Free for academic non-profit institutions. Other users need a Commercial license

Aliases for P3H4 Gene

Aliases for P3H4 Gene

  • Prolyl 3-Hydroxylase Family Member 4 (Non-Enzymatic) 2 3 5
  • Synaptonemal Complex Protein SC65 3 4
  • Nucleolar Autoantigen (55kD) 2 3
  • Nucleolar Autoantigen No55 3 4
  • Leprecan-Like Protein 4 3 4
  • Leprecan-Like 4 2 3
  • LEPREL4 3 4
  • NOL55 3 4
  • SC65 3 4
  • Prolyl 3-Hydroxylase Family Member 4 4
  • Endoplasmic Reticulum Protein SC65 3
  • Rat Synaptonemal Complex Protein 2
  • Nucleolar Autoantigen, 55kDa 3
  • NO55 3

External Ids for P3H4 Gene

Previous HGNC Symbols for P3H4 Gene

  • LEPREL4

Summaries for P3H4 Gene

Entrez Gene Summary for P3H4 Gene

  • This nucleolar protein was first characterized because it was an autoantigen in cases on interstitial cystitis. The protein, with a predicted molecular weight of 50 kDa, appears to be localized in the particulate compartment of the interphase nucleolus, with a distribution distinct from that of nucleolar protein B23. During mitosis it is associated with chromosomes. [provided by RefSeq, Jul 2008]

GeneCards Summary for P3H4 Gene

P3H4 (Prolyl 3-Hydroxylase Family Member 4 (Non-Enzymatic)) is a Protein Coding gene. Diseases associated with P3H4 include Cystitis. An important paralog of this gene is CRTAP.

UniProtKB/Swiss-Prot for P3H4 Gene

  • Part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linking of collagen fibrils. Required for normal bone density and normal skin stability via its role in hydroxylation of lysine residues in collagen alpha chains and in collagen fibril assembly.

Gene Wiki entry for P3H4 Gene

Additional gene information for P3H4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for P3H4 Gene

Genomics for P3H4 Gene

GeneHancer (GH) Regulatory Elements for P3H4 Gene

Promoters and enhancers for P3H4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J041810 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 665.4 -0.2 -196 4.4 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF766 ZNF213 ZNF207 ZNF143 P3H4 FKBP10 PIR33798 DHX58 NT5C3B CNTD1 CAVIN1 RETREG3 KAT2A HSD17B1
GH17J041687 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 10.4 +122.2 122217 6.1 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 EIF1 GC17P041691 GC17P041692 ENSG00000267758 ENSG00000259623 KLHL10 CNTNAP1 HSD17B1 NT5C3B KAT2A
GH17J042386 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.2 -575.8 -575832 4.3 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 STAT3 GC17M042386 NBR1 ENSG00000267765 ENSG00000267002 KLHL10 HMGN1P29 ENSG00000267758 ENSG00000267340 TUBG2
GH17J042515 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -709.3 -709277 12.2 PKNOX1 SMAD1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 NBR2 MLX TUBG2 ENSG00000266962 ENSG00000267002 CAVIN1 NAGLU ENSG00000267340 RAB5C KAT2A
GH17J041737 Promoter/Enhancer 1.7 VISTA EPDnew ENCODE 11.7 +73.2 73241 3.7 HDGF ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 ZNF766 HAP1 JUP GAST P3H4 FKBP10 KLHL11 KAT2A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around P3H4 on UCSC Golden Path with GeneCards custom track

Genomic Locations for P3H4 Gene

Genomic Locations for P3H4 Gene
chr17:41,801,947-41,812,616
(GRCh38/hg38)
Size:
10,670 bases
Orientation:
Minus strand
chr17:39,958,199-39,968,856
(GRCh37/hg19)
Size:
10,658 bases
Orientation:
Minus strand

Genomic View for P3H4 Gene

Genes around P3H4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
P3H4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for P3H4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for P3H4 Gene

Proteins for P3H4 Gene

  • Protein details for P3H4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92791-SC65_HUMAN
    Recommended name:
    Endoplasmic reticulum protein SC65
    Protein Accession:
    Q92791
    Secondary Accessions:
    • Q53GI6
    • Q9H4F6

    Protein attributes for P3H4 Gene

    Size:
    437 amino acids
    Molecular mass:
    50381 Da
    Quaternary structure:
    • Interacts with PLOD1, P3H3 and PPIB. Identified in a complex with PLOD1 and P3H3.

neXtProt entry for P3H4 Gene

Post-translational modifications for P3H4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for P3H4 Gene

No data available for DME Specific Peptides for P3H4 Gene

Domains & Families for P3H4 Gene

Gene Families for P3H4 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for P3H4 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for P3H4 Gene

Graphical View of Domain Structure for InterPro Entry

Q92791

UniProtKB/Swiss-Prot:

SC65_HUMAN :
  • Belongs to the leprecan family.
Family:
  • Belongs to the leprecan family.
genes like me logo Genes that share domains with P3H4: view

Function for P3H4 Gene

Molecular function for P3H4 Gene

UniProtKB/Swiss-Prot Function:
Part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linking of collagen fibrils. Required for normal bone density and normal skin stability via its role in hydroxylation of lysine residues in collagen alpha chains and in collagen fibril assembly.

Phenotypes From GWAS Catalog for P3H4 Gene

Gene Ontology (GO) - Molecular Function for P3H4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with P3H4: view
genes like me logo Genes that share phenotypes with P3H4: view

Animal Models for P3H4 Gene

MGI Knock Outs for P3H4:
  • P3h4 P3h4<tm1.2Rmr>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for P3H4

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for P3H4 Gene

Localization for P3H4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for P3H4 Gene

Endoplasmic reticulum.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for P3H4 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
extracellular 2
mitochondrion 1
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for P3H4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000794 condensed nuclear chromosome TAS 8862517
GO:0000795 synaptonemal complex TAS,IEA --
GO:0005730 nucleolus TAS 8862517
GO:0005783 endoplasmic reticulum IDA,IEA 23959653
GO:1902494 catalytic complex IEA --
genes like me logo Genes that share ontologies with P3H4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for P3H4 Gene

Pathways & Interactions for P3H4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for P3H4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007130 synaptonemal complex assembly TAS 8862517
GO:0017185 peptidyl-lysine hydroxylation ISS --
GO:0030199 collagen fibril organization ISS --
GO:0032964 collagen biosynthetic process ISS --
GO:0046849 bone remodeling ISS --
genes like me logo Genes that share ontologies with P3H4: view

No data available for Pathways by source and SIGNOR curated interactions for P3H4 Gene

Drugs & Compounds for P3H4 Gene

No Compound Related Data Available

Transcripts for P3H4 Gene

mRNA/cDNA for P3H4 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for P3H4

Alternative Splicing Database (ASD) splice patterns (SP) for P3H4 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b ^ 10
SP1: - - - -
SP2: - - - -
SP3:
SP4:
SP5: - - -
SP6:

Relevant External Links for P3H4 Gene

GeneLoc Exon Structure for
P3H4
ECgene alternative splicing isoforms for
P3H4

Expression for P3H4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for P3H4 Gene

Protein differential expression in normal tissues from HIPED for P3H4 Gene

This gene is overexpressed in Bone (50.1) and Fetal ovary (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for P3H4 Gene



Protein tissue co-expression partners for P3H4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of P3H4 Gene:

P3H4

mRNA Expression by UniProt/SwissProt for P3H4 Gene:

Q92791-SC65_HUMAN
Tissue specificity: Detected in fibroblasts (at protein level) (PubMed:23959653). Detected in spleen, prostate, testis, ovary, colon, pancreas, kidney, placenta and heart (PubMed:10952778).

Evidence on tissue expression from TISSUES for P3H4 Gene

  • Nervous system(4.6)
  • Kidney(4.1)
genes like me logo Genes that share expression patterns with P3H4: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for P3H4 Gene

Orthologs for P3H4 Gene

This gene was present in the common ancestor of animals.

Orthologs for P3H4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LEPREL4 34 33
  • 99.11 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LEPREL4 34
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LEPREL4 34 33
  • 90.21 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Leprel4 34 33
  • 88.03 (n)
OneToOne
P3h4 16
rat
(Rattus norvegicus)
Mammalia Leprel4 33
  • 88.02 (n)
oppossum
(Monodelphis domestica)
Mammalia LEPREL4 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LEPREL4 34
  • 60 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC430099 33
  • 73.74 (n)
LEPREL4 34
  • 66 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LEPREL4 34
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia leprel4 33
  • 64.7 (n)
Str.16255 33
zebrafish
(Danio rerio)
Actinopterygii leprel4 34 33
  • 58.33 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y73F8A.26 34
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 26 (a)
OneToMany
Species where no ortholog for P3H4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for P3H4 Gene

ENSEMBL:
Gene Tree for P3H4 (if available)
TreeFam:
Gene Tree for P3H4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for P3H4: view image

Paralogs for P3H4 Gene

Paralogs for P3H4 Gene

genes like me logo Genes that share paralogs with P3H4: view

Variants for P3H4 Gene

Sequence variations from dbSNP and Humsavar for P3H4 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs114527140 uncertain-significance, Osteogenesis Imperfecta, Recessive 41,812,768(-) G/A/T upstream_transcript_variant
rs533813401 uncertain-significance, Osteogenesis Imperfecta, Recessive 41,812,852(-) C/G upstream_transcript_variant
rs555053677 uncertain-significance, Osteogenesis Imperfecta, Recessive 41,812,858(-) C/G upstream_transcript_variant
rs782363137 uncertain-significance, Osteogenesis Imperfecta, Recessive 41,812,828(-) C/T upstream_transcript_variant
rs886052922 uncertain-significance, Osteogenesis Imperfecta, Recessive 41,812,732(-) G/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for P3H4 Gene

Variant ID Type Subtype PubMed ID
dgv3174n100 CNV gain 25217958
esv2664779 CNV deletion 23128226
esv3640595 CNV loss 21293372
nsv1060502 CNV gain 25217958
nsv1109076 CNV deletion 24896259
nsv1146669 OTHER inversion 26484159
nsv833447 CNV loss 17160897

Variation tolerance for P3H4 Gene

Residual Variation Intolerance Score: 31.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.98; 89.94% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for P3H4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
P3H4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for P3H4 Gene

Disorders for P3H4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for P3H4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
cystitis
  • infective cystitis
- elite association - COSMIC cancer census association via MalaCards
Search P3H4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for P3H4

genes like me logo Genes that share disorders with P3H4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for P3H4 Gene

Publications for P3H4 Gene

  1. cDNA cloning and characterization of a novel nucleolar protein. (PMID: 8862517) Ochs RL … Tan EM (Molecular biology of the cell 1996) 2 3 4 58
  2. Sc65 is a novel endoplasmic reticulum protein that regulates bone mass homeostasis. (PMID: 23959653) Gruenwald K … Morello R (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2014) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Identification of nucleolar protein No55 as a tumour-associated autoantigen in patients with prostate cancer. (PMID: 10952778) Fosså A … Gaudernack G (British journal of cancer 2000) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for P3H4 Gene

Sources for P3H4 Gene

Content
Loading form....