PGC

progastricsin, the group of Pepsinogens

Basic information

Region (hg38): 6:41736710-41754109

Links

ENSG00000096088 ∙ NCBI:5225 ∙ OMIM:169740 ∙ HGNC:8890 ∙ Uniprot:P20142 ∙ 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 PGC gene.

• Inborn genetic diseases (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGC 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in PGC

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

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

Position	Type	Phenotype	Significance	ClinVar
6-41736917-G-A		not specified	Uncertain significance (May 10, 2022)
6-41736935-T-G		not specified	Uncertain significance (Dec 18, 2023)
6-41736949-C-T		not specified	Uncertain significance (Jul 06, 2022)
6-41736962-A-T		not specified	Uncertain significance (Jul 25, 2023)
6-41736992-A-G		not specified	Uncertain significance (Feb 24, 2022)
6-41737773-T-C		not specified	Likely benign (Feb 27, 2023)
6-41739845-C-T		not specified	Uncertain significance (Jul 09, 2021)
6-41739909-C-T		not specified	Uncertain significance (Jun 16, 2023)
6-41739946-C-T		not specified	Likely benign (Sep 26, 2023)
6-41740497-A-G		not specified	Uncertain significance (Jan 03, 2022)
6-41740533-G-A		not specified	Uncertain significance (Oct 03, 2022)
6-41740563-C-T		not specified	Likely benign (Feb 05, 2024)
6-41740594-C-G		not specified	Uncertain significance (Aug 08, 2022)
6-41740595-G-T		not specified	Uncertain significance (May 31, 2022)
6-41742372-C-T		Inborn genetic diseases	Uncertain significance (Dec 15, 2021)
6-41742390-C-T		not specified	Uncertain significance (Aug 30, 2022)
6-41742416-G-A		not specified	Uncertain significance (Jun 29, 2023)
6-41742437-G-C		not specified	Uncertain significance (Nov 08, 2022)
6-41742456-C-T		not specified	Uncertain significance (Apr 19, 2023)
6-41743278-G-T		not specified	Uncertain significance (Dec 17, 2021)
6-41743288-C-A		not specified	Uncertain significance (Dec 07, 2022)
6-41743300-T-C		not specified	Uncertain significance (Jun 02, 2023)
6-41743359-G-A		not specified	Uncertain significance (Mar 11, 2024)
6-41744448-C-T		not specified	Uncertain significance (Sep 25, 2023)
6-41744668-G-A		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGC	protein_coding	protein_coding	ENST00000373025	9	17399

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.75e-11	0.131	125648	0	100	125748	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0484	228	230	0.991	0.0000128	2544
Missense in Polyphen		77	76.771	1.003		897
Synonymous	0.588	95	103	0.926	0.00000680	760
Loss of Function	0.490	17	19.3	0.880	8.23e-7	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00148	0.00145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000467	0.000462
European (Non-Finnish)	0.000410	0.000404
Middle Eastern	0.000163	0.000163
South Asian	0.000197	0.000196
Other	0.000661	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes a variety of proteins.
• Pathway: miR-targeted genes in epithelium - TarBase (Consensus)

Intolerance Scores

• loftool: 0.901
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.52

Haploinsufficiency Scores

• pHI: 0.0900
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.722

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgc

Gene ontology

• Biological process: positive regulation of antibacterial peptide production;proteolysis;digestion;protein catabolic process
• Cellular component: extracellular space
• Molecular function: aspartic-type endopeptidase activity