PA2G4

proliferation-associated 2G4, the group of M24 metallopeptidase family

Basic information

Region (hg38): 12:56104537-56113910

Links

ENSG00000170515

∙ NCBI:5036 ∙ OMIM:602145 ∙ HGNC:8550 ∙ Uniprot:Q9UQ80 ∙ 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 PA2G4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PA2G4 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 clinvar			3
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	0	0

Variants in PA2G4

This is a list of pathogenic ClinVar variants found in the PA2G4 region.

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

Position	Phenotype	Significance	ClinVar
12-56106992-A-G	not specified	Uncertain significance (Feb 12, 2025)	3884993
12-56109923-C-T	not specified	Uncertain significance (Nov 03, 2022)	2322061
12-56111227-A-G	not specified	Uncertain significance (May 12, 2024)	3303842
12-56111262-C-T	not specified	Uncertain significance (May 21, 2024)	3303843
12-56111275-A-G	not specified	Uncertain significance (Feb 20, 2025)	3884994

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PA2G4	protein_coding	protein_coding	ENST00000303305	13	9589

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00124	125745	0	2	125747	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.52	74	222	0.334	0.0000113	2619
Missense in Polyphen		6	53.461	0.11223		715
Synonymous	1.33	65	80.1	0.811	0.00000427	715
Loss of Function	4.34	1	23.9	0.0419	0.00000117	289

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)	0.0000183	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May play a role in a ERBB3-regulated signal transduction pathway. Seems be involved in growth regulation. Acts a corepressor of the androgen receptor (AR) and is regulated by the ERBB3 ligand neuregulin-1/heregulin (HRG). Inhibits transcription of some E2F1-regulated promoters, probably by recruiting histone acetylase (HAT) activity. Binds RNA. Associates with 28S, 18S and 5.8S mature rRNAs, several rRNA precursors and probably U3 small nucleolar RNA. May be involved in regulation of intermediate and late steps of rRNA processing. May be involved in ribosome assembly. Mediates cap-independent translation of specific viral IRESs (internal ribosomal entry site) (By similarity). Regulates cell proliferation, differentiation, and survival. Isoform 1 suppresses apoptosis whereas isoform 2 promotes cell differentiation (By similarity). {ECO:0000250|UniProtKB:P50580, ECO:0000250|UniProtKB:Q6AYD3, ECO:0000269|PubMed:11268000, ECO:0000269|PubMed:12682367, ECO:0000269|PubMed:15064750, ECO:0000269|PubMed:15583694, ECO:0000269|PubMed:16832058}.;
Pathway: Neutrophil degranulation;Innate Immune System;Immune System;Coregulation of Androgen receptor activity (Consensus)

Recessive Scores

pRec: 0.223

Intolerance Scores

loftool
rvis_EVS: -0.3
rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

pHI: 0.960
hipred: Y
hipred_score: 0.681
ghis: 0.647

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.444

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pa2g4
Phenotype: growth/size/body region phenotype; cellular phenotype; hematopoietic system phenotype; reproductive system phenotype; limbs/digits/tail phenotype;

Gene ontology

Biological process: rRNA processing;regulation of translation;cell cycle arrest;cell population proliferation;negative regulation of apoptotic process;neutrophil degranulation;positive regulation of cell differentiation;negative regulation of transcription, DNA-templated
Cellular component: extracellular region;nucleus;nucleolus;cytoplasm;membrane;azurophil granule lumen;extracellular exosome
Molecular function: nucleic acid binding;DNA binding;DNA-binding transcription factor activity;RNA binding;protein binding;ubiquitin protein ligase binding