PDZRN3 (PDZ domain containing ring finger 3)

Gene

• Entrez ID: 23024
• Gene name: PDZ domain containing ring finger 3
• Gene symbol: PDZRN3
• Synonyms: LNX3, SEMACAP3, SEMCAP3
• Chromosome: 3
• Chromosome location: 3p13
• Summary: This gene encodes a member of the LNX (Ligand of Numb Protein-X) family of RING-type ubiquitin E3 ligases. This protein may function in vascular morphogenesis and the differentiation of adipocytes, osteoblasts and myoblasts. This protein may be targeted f

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs747762087	T>A,G	Likely-pathogenic	Missense variant, coding sequence variant
rs748809996	C>T	Likely-pathogenic	Missense variant, coding sequence variant, genic upstream transcript variant
rs778037798	A>G	Likely-pathogenic	Intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT048113	hsa-miR-197-3p	CLASH	23622248
MIRT1224097	hsa-miR-136	CLIP-seq
MIRT1224098	hsa-miR-140-5p	CLIP-seq
MIRT1224099	hsa-miR-1537	CLIP-seq
MIRT1224100	hsa-miR-1827	CLIP-seq
MIRT1224101	hsa-miR-298	CLIP-seq
MIRT1224102	hsa-miR-3074-5p	CLIP-seq
MIRT1224103	hsa-miR-3124-3p	CLIP-seq
MIRT1224104	hsa-miR-3545-5p	CLIP-seq
MIRT1224105	hsa-miR-3663-3p	CLIP-seq
MIRT1224106	hsa-miR-3692	CLIP-seq
MIRT1224107	hsa-miR-3924	CLIP-seq
MIRT1224108	hsa-miR-4282	CLIP-seq
MIRT1224109	hsa-miR-4460	CLIP-seq
MIRT1224110	hsa-miR-4536	CLIP-seq
MIRT1224111	hsa-miR-486-5p	CLIP-seq
MIRT1224112	hsa-miR-940	CLIP-seq
MIRT2065333	hsa-miR-1912	CLIP-seq
MIRT2065334	hsa-miR-296-3p	CLIP-seq
MIRT2065335	hsa-miR-450b-5p	CLIP-seq
MIRT2065336	hsa-miR-518a-5p	CLIP-seq
MIRT2065337	hsa-miR-527	CLIP-seq
MIRT2065334	hsa-miR-296-3p	CLIP-seq
MIRT2591196	hsa-miR-1269	CLIP-seq
MIRT2591197	hsa-miR-1269b	CLIP-seq
MIRT2065333	hsa-miR-1912	CLIP-seq
MIRT2591198	hsa-miR-2682	CLIP-seq
MIRT2065334	hsa-miR-296-3p	CLIP-seq
MIRT2591199	hsa-miR-300	CLIP-seq
MIRT2591200	hsa-miR-3148	CLIP-seq
MIRT2591201	hsa-miR-34a	CLIP-seq
MIRT2591202	hsa-miR-34c-5p	CLIP-seq
MIRT2591203	hsa-miR-3676	CLIP-seq
MIRT2591204	hsa-miR-381	CLIP-seq
MIRT2591205	hsa-miR-4423-3p	CLIP-seq
MIRT2591206	hsa-miR-449a	CLIP-seq
MIRT2591207	hsa-miR-449b	CLIP-seq
MIRT2591208	hsa-miR-449c	CLIP-seq
MIRT2065335	hsa-miR-450b-5p	CLIP-seq
MIRT2591209	hsa-miR-4520b-3p	CLIP-seq
MIRT2591210	hsa-miR-4529-3p	CLIP-seq
MIRT2591211	hsa-miR-4666-3p	CLIP-seq
MIRT2065336	hsa-miR-518a-5p	CLIP-seq
MIRT2065337	hsa-miR-527	CLIP-seq
MIRT2591212	hsa-miR-548ae	CLIP-seq
MIRT2591213	hsa-miR-548aj	CLIP-seq
MIRT2591214	hsa-miR-548am	CLIP-seq
MIRT2591215	hsa-miR-548x	CLIP-seq
MIRT2591216	hsa-miR-599	CLIP-seq
MIRT1224112	hsa-miR-940	CLIP-seq
MIRT2591196	hsa-miR-1269	CLIP-seq
MIRT2591197	hsa-miR-1269b	CLIP-seq
MIRT2065333	hsa-miR-1912	CLIP-seq
MIRT2591198	hsa-miR-2682	CLIP-seq
MIRT2065334	hsa-miR-296-3p	CLIP-seq
MIRT2591201	hsa-miR-34a	CLIP-seq
MIRT2591202	hsa-miR-34c-5p	CLIP-seq
MIRT2591205	hsa-miR-4423-3p	CLIP-seq
MIRT2591206	hsa-miR-449a	CLIP-seq
MIRT2591207	hsa-miR-449b	CLIP-seq
MIRT2591208	hsa-miR-449c	CLIP-seq
MIRT2065335	hsa-miR-450b-5p	CLIP-seq
MIRT2591209	hsa-miR-4520b-3p	CLIP-seq
MIRT2591210	hsa-miR-4529-3p	CLIP-seq
MIRT2065336	hsa-miR-518a-5p	CLIP-seq
MIRT2065337	hsa-miR-527	CLIP-seq
MIRT2591216	hsa-miR-599	CLIP-seq
MIRT1224112	hsa-miR-940	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004842	Function	Ubiquitin-protein transferase activity	ISS
GO:0005737	Component	Cytoplasm	IEA
GO:0007528	Process	Neuromuscular junction development	IBA	21873635
GO:0008270	Function	Zinc ion binding	IEA
GO:0016567	Process	Protein ubiquitination	IBA	21873635
GO:0016567	Process	Protein ubiquitination	IEA
GO:0016567	Process	Protein ubiquitination	ISS
GO:0031594	Component	Neuromuscular junction	IBA	21873635
GO:0061630	Function	Ubiquitin protein ligase activity	IBA	21873635

Other IDs

• MIM: 609729
• HGNC: 17704
• e!Ensembl: ENSG00000121440

Protein

• UniProt ID: Q9UPQ7
• Protein name: E3 ubiquitin-protein ligase PDZRN3 (EC 2.3.2.27) (Ligand of Numb protein X 3) (PDZ domain-containing RING finger protein 3) (RING-type E3 ubiquitin transferase PDZRN3) (Semaphorin cytoplasmic domain-associated protein 3) (Protein SEMACAP3)
• Protein 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 differentia
• PDB: 1UHP, 1WH1
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13923	zf-C3HC4_2	17 → 56		Domain
  PF00595	PDZ	249 → 336	PDZ domain	Domain
  PF00595	PDZ	419 → 501	PDZ domain	Domain

• Sequence:

  MGFELDRFDGDVDPDLKCALCHKVLEDPLTTPCGHVFCAGCVLPWVVQEGSCPARCRGRL
  SAKELNHVLPLKRLILKLDIKCAYATRGCGRVVKLQQLPEHLERCDFAPARCRHAGCGQV
  LLRRDVEAHMRDACDARPVGRCQEGCGLPLTHGEQRAGGHCCARALRAHNGALQARLGAL
  HKALKKEALRAGKREKSLVAQLAAAQLELQMTALRYQKKFTEYSARLDSLSRCVAAPPGG
  KGEETKSLTLVLHRDSGSLGFNIIGGRPSVDNHDGSSSEGIFVSKIVDSGPAAKEGGLQI
  HDRIIEVNGRDLSRATHDQAVEAFKTAKEPIVVQVLRRTPRTKMFTPPSESQLVDTGTQT
  DITFEHIMALTKMSSPSPPVLDPYLLPEEHPSAHEYYDPNDYIGDIHQEMDREELELEEV
  DLYRMNSQDKLGLTVCYRTDDEDDIGIYISEIDPNSIAAKDGRIREGDRIIQINGIEVQN
  REEAVALLTSEENKNFSLLIARPELQLDEGWMDDDRNDFLDDLHMDMLEEQHHQAMQFTA
  SVLQQKKHDEDGGTTDTATILSNQHEKDSGVGRTDESTRNDESSEQENNGDDATASSNPL
  AGQRKLTCSQDTLGSGDLPFSNESFISADCTDADYLGIPVDECERFRELLELKCQVKSAT
  PYGLYYPSGPLDAGKSDPESVDKELELLNEELRSIELECLSIVRAHKMQQLKEQYRESWM
  LHNSGFRNYNTSIDVRRHELSDITELPEKSDKDSSSAYNTGESCRSTPLTLEISPDNSLR
  RAAEGISCPSSEGAVGTTEAYGPASKNLLSITEDPEVGTPTYSPSLKELDPNQPLESKER
  RASDGSRSPTPSQKLGSAYLPSYHHSPYKHAHIPAHAQHYQSYMQLIQQKSAVEYAQSQM
  SLVSMCKDLSSPTPSEPRMEWKVKIRSDGTRYITKRPVRDRLLRERALKIREERSGMTTD
  DDAVSEMKMGRYWSKEERKQHLVKAKEQRRRREFMMQSRLDCLKEQQAADDRKEMNILEL
  SHKKMMKKRNKKIFDNWMTIQELLTHGTKSPDGTRVYNSFLSVTTV

• Sequence length: 1066

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Leukemia	Leukemia, Myelocytic, Acute	rs121909646, rs121913488, rs587776834, rs752746786, rs869312821, rs767454740, rs1554564297, rs11978267, rs4132601	27903959
Schizophrenia	Schizophrenia, Childhood	rs74315508, rs74315509, rs13447324, rs1558507406, rs387906932, rs387906933, rs863223354, rs863223355, rs776061422, rs863223349, rs748809996, rs759748655, rs863223353, rs863223350, rs863223356, rs781821239, rs863223348, rs863223346, rs863223347, rs863223351, rs863223352, rs61734270, rs797045205, rs869312829, rs869312830, rs770913157, rs869312832, rs869312831, rs781720548, rs1262969313	26508570

Unknown
Disease name	Disease term	dbSNP ID	References
Kidney failure	Kidney Failure, Chronic		21546767