PTX4

Chr 16

pentraxin 4

Also known as: C16orf38

NCBI Gene: 390667ENSG00000251692UniProt: Q96A99OMIM: 613442

The encoded protein is a member of the pentraxin superfamily containing a conserved pentraxin domain at the C-terminus, with highest expression in bone marrow, small intestine and testes. This gene is not highly constrained against loss-of-function variants (pLI near zero, LOEUF 1.64), and no established Mendelian diseases have been definitively linked to PTX4 mutations in current clinical practice. Additional research may be needed to establish clear genotype-phenotype correlations for this gene.

OMIMResearchSummary from RefSeq
DNmechanismLOEUF 1.64
Clinical Summary— PTX4
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
45 unique Pathogenic / Likely Pathogenic· 122 VUS of 183 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.64LOEUF
pLI 0.000
Z-score -0.43
OE 1.12 (0.77–1.64)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.61Z-score
OE missense 1.10 (1.00–1.20)
334 obs / 304.1 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.12 (0.77–1.64)
0≤0.351.4
Missense OE1.10 (1.00–1.20)
0≤0.61.4
Synonymous OE0.99
0≤1.21.6
LoF obs/exp: 18 / 16.1Missense obs/exp: 334 / 304.1Syn Z: 0.05
DN
0.6647th %ile
GOF
0.6053th %ile
LOF
0.3940th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

183 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic44
Likely Pathogenic1
VUS122
Likely Benign15
44
Pathogenic
1
Likely Pathogenic
122
VUS
15
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
44
0
44
Likely Pathogenic
0
0
1
0
1
VUS
0
107
15
0
122
Likely Benign
0
14
0
1
15
Benign
0
0
0
0
0
Total0121601182

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PTX4 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Binding of anionic Pt(ii) complexes in a dedicated organic matrix: towards new binary crystalline composites.
Kuzniak-Glanowska E et al.·Dalton Trans
2021
Pentraxin family members of largemouth bass (Micropterus salmoides): Cloning, characterization and expression responses to LPS, Poly (I:C) and Nocardia seriolae.
Yang Y et al.·Dev Comp Immunol
2025
Comorbidity between Alzheimer's disease and major depression: a behavioural and transcriptomic characterization study in mice
Martín-Sánchez A et al.·Alzheimers Res Ther
2021
Long pentraxin PTX3 is upregulated systemically and centrally after experimental neurotrauma, but its depletion leaves unaltered sensorimotor deficits or histopathology
Oggioni M et al.·Sci Rep
2021
High Levels of C-Reactive Protein with Low Levels of Pentraxin 3 as Biomarkers for Central Serous Chorioretinopathy
Bousquet E et al.·Ophthalmol Sci
2023
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Evolution of the pentraxin family: the new entry PTX4.
Martinez de la Torre Y et al.·J Immunol
2010
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients