PCOLCE2

procollagen C-endopeptidase enhancer 2

Basic information

Region (hg38): 3:142815922-142889206

Links

ENSG00000163710 ∙ NCBI:26577 ∙ OMIM:607064 ∙ HGNC:8739 ∙ Uniprot:Q9UKZ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCOLCE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCOLCE2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in PCOLCE2

This is a list of pathogenic ClinVar variants found in the PCOLCE2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-142818389-C-T		not specified	Uncertain significance (Jun 16, 2022)
3-142818402-C-T		not specified	Uncertain significance (Mar 21, 2023)
3-142818445-C-T		not specified	Uncertain significance (Feb 21, 2024)
3-142820963-C-G		not specified	Uncertain significance (Aug 02, 2023)
3-142821010-C-T		not specified	Uncertain significance (May 09, 2022)
3-142821013-G-A		not specified	Uncertain significance (May 13, 2024)
3-142823567-C-T		not specified	Uncertain significance (Jan 29, 2024)
3-142829694-G-A		not specified	Uncertain significance (Mar 06, 2023)
3-142829733-G-C		not specified	Uncertain significance (Dec 20, 2023)
3-142829814-A-G		not specified	Uncertain significance (Oct 05, 2022)
3-142838813-C-T		not specified	Uncertain significance (Oct 22, 2021)
3-142838860-T-G		not specified	Uncertain significance (Mar 28, 2024)
3-142842928-T-C		not specified	Uncertain significance (Oct 12, 2022)
3-142842938-C-T		not specified	Uncertain significance (Mar 20, 2024)
3-142842962-C-T		not specified	Uncertain significance (Jan 29, 2024)
3-142842964-C-A		not specified	Uncertain significance (Jun 17, 2024)
3-142842980-G-A		not specified	Uncertain significance (Aug 21, 2023)
3-142843013-A-C		not specified	Uncertain significance (Feb 28, 2023)
3-142848229-G-A		not specified	Uncertain significance (Jul 14, 2023)
3-142848238-C-T		not specified	Uncertain significance (Jul 09, 2021)
3-142848264-C-T		not specified	Uncertain significance (Aug 22, 2023)
3-142848333-C-T		not specified	Uncertain significance (May 11, 2022)
3-142848361-G-A		not specified	Uncertain significance (Aug 11, 2022)
3-142848387-A-G		not specified	Uncertain significance (May 09, 2022)
3-142848433-T-C		not specified	Uncertain significance (Nov 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCOLCE2	protein_coding	protein_coding	ENST00000295992	9	73282

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.46e-11	0.214	125633	0	115	125748	0.000457

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.587	213	238	0.893	0.0000131	2709
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00195	0.00195
Ashkenazi Jewish	0.000795	0.000794
East Asian	0.000436	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000355	0.000352
Middle Eastern	0.000436	0.000435
South Asian	0.000627	0.000621
Other	0.000493	0.000489

dbNSFP

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}.
• Pathway: Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.0846

Intolerance Scores

• loftool: 0.912
• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.251
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.216

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcolce2
• Phenotype: normal phenotype

Gene ontology

• Biological process: positive regulation of peptidase activity;cellular response to leukemia inhibitory factor
• Cellular component: extracellular region
• Molecular function: collagen binding;heparin binding;peptidase activator activity