PDZRN4

PDZ domain containing ring finger 4, the group of PDZ domain containing|Ring finger proteins

Basic information

Region (hg38): 12:41188320-41574745

Links

ENSG00000165966 ∙ NCBI:29951 ∙ OMIM:609730 ∙ HGNC:30552 ∙ Uniprot:Q6ZMN7 ∙ 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 PDZRN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZRN4 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			68	1		69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	1	0

Variants in PDZRN4

This is a list of pathogenic ClinVar variants found in the PDZRN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-41188505-A-G		not specified	Uncertain significance (Dec 07, 2021)
12-41188520-G-A		not specified	Uncertain significance (Dec 12, 2023)
12-41188534-G-C		not specified	Uncertain significance (Dec 28, 2023)
12-41188585-C-T		not specified	Uncertain significance (Jan 29, 2024)
12-41188626-G-T		not specified	Uncertain significance (Dec 20, 2023)
12-41188636-C-G		not specified	Uncertain significance (Dec 15, 2023)
12-41188727-C-T		not specified	Uncertain significance (Nov 05, 2021)
12-41188733-G-A		not specified	Uncertain significance (Jan 16, 2024)
12-41188762-C-G		not specified	Uncertain significance (Apr 11, 2023)
12-41188780-G-A		not specified	Uncertain significance (Jun 18, 2021)
12-41188786-C-G		not specified	Uncertain significance (Jan 03, 2024)
12-41188796-G-A		not specified	Uncertain significance (Jun 07, 2023)
12-41188802-G-C		not specified	Uncertain significance (Dec 03, 2021)
12-41188805-G-C		not specified	Uncertain significance (Jan 03, 2024)
12-41188822-G-C		not specified	Uncertain significance (May 20, 2024)
12-41188846-G-C		not specified	Uncertain significance (Jun 03, 2024)
12-41188849-G-A		not specified	Uncertain significance (Jun 11, 2021)
12-41188849-G-C		not specified	Uncertain significance (Jan 24, 2024)
12-41188859-C-G		not specified	Uncertain significance (Mar 29, 2023)
12-41188889-C-A		not specified	Uncertain significance (Dec 19, 2022)
12-41188915-T-G		not specified	Uncertain significance (Oct 19, 2021)
12-41189014-C-T		not specified	Uncertain significance (Jul 11, 2023)
12-41189071-T-A		not specified	Uncertain significance (Dec 14, 2023)
12-41506460-A-G		not specified	Uncertain significance (Jul 14, 2021)
12-41506519-A-G		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDZRN4	protein_coding	protein_coding	ENST00000402685	10	386143

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.14e-7	1.00	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0596	535	531	1.01	0.0000289	6743
Missense in Polyphen		211	221.37	0.95313		2577
Synonymous	-0.130	205	203	1.01	0.0000111	1949
Loss of Function	3.61	18	43.7	0.412	0.00000258	521

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000376	0.000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.000450	0.000435
Finnish	0.000178	0.000139
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000450	0.000435
South Asian	0.000243	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.733
• rvis_EVS: 1.41
• rvis_percentile_EVS: 94.77

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.436
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.301

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdzrn4

Gene ontology

• Biological process: protein ubiquitination
• Molecular function: metal ion binding;ubiquitin protein ligase activity