PJA1

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

Basic information

Region (hg38): X:69160850-69165521

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.

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.

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				4		4
missense			25	3	2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	7	2

Variants in PJA1

This is a list of pathogenic ClinVar variants found in the PJA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-69161314-G-A		not specified	Uncertain significance (Jan 31, 2024)
X-69161322-G-C			Benign (Dec 31, 2019)
X-69161432-C-T		not specified	Uncertain significance (Aug 30, 2022)
X-69161477-C-T		not specified	Uncertain significance (Nov 04, 2021)
X-69161518-A-G		not specified	Uncertain significance (Aug 12, 2022)
X-69161564-C-T		not specified	Uncertain significance (Jan 27, 2022)
X-69161581-G-T		not specified	Uncertain significance (Aug 26, 2022)
X-69161752-T-C		not specified	Uncertain significance (Jan 17, 2024)
X-69161797-T-C		not specified	Uncertain significance (Dec 28, 2022)
X-69161814-C-T			Likely benign (Mar 01, 2022)
X-69161925-G-T		not specified	Uncertain significance (Oct 05, 2023)
X-69161929-C-G		not specified	Uncertain significance (Oct 05, 2021)
X-69161954-C-T			Benign (Dec 31, 2019)
X-69161964-G-A			Likely benign (Sep 01, 2022)
X-69161971-G-A		not specified	Uncertain significance (Oct 16, 2023)
X-69161989-G-A		not specified	Uncertain significance (Feb 12, 2024)
X-69161999-C-T		not specified	Likely benign (Apr 26, 2023)
X-69162074-T-C		not specified	Uncertain significance (Jul 13, 2021)
X-69162113-G-A			Uncertain significance (Sep 21, 2022)
X-69162157-C-T		not specified	Uncertain significance (Apr 26, 2024)
X-69162196-G-T		not specified	Uncertain significance (May 03, 2023)
X-69162209-T-C		not specified	Uncertain significance (Sep 16, 2021)
X-69162211-C-T		not specified	Likely benign (Nov 08, 2021)
X-69162434-C-T		not specified	Uncertain significance (Aug 28, 2023)
X-69162479-G-T		not specified	Uncertain significance (May 02, 2024)

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