PGA4

pepsinogen A4, the group of Pepsinogens

Basic information

Region (hg38): 11:61222347-61231694

Links

ENSG00000229183 ∙ NCBI:643847 ∙ OMIM:169720 ∙ HGNC:8886 ∙ Uniprot:P0DJD7 ∙ 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 PGA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGA4 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in PGA4

This is a list of pathogenic ClinVar variants found in the PGA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61230205-A-G		not specified	Uncertain significance (Mar 07, 2025)
11-61230238-G-A		not specified	Uncertain significance (Aug 02, 2022)
11-61230248-G-A		not specified	Uncertain significance (Aug 02, 2023)
11-61231421-C-G		not specified	Likely benign (Apr 12, 2022)
11-61231490-G-A		not specified	Uncertain significance (Jan 19, 2025)
11-61231506-A-T		not specified	Uncertain significance (Jul 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGA4	protein_coding	protein_coding	ENST00000378149	9	29242

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.305	0.500	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.155	5	4.11	1.22	2.16e-7	2516
Missense in Polyphen		2	1.1901	1.6805		1021
Synonymous	0.0162	2	2.03	0.986	1.44e-7	787
Loss of Function	0.445	0	0.231	0.00	9.78e-9	192

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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: 0.207

Haploinsufficiency Scores

• pHI: 0.156
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

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