CTRC

chymotrypsin C

Basic information

Region (hg38): 1:15438442-15449242

Links

ENSG00000162438 ∙ NCBI:11330 ∙ OMIM:601405 ∙ HGNC:2523 ∙ Uniprot:Q99895 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary chronic pancreatitis (Definitive), mode of inheritance: AD
• hereditary chronic pancreatitis (Strong), mode of inheritance: AD

ClinVar

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

• Hereditary pancreatitis (9 variants)
• Pancreatitis, chronic, susceptibility to (2 variants)
• not specified (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTRC 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			1	127	3	131
missense		1	264	28	1	294
nonsense	5	2	3	2		12
start loss		1				1
frameshift	3	2	5			10
inframe indel	1		1			2
splice donor/acceptor (+/-2bp)		1	4			5
splice region			5	5		10
non coding			4	42	16	62
Total	9	7	282	199	20

Highest pathogenic variant AF is 0.0000789

Variants in CTRC

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

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

Position	Type	Phenotype	Significance	ClinVar
1-15438463-C-T		Hereditary pancreatitis	Uncertain significance (Aug 07, 2023)
1-15438464-C-T		Hereditary pancreatitis	Uncertain significance (Dec 07, 2021)
1-15438465-A-G		Hereditary pancreatitis	Conflicting classifications of pathogenicity (Nov 24, 2023)
1-15438466-T-C		Hereditary pancreatitis	Likely pathogenic (Feb 10, 2022)
1-15438469-T-G		Hereditary pancreatitis	Uncertain significance (Aug 15, 2022)
1-15438470-G-A		Hereditary pancreatitis	Likely benign (Aug 29, 2023)
1-15438471-G-T		Hereditary pancreatitis	Uncertain significance (Nov 16, 2023)
1-15438472-G-A		Hereditary pancreatitis	Uncertain significance (Jul 29, 2023)
1-15438475-T-C		Hereditary pancreatitis	Uncertain significance (Dec 30, 2020)
1-15438476-C-T		Hereditary pancreatitis	Likely benign (Sep 06, 2019)
1-15438477-A-C		Hereditary pancreatitis	Uncertain significance (Nov 18, 2022)
1-15438477-A-G		Hereditary pancreatitis	Uncertain significance (Apr 24, 2024)
1-15438477-A-T		Hereditary pancreatitis	Uncertain significance (Jun 16, 2024)
1-15438479-T-C		Hereditary pancreatitis	Likely benign (Dec 21, 2020)
1-15438480-G-A		Hereditary pancreatitis	Uncertain significance (Sep 25, 2023)
1-15438485-C-A		Hereditary pancreatitis	Likely benign (Jan 16, 2022)
1-15438485-C-T		Hereditary pancreatitis	Likely benign (Aug 01, 2022)
1-15438486-G-A		Hereditary pancreatitis	Uncertain significance (Feb 03, 2023)
1-15438487-C-G		Hereditary pancreatitis	Uncertain significance (May 04, 2022)
1-15438489-G-T		Hereditary pancreatitis	Uncertain significance (Aug 29, 2023)
1-15438490-C-A		Hereditary pancreatitis	Uncertain significance (May 26, 2020)
1-15438490-C-T		Hereditary pancreatitis	Uncertain significance (Oct 10, 2023)
1-15438491-G-A		Hereditary pancreatitis	Conflicting classifications of pathogenicity (Sep 12, 2023)
1-15438491-G-C		Hereditary pancreatitis	Likely benign (Sep 14, 2023)
1-15438493-T-A		CTRC-related disorder	Uncertain significance (Jul 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTRC	protein_coding	protein_coding	ENST00000375949	8	10803

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-12	0.0134	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.134	168	163	1.03	0.0000114	1740
Missense in Polyphen		74	68.744	1.0765		733
Synonymous	-0.198	72	69.9	1.03	0.00000531	535
Loss of Function	-0.521	17	14.8	1.15	7.38e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00101
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000219	0.000217
South Asian	0.000361	0.000359
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates activation and degradation of trypsinogens and procarboxypeptidases by targeting specific cleavage sites within their zymogen precursors. Has chymotrypsin-type protease activity and hypocalcemic activity. {ECO:0000269|PubMed:23430245}.
• Pathway: Cobalamin (Cbl, vitamin B12) transport and metabolism;Metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling (Consensus)

Intolerance Scores

• loftool: 0.280
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• pHI: 0.355
• hipred: N
• hipred_score: 0.170
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.271

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctrc

Gene ontology

• Biological process: proteolysis;cobalamin metabolic process
• Cellular component: extracellular region
• Molecular function: serine-type endopeptidase activity;protein binding;peptidase activity