PCOLCE2

Chr 3

procollagen C-endopeptidase enhancer 2

Also known as: PCPE2

NCBI Gene: 26577 ENSG00000163710 UniProt: Q9UKZ9 OMIM: 607064

Enables collagen binding activity; heparin binding activity; and peptidase activator activity. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 1.22

Clinical Summary— PCOLCE2

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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

75 VUS of 85 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?

1.22LOEUF

pLI 0.000

Z-score 0.76

OE 0.82 (0.57–1.22)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.59Z-score

OE missense 0.89 (0.80–1.00)

213 obs / 238.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.82 (0.57–1.22)

0≤0.351.4

Missense OE?0.89 (0.80–1.00)

0≤0.61.4

Synonymous OE?0.84

0≤1.21.6

LoF obs/exp: 18 / 21.9Missense obs/exp: 213 / 238.5Syn Z: 1.21

This gene — mechanism propensity

0.6937th %ile

GOF

0.5954th %ile

LOF

0.3843th %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

85 submitted variants in ClinVar

ClinVar

Classification Summary

VUS75

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	75	75
Likely Benign	0	0
Benign	0	0
Total	75	75

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

View in ClinVar →

18 pathogenic / likely-pathogenic (of 23) ClinVar copy-number / structural variants overlap PCOLCE2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →