PCOLCE2

protein-coding

procollagen C-endopeptidase enhancer 2

Gene summary

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. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_013363.4

Inheritance

—

ClinVar variants

U:77

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr3:142,815,922-142,889,206

External References & Databases

Ensembl (ENSG00000163710)

Transcript & Mutation Effects

hg38 • Region Span ~73.3 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 PCOLCE2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 75

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013363.4. 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						0
missense			76 clinvar			76
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	77	0	0	77

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013363.4	RefSeq	NP_037495.1	9	MANE Select
ENST00000295992.8	Ensembl	ENSP00000295992.3	9	MANE Select
ENST00000470310.5	Ensembl	ENSP00000419643.1	4	Standard
ENST00000480473.5	Ensembl	ENSP00000418782.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Collagen biosynthesis and modifying enzymes
Collagen formation
Extracellular matrix organization

Biological Process

positive regulation of peptidase activity
cellular response to leukemia inhibitory factor

Molecular Function

collagen binding
heparin binding
peptidase activator activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295992
Coding exons: 9
Length: 73282
Individuals with no LoFs: 125633
Homozygous LoFs: 0
Heterozygous LoFs: 115
Defined: 125748
p: 0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.587	213	238	0.893	0.0000131	2709
Missense (PolyPhen)		70	81.391	0.86004		936
Synonymous	1.21	76	90.7	0.838	0.00000533	800
Loss of Function	0.764	18	21.9	0.824	0.00000136	236

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0017	0.0017	notable
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.00079	0.00079	rare
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00035	0.00035	rare
South Asian	0.00063	0.00062	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to the C-terminal propeptide of types I and II procollagens and may enhance the cleavage of that propeptide by BMP1. {ECO:0000269|PubMed:12393877}.;

Recessive Scores

pRec: 0.0846

Intolerance Scores

LoFtool: 0.912
RVIS EVS: 0.07
RVIS percentile EVS: 58.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.216

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium