PGA3

pepsinogen A3, the group of Pepsinogens

Basic information

Region (hg38): 11:61203307-61213098

Links

ENSG00000229859 ∙ NCBI:643834 ∙ OMIM:169710 ∙ HGNC:8885 ∙ Uniprot:P0DJD8 ∙ 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 PGA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGA3 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		1
missense			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	3	0

Variants in PGA3

This is a list of pathogenic ClinVar variants found in the PGA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-61203595-G-A		not specified	Uncertain significance (May 17, 2023)
11-61204138-C-T		not specified	Uncertain significance (Dec 24, 2024)
11-61204139-G-A		not specified	Uncertain significance (Feb 13, 2024)
11-61204153-C-T		not specified	Uncertain significance (Jun 09, 2022)
11-61204232-C-G		not specified	Uncertain significance (Dec 15, 2024)
11-61207571-G-A		not specified	Uncertain significance (May 23, 2024)
11-61207577-G-A		not specified	Uncertain significance (May 23, 2024)
11-61211183-C-T			Likely benign (Mar 01, 2025)
11-61211193-A-G		not specified	Uncertain significance (Feb 09, 2022)
11-61211216-C-T			Likely benign (Feb 01, 2025)
11-61211232-G-A		not specified	Uncertain significance (Jun 30, 2023)
11-61211355-G-T		not specified	Likely benign (Aug 12, 2021)
11-61211393-T-C			Likely benign (Jul 01, 2022)
11-61212592-C-G		not specified	Likely benign (Mar 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGA3	protein_coding	protein_coding	ENST00000325558	9	9792

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.105	0.785	125418	2	6	125426	0.0000319

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	28	50.9	0.550	0.00000234	2481
Missense in Polyphen		6	12.773	0.46974		968
Synonymous	1.15	16	23.0	0.696	0.00000118	765
Loss of Function	1.24	2	4.99	0.401	2.57e-7	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000592	0.0000592
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000539	0.0000462
European (Non-Finnish)	0.0000594	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.0000347	0.0000327
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: 0.104

Haploinsufficiency Scores

• pHI: 0.0804
• hipred: N
• hipred_score: 0.218
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.221

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