PJA1

praja ring finger ubiquitin ligase 1, the group of Ring finger proteins

Basic information

Region (hg38): X:69160851-69165521

Links

ENSG00000181191 ∙ NCBI:64219 ∙ OMIM:300420 ∙ HGNC:16648 ∙ Uniprot:Q8NG27 ∙ 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 PJA1 gene.

• not_specified (56 variants)
• not_provided (7 variants)
• PJA1-related_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PJA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001032396.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			49	8	2	59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	12	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PJA1	protein_coding	protein_coding	ENST00000361478	1	4943

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.928	0.0724	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	226	273	0.827	0.0000223	4256
Missense in Polyphen		29	66.949	0.43316		1193
Synonymous	2.02	85	112	0.758	0.00000988	1265
Loss of Function	3.39	2	17.2	0.116	0.00000166	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000763	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000244	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000106	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has E2-dependent E3 ubiquitin-protein ligase activity. Ubiquitinates MAGED1 antigen leading to its subsequent degradation by proteasome (By similarity). May be involved in protein sorting. {ECO:0000250, ECO:0000269|PubMed:12036302}.
• Pathway: TGF-beta Signaling Pathway;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;TGF_beta_Receptor (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.396
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.85

Haploinsufficiency Scores

• pHI: 0.0601
• hipred: Y
• hipred_score: 0.681
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pja1
• Phenotype: normal phenotype

Gene ontology

• Biological process: protein ubiquitination;protein catabolic process
• Cellular component: cytoplasm
• Molecular function: protein binding;metal ion binding;ubiquitin protein ligase activity