PCOLCE

procollagen C-endopeptidase enhancer

Basic information

Region (hg38): 7:100602363-100608175

Links

ENSG00000106333 ∙ NCBI:5118 ∙ OMIM:600270 ∙ HGNC:8738 ∙ Uniprot:Q15113 ∙ 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 PCOLCE gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCOLCE 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			28	2	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	1

Variants in PCOLCE

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

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

Position	Type	Phenotype	Significance	ClinVar
7-100602473-C-G		not specified	Uncertain significance (Oct 07, 2024)
7-100602476-C-A		not specified	Uncertain significance (Sep 22, 2023)
7-100602528-G-C		not specified	Uncertain significance (Nov 22, 2023)
7-100603459-A-T		not specified	Uncertain significance (Nov 13, 2024)
7-100603466-A-T		not specified	Uncertain significance (Jul 25, 2024)
7-100603509-C-G		not specified	Uncertain significance (Mar 29, 2022)
7-100603513-A-G		not specified	Uncertain significance (Mar 12, 2024)
7-100603526-C-G		not specified	Uncertain significance (Dec 08, 2023)
7-100603966-A-G		not specified	Uncertain significance (Jan 03, 2024)
7-100604010-C-A		not specified	Uncertain significance (Jan 26, 2022)
7-100604016-C-G		not specified	Uncertain significance (Jan 24, 2024)
7-100604046-T-C		not specified	Uncertain significance (Jan 06, 2023)
7-100604059-G-C		not specified	Uncertain significance (Oct 21, 2021)
7-100604128-A-G		not specified	Uncertain significance (Sep 17, 2021)
7-100605094-A-G		not specified	Uncertain significance (Feb 07, 2025)
7-100605117-G-A		not specified	Uncertain significance (Jan 03, 2025)
7-100605182-C-G		not specified	Uncertain significance (Oct 22, 2021)
7-100605208-C-G		not specified	Likely benign (Jan 02, 2024)
7-100605679-A-T		not specified	Uncertain significance (Apr 08, 2024)
7-100605757-G-T		not specified	Uncertain significance (Jan 17, 2025)
7-100605785-G-A		not specified	Uncertain significance (Feb 01, 2025)
7-100605805-G-A		not specified	Uncertain significance (Dec 25, 2024)
7-100606444-C-T		not specified	Uncertain significance (Nov 26, 2024)
7-100606512-G-A		PCOLCE-related disorder	Likely benign (Aug 06, 2019)
7-100606513-C-A		PCOLCE-related disorder	Likely benign (Aug 06, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PCOLCE	protein_coding	protein_coding	ENST00000223061	9	5999

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000584	0.975	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.160	256	263	0.972	0.0000142	2828
Missense in Polyphen		90	97.372	0.92429		1127
Synonymous	-1.05	130	116	1.12	0.00000649	966
Loss of Function	2.02	10	19.6	0.509	8.52e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000647	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000801	0.0000791
Middle Eastern	0.000218	0.000217
South Asian	0.0000660	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the C-terminal propeptide of type I procollagen and enhances procollagen C-proteinase activity.
• Pathway: Crosslinking of collagen fibrils;Assembly of collagen fibrils and other multimeric structures;Collagen biosynthesis and modifying enzymes;Collagen formation;Extracellular matrix organization (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.580
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.758
• hipred: Y
• hipred_score: 0.580
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.215

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pcolce
• Phenotype: limbs/digits/tail phenotype; muscle phenotype; skeleton phenotype

Gene ontology

• Biological process: proteolysis;multicellular organism development;positive regulation of peptidase activity;cellular response to leukemia inhibitory factor
• Cellular component: extracellular region;extracellular space;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: extracellular matrix structural constituent;protein binding;collagen binding;heparin binding;peptidase activator activity