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P3H4 prolyl 3-hydroxylase family member 4 (inactive) [ Homo sapiens (human) ]

Gene ID: 10609, updated on 3-Apr-2024

Summary

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Official Symbol
P3H4provided by HGNC
Official Full Name
prolyl 3-hydroxylase family member 4 (inactive)provided by HGNC
Primary source
HGNC:HGNC:16946
See related
Ensembl:ENSG00000141696 MIM:617419; AllianceGenome:HGNC:16946
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
NO55; SC65; NOL55; LEPREL4
Summary
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]
Expression
Ubiquitous expression in placenta (RPKM 4.3), thyroid (RPKM 4.3) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
17q21.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (41801953..41811949, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (42658495..42669488, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (39958205..39968201, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene huntingtin associated protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39889784-39890326 Neighboring gene RNA, 7SL, cytoplasmic 399, pseudogene Neighboring gene junction plakoglobin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39927459-39927963 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39927964-39928467 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39932003-39932506 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:39942255-39942467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39947785-39948448 Neighboring gene CRISPRi-validated cis-regulatory element chr17.2540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39956106-39956612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39956613-39957119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39971057-39971558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39971559-39972058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39974907-39975818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:39975819-39976730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39977650-39978248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:39978249-39978845 Neighboring gene FKBP prolyl isomerase 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8501 Neighboring gene 5'-nucleotidase, cytosolic IIIB Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8502 Neighboring gene kelch like family member 10

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. P3H4 Overexpression Serves as a Prognostic Factor in Lung Adenocarcinoma. Jin X, et al. Comput Math Methods Med, 2021. PMID 34257701, Free PMC Article
  2. P3H4 is correlated with clinicopathological features and prognosis in bladder cancer. Li W, et al. World J Surg Oncol, 2018 Oct 15. PMID 30322400, Free PMC Article
  3. Identification and characterization of a new autoimmune protein in membranous nephropathy by immunoscreening of a renal cDNA library. Cavazzini F, et al. PLoS One, 2012. PMID 23144993, Free PMC Article
  4. Identification of nucleolar protein No55 as a tumour-associated autoantigen in patients with prostate cancer. Fosså A, et al. Br J Cancer, 2000 Sep. PMID 10952778, Free PMC Article
  5. cDNA cloning and characterization of a novel nucleolar protein. Ochs RL, et al. Mol Biol Cell, 1996 Jul. PMID 8862517, Free PMC Article

See all (34) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. P3H4 and PLOD1 expression associates with poor prognosis in bladder cancer.
    Title: P3H4 and PLOD1 expression associates with poor prognosis in bladder cancer.
  2. P3H4 Overexpression Serves as a Prognostic Factor in Lung Adenocarcinoma.
    Title: P3H4 Overexpression Serves as a Prognostic Factor in Lung Adenocarcinoma.
  3. Knockdown of P3H4 inhibits proliferation and invasion of bladder cancer.
    Title: Knockdown of P3H4 inhibits proliferation and invasion of bladder cancer.
  4. High P3H4 expression is associated with bladder cancer.
    Title: P3H4 is correlated with clinicopathological features and prognosis in bladder cancer.
  5. SC65 protein is identified as an autoimmune target in idiopathic membranous nephropathy.
    Title: Identification and characterization of a new autoimmune protein in membranous nephropathy by immunoscreening of a renal cDNA library.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to collagen binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in bone remodeling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in collagen biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in collagen fibril organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in peptidyl-lysine hydroxylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in peptidyl-lysine hydroxylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in synaptonemal complex assembly TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of catalytic complex IEA
Inferred from Electronic Annotation
more info
  
located_in condensed nuclear chromosome TAS
Traceable Author Statement
more info
 PubMed 
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nucleolus TAS
Traceable Author Statement
more info
 PubMed 
located_in synaptonemal complex TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
endoplasmic reticulum protein SC65
Names
leprecan-like 4
leprecan-like protein 4
nucleolar autoantigen (55kD)
nucleolar autoantigen No55
nucleolar autoantigen, 55kDa
prolyl 3-hydroxylase family member 4 (non-enzymatic)
synaptonemal complex 65
synaptonemal complex protein SC65

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)

  1. NM_006455.3 → NP_006446.1  endoplasmic reticulum protein SC65 precursor

    See identical proteins and their annotated locations for NP_006446.1

    Status: VALIDATED

    Source sequence(s)
    AK056085, BC007942, U47621
    Consensus CDS
    CCDS11408.1
    UniProtKB/Swiss-Prot
    Q53GI6, Q92791, Q9H4F6
    UniProtKB/TrEMBL
    B4DVZ5
    Related
    ENSP00000377505.1, ENST00000393928.6

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    41801953..41811949 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006721640.5 → XP_006721703.2  endoplasmic reticulum protein SC65 isoform X2

  2. XM_047435138.1 → XP_047291094.1  endoplasmic reticulum protein SC65 isoform X1

  3. XM_047435137.1 → XP_047291093.1  endoplasmic reticulum protein SC65 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    42658495..42669488 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314726.1 → XP_054170701.1  endoplasmic reticulum protein SC65 isoform X5

  2. XM_054314724.1 → XP_054170699.1  endoplasmic reticulum protein SC65 isoform X4

  3. XM_054314725.1 → XP_054170700.1  endoplasmic reticulum protein SC65 isoform X2

  4. XM_054314723.1 → XP_054170698.1  endoplasmic reticulum protein SC65 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92791.1 GenPept UniProtKB/Swiss-Prot:Q92791

Gene LinkOut

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