PDZRN4 PDZ domain containing ring finger 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDZRN4provided by HGNC
Official Full Name: PDZ domain containing ring finger 4provided by HGNC
Primary source: HGNC:HGNC:30552
See related: Ensembl:ENSG00000165966 MIM:609730; AllianceGenome:HGNC:30552
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: LNX4; SAMCAP3L
Summary: Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in prostate (RPKM 5.3), urinary bladder (RPKM 3.3) and 15 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q12

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (41188320..41574745)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (41147522..41533404)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (41582122..41968547)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Results showed that PDZRN4 might be a potential tumour suppressor gene and had anti-proliferative effect on hepatocellular carcinoma cell proliferation.
Title: PDZRN4 acts as a suppressor of cell proliferation in human liver cancer cell lines.
Observational study of gene-disease association. (HuGE Navigator)
Title: Replication of top markers of a genome-wide association study in multiple sclerosis in Spain.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study identifies protein quantitative trait loci (pQTLs). EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study identifies susceptibility loci of silica related pneumoconiosis in Han Chinese. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-106266 (e-PCR)
- UniSTS:169732

D12S1271 (e-PCR)
- UniSTS:69637

G64335 (e-PCR)
- UniSTS:163856

G64336 (e-PCR)
- UniSTS:163857

SHGC-81442 (e-PCR)
- UniSTS:103197

SHGC-146391 (e-PCR)
- UniSTS:175195

RH11208 (e-PCR)
- UniSTS:70239

G62896 (e-PCR)
- UniSTS:139871

WI-21835 (e-PCR)
- UniSTS:74931

SHGC-31383 (e-PCR)
- UniSTS:32987

SHGC-79515 (e-PCR)
- UniSTS:103645

RH123701 (e-PCR)
- UniSTS:135905

G64333 (e-PCR)
- UniSTS:163821

SHGC-57125 (e-PCR)
- UniSTS:2036

G63423 (e-PCR)
- UniSTS:140535

G64334 (e-PCR)
- UniSTS:163837

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: PDZ domain-containing RING finger protein 4

Names: IMAGE5767589; SEMACAP3-like protein; ligand of Numb protein X 4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001164595.2 → NP_001158067.1 PDZ domain-containing RING finger protein 4 isoform 1

See identical proteins and their annotated locations for NP_001158067.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC021651, AC090531, AK294535, AW297403, BX640695

Consensus CDS

CCDS53777.1

UniProtKB/Swiss-Prot

Q52LY3, Q52LY4, Q6N052, Q6ZMN7, Q8IUU1, Q9NTP7

UniProtKB/TrEMBL

B4DGD1

Related

ENSP00000384197.2, ENST00000402685.7

Conserved Domains (4) summary

smart00228
Location:221 → 313

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00162
Location:17 → 54

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

cd00992
Location:402 → 484

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cl19105
Location:66 → 108

Sina; Seven in absentia (Sina) protein family, C-terminal substrate binding domain; composed of the Drosophila Sina protein, the mammalian Sina homolog (Siah), the plant protein SINAT5, and similar proteins. Sina, Siah and SINAT5 are RING-containing proteins ...
NM_013377.4 → NP_037509.3 PDZ domain-containing RING finger protein 4 isoform 2

See identical proteins and their annotated locations for NP_037509.3

Status: VALIDATED

Description

Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses a distinct start codon, compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.

Source sequence(s)

AC090531, AK131554, BC093744, BX640695

Consensus CDS

CCDS8739.1

UniProtKB/TrEMBL

B4DG65

Related

ENSP00000439990.2, ENST00000539469.6

Conserved Domains (2) summary

smart00228
Location:24 → 55

PDZ; Domain present in PSD-95, Dlg, and ZO-1/2

cd00992
Location:144 → 226

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...