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.

• not_specified (131 variants)

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. These statistics are base on transcript: NM_001164595.2. 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						0
missense			128	3		131
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	128	3	0

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