		108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	96	13	0	109

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001328608.2	RefSeq	NP_001315537.1	3	MANE Select
ENST00000447419.7	Ensembl	ENSP00000445277.2	3	MANE Select
NM_001013658.1	RefSeq	NP_001013680.1	3	Standard
ENST00000293922.1	Ensembl	ENSP00000293922.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

metal ion binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293922
Coding exons: 3
Length: 3096
Individuals with no LoFs: 125672
Homozygous LoFs: 0
Heterozygous LoFs: 67
Defined: 125739
p: 0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.609	334	304	1.10	0.0000214	2941
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00069	0.00068	rare
Latino/Admixed American	0.00045	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00065	0.00062	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 2.65
RVIS percentile EVS: 98.84

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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