PTX4

Chr 16

pentraxin 4

Also known as: C16orf38

NCBI Gene: 390667 ENSG00000251692 UniProt: Q96A99 OMIM: 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.

OMIM ResearchSummary from RefSeq

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]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.64

Clinical Summary— PTX4

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

110 VUS of 126 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 OE?1.12 (0.77–1.64)

0≤0.351.4

Missense OE?1.10 (1.00–1.20)

0≤0.61.4

Synonymous OE?0.99

0≤1.21.6

LoF obs/exp: 18 / 16.1Missense obs/exp: 334 / 304.1Syn Z: 0.05

This gene — mechanism propensity

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

126 submitted variants in ClinVar

ClinVar

Classification Summary

VUS110

Likely Benign15

110

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	107	3	0	110
Likely Benign	14	0	1	15
Benign	0	0	0	0
Total	121	3	1	125

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

View in ClinVar →

45 pathogenic / likely-pathogenic (of 57) ClinVar copy-number / structural variants overlap PTX4 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →