PJA2

praja ring finger ubiquitin ligase 2, the group of Ring finger proteins

Basic information

Region (hg38): 5:109334712-109409974

Previous symbols: [ "RNF131" ]

Links

ENSG00000198961 ∙ NCBI:9867 ∙ OMIM:619341 ∙ HGNC:17481 ∙ Uniprot:O43164 ∙ 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 PJA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PJA2 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			34			34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	0	0

Variants in PJA2

This is a list of pathogenic ClinVar variants found in the PJA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-109337295-G-A		not specified	Uncertain significance (Jun 07, 2024)
5-109344287-G-C		not specified	Uncertain significance (Apr 08, 2023)
5-109355935-G-A		not specified	Uncertain significance (Feb 13, 2023)
5-109356003-C-G		not specified	Uncertain significance (Nov 17, 2022)
5-109362916-G-A		not specified	Uncertain significance (Jun 28, 2022)
5-109362994-T-C		not specified	Uncertain significance (May 27, 2022)
5-109368603-C-T		not specified	Uncertain significance (Feb 13, 2024)
5-109368635-A-T		not specified	Uncertain significance (Jan 02, 2024)
5-109368693-C-T		not specified	Uncertain significance (Dec 06, 2022)
5-109368709-G-A		not specified	Uncertain significance (Mar 30, 2024)
5-109378243-C-T		not specified	Uncertain significance (Aug 16, 2022)
5-109378267-A-G		not specified	Uncertain significance (May 28, 2024)
5-109378375-T-C		not specified	Uncertain significance (Nov 10, 2022)
5-109378406-A-C		not specified	Uncertain significance (May 20, 2024)
5-109378451-A-G		not specified	Uncertain significance (May 18, 2022)
5-109378457-G-C		not specified	Uncertain significance (May 18, 2023)
5-109378474-G-A		not specified	Uncertain significance (Apr 07, 2022)
5-109378496-T-C		not specified	Uncertain significance (Sep 14, 2022)
5-109378505-C-A		not specified	Uncertain significance (Aug 08, 2022)
5-109378570-T-C		not specified	Uncertain significance (Jan 24, 2024)
5-109378630-G-C		not specified	Uncertain significance (Nov 22, 2021)
5-109378690-C-T		not specified	Uncertain significance (Mar 26, 2024)
5-109378708-G-A		not specified	Uncertain significance (Dec 01, 2022)
5-109378738-T-C		not specified	Uncertain significance (Dec 07, 2023)
5-109378798-A-T		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PJA2	protein_coding	protein_coding	ENST00000361189	9	75286

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0237	0.976	125729	0	15	125744	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.426	339	362	0.937	0.0000165	4709
Missense in Polyphen		38	87.29	0.43533		1193
Synonymous	-0.982	138	124	1.11	0.00000568	1274
Loss of Function	3.69	9	31.3	0.288	0.00000139	410

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000909	0.0000909
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.000163	0.000163
South Asian	0.000166	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has E2-dependent E3 ubiquitin-protein ligase activity. Responsible for ubiquitination of cAMP-dependent protein kinase type I and type II-alpha/beta regulatory subunits and for targeting them for proteasomal degradation. Essential for PKA- mediated long-term memory processes. Through the ubiquitination of MFHAS1, positively regulates the TLR2 signaling pathway that leads to the activation of the downstream p38 and JNK MAP kinases and promotes the polarization of macrophages toward the pro- inflammatory M1 phenotype (PubMed:28471450). {ECO:0000269|PubMed:12036302, ECO:0000269|PubMed:21423175, ECO:0000269|PubMed:28471450}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.0951

Intolerance Scores

• loftool: 0.489
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.98

Haploinsufficiency Scores

• pHI: 0.324
• hipred: Y
• hipred_score: 0.583
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pja2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; skeleton phenotype; immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: pja2
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: deformed

Gene ontology

• Biological process: inflammatory response;long-term memory;regulation of protein kinase A signaling;protein ubiquitination;positive regulation of toll-like receptor 2 signaling pathway;hippo signaling;regulation of macrophage activation;innate immune response;positive regulation of JNK cascade;positive regulation of p38MAPK cascade
• Cellular component: Golgi membrane;cytoplasm;endoplasmic reticulum membrane;plasma membrane;postsynaptic density;cell junction;intermediate filament cytoskeleton;postsynaptic membrane
• Molecular function: ubiquitin-protein transferase activity;protein binding;protein kinase A catalytic subunit binding;protein kinase A regulatory subunit binding;metal ion binding;ubiquitin protein ligase activity