PDZRN3

PDZ domain containing ring finger 3, the group of Zinc fingers TRAF-type|PDZ domain containing|Ring finger proteins

Basic information

Region (hg38): 3:73382431-73624941

Links

ENSG00000121440 ∙ NCBI:23024 ∙ OMIM:609729 ∙ HGNC:17704 ∙ Uniprot:Q9UPQ7 ∙ 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 PDZRN3 gene.

• not_specified (167 variants)
• not_provided (8 variants)
• Short_stature (2 variants)
• Childhood-onset_schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZRN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015009.3. 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				3	2	5
missense		2	164	3	1	170
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)					1	1
Total	0	2	164	6	4

Highest pathogenic variant AF is 0.0000180919

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDZRN3	protein_coding	protein_coding	ENST00000263666	10	242508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0153	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00506	623	623	1.00	0.0000410	6941
Missense in Polyphen		188	219.42	0.85679		2365
Synonymous	-2.02	322	279	1.15	0.0000219	2050
Loss of Function	4.68	5	34.7	0.144	0.00000157	443

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.0000978	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase. Plays an important role in regulating the surface level of MUSK on myotubes. Mediates the ubiquitination of MUSK, promoting its endocytosis and lysosomal degradation. Might contribute to terminal myogenic differentiation. {ECO:0000250|UniProtKB:Q69ZS0}.

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.280
• rvis_EVS: -0.99
• rvis_percentile_EVS: 8.63

Haploinsufficiency Scores

• pHI: 0.472
• hipred: Y
• hipred_score: 0.768
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.741

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdzrn3
• Phenotype: growth/size/body region phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: neuromuscular junction development;protein ubiquitination
• Cellular component: nucleus;nucleoplasm;cytosol;cell junction;neuromuscular junction
• Molecular function: ubiquitin-protein transferase activity;zinc ion binding;ubiquitin protein ligase activity