PGA5

pepsinogen A5, the group of Pepsinogens

Basic information

Region (hg38): 11:61241175-61251444

Links

ENSG00000256713 ∙ NCBI:5222 ∙ OMIM:169730 ∙ HGNC:8887 ∙ Uniprot:P0DJD9 ∙ 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 PGA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGA5 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			19	2		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	19	2	0

Variants in PGA5

This is a list of pathogenic ClinVar variants found in the PGA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61248420-G-A		not specified	Likely benign (Mar 24, 2023)
11-61248426-A-C			Likely benign (Mar 01, 2023)
11-61248433-G-T		not specified	Uncertain significance (Apr 09, 2024)
11-61248457-T-C		not specified	Uncertain significance (Feb 28, 2025)
11-61248504-G-A		not specified	Uncertain significance (Jun 07, 2024)
11-61248507-G-A		not specified	Uncertain significance (Jan 29, 2024)
11-61248516-T-C		not specified	Uncertain significance (Aug 02, 2022)
11-61248528-G-A		not specified	Uncertain significance (May 05, 2023)
11-61249694-G-A		not specified	Uncertain significance (May 11, 2022)
11-61249710-G-T		not specified	Uncertain significance (Dec 05, 2022)
11-61249730-G-A		not specified	Uncertain significance (Nov 10, 2024)
11-61249748-G-A		not specified	Uncertain significance (Aug 20, 2024)
11-61249751-C-G		not specified	Uncertain significance (Jun 23, 2021)
11-61249779-G-A		not specified	Uncertain significance (Apr 08, 2022)
11-61249811-G-A		not specified	Uncertain significance (May 27, 2022)
11-61249955-A-C		not specified	Uncertain significance (Oct 31, 2024)
11-61249955-A-G		not specified	Uncertain significance (Feb 15, 2023)
11-61250009-C-A		not specified	Uncertain significance (Sep 18, 2024)
11-61250012-C-A		not specified	Uncertain significance (Jun 16, 2023)
11-61251183-T-C		not specified	Uncertain significance (Aug 20, 2024)
11-61251240-G-A		not specified	Uncertain significance (Sep 04, 2024)
11-61251240-G-C		not specified	Uncertain significance (Jan 16, 2025)
11-61251250-A-C		not specified	Uncertain significance (Aug 02, 2023)
11-61251262-G-C		not specified	Uncertain significance (Dec 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGA5	protein_coding	protein_coding	ENST00000312403	9	10407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.61e-10	0.0161	125333	6	251	125590	0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.432	125	112	1.11	0.00000723	2528
Missense in Polyphen		49	39.615	1.2369		948
Synonymous	-0.519	51	46.5	1.10	0.00000358	787
Loss of Function	-1.30	12	8.02	1.50	4.81e-7	193

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000812	0.000812
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000888	0.0000881
Middle Eastern	0.000326	0.000326
South Asian	0.00712	0.00698
Other	0.000335	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Shows particularly broad specificity; although bonds involving phenylalanine and leucine are preferred, many others are also cleaved to some extent.
• Pathway: Protein digestion and absorption - Homo sapiens (human);Surfactant metabolism;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.105

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.263

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pga5

Gene ontology

• Biological process: proteolysis;digestion;protein catabolic process;cellular protein metabolic process
• Cellular component: extracellular exosome;multivesicular body lumen
• Molecular function: aspartic-type endopeptidase activity;peptidase activity