Aliases for SCCPDH Gene

Aliases for SCCPDH Gene

  • Saccharopine Dehydrogenase (Putative) 2 3 5
  • Saccharopine Dehydrogenase-Like Oxidoreductase 3 4
  • Epididymis Secretory Sperm Binding Protein 3
  • Probable Saccharopine Dehydrogenase 3
  • EC 1.-.-.- 4
  • CGI-49 3
  • NET11 3

External Ids for SCCPDH Gene

Previous GeneCards Identifiers for SCCPDH Gene

  • GC01P243214
  • GC01P244953
  • GC01P246887
  • GC01P217253

Summaries for SCCPDH Gene

GeneCards Summary for SCCPDH Gene

SCCPDH (Saccharopine Dehydrogenase (Putative)) is a Protein Coding gene. Diseases associated with SCCPDH include Hyperlysinemia, Type I and L-2-Hydroxyglutaric Aciduria. Among its related pathways are Response to elevated platelet cytosolic Ca2+. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity.

Additional gene information for SCCPDH Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCCPDH Gene

Genomics for SCCPDH Gene

GeneHancer (GH) Regulatory Elements for SCCPDH Gene

Promoters and enhancers for SCCPDH 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
GH01J246723 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 514.1 +2.3 2312 6 EP300 SIN3A NRF1 POLR2G GTF2E2 PHF8 ZFX POLR2A ZBTB26 TARDBP SCCPDH ENSG00000260855 KIF28P piR-60921
GH01J246703 Enhancer 1.1 Ensembl ENCODE 12.5 -17.3 -17275 8 EP300 FOXK2 ZNF217 NCOR1 FOS KDM6A FOXA1 KLF4 CUX1 ZBTB25 SCCPDH KIF28P ENSG00000235021 piR-38423-003
GH01J246768 Enhancer 0.8 Ensembl ENCODE 11 +44.8 44759 2.5 CUX1 ZNF316 FOS CEBPB POLR3A RCOR1 TBP RXRA MAX HNF4A HE855972 ENSG00000260855 SCCPDH lnc-CNST-3
GH01J246698 Enhancer 1.2 FANTOM5 ENCODE 6.4 -24.9 -24922 1.5 FOXK2 ZNF217 CTCF ZBTB5 AFF1 TRIM28 REST MEF2C MYC RCOR1 ENSG00000235021 SCCPDH ENSG00000260855 piR-38423-003
GH01J246784 Promoter/Enhancer 0.9 Ensembl ENCODE CraniofacialAtlas 7.5 +61.0 61013 1.8 AGO2 MYC MAX POLR2A lnc-AHCTF1-1 lnc-AHCTF1-2 ENSG00000260855 SCCPDH LINC01341 KIF28P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCCPDH on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCCPDH

Top Transcription factor binding sites by QIAGEN in the SCCPDH gene promoter:
  • E47
  • GATA-1
  • Hand1
  • HFH-1
  • MRF-2
  • Nkx5-1
  • NRSF form 1
  • NRSF form 2
  • TBP

Genomic Locations for SCCPDH Gene

Genomic Locations for SCCPDH Gene
chr1:246,724,076-246,768,137
(GRCh38/hg38)
Size:
44,062 bases
Orientation:
Plus strand
chr1:246,887,349-246,931,439
(GRCh37/hg19)
Size:
44,091 bases
Orientation:
Plus strand

Genomic View for SCCPDH Gene

Genes around SCCPDH on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SCCPDH Gene

Proteins for SCCPDH Gene

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

    Protein Symbol:
    Q8NBX0-SCPDL_HUMAN
    Recommended name:
    Saccharopine dehydrogenase-like oxidoreductase
    Protein Accession:
    Q8NBX0
    Secondary Accessions:
    • Q8TAR0
    • Q9Y363

    Protein attributes for SCCPDH Gene

    Size:
    429 amino acids
    Molecular mass:
    47151 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SCCPDH Gene

Post-translational modifications for SCCPDH Gene

  • Ubiquitination at Lys136, Lys220, Lys242, and Lys394
  • Modification sites at PhosphoSitePlus

Other Protein References for SCCPDH Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SCCPDH Gene

Domains & Families for SCCPDH Gene

Gene Families for SCCPDH Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SCCPDH Gene

Suggested Antigen Peptide Sequences for SCCPDH Gene

GenScript: Design optimal peptide antigens:
  • Saccharopine dehydrogenase (Putative) (Q5VTK4_HUMAN)
  • Probable saccharopine dehydrogenase (SCPDH_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NBX0

UniProtKB/Swiss-Prot:

SCPDL_HUMAN :
  • Belongs to the saccharopine dehydrogenase family.
Family:
  • Belongs to the saccharopine dehydrogenase family.
genes like me logo Genes that share domains with SCCPDH: view

Function for SCCPDH Gene

Enzyme Numbers (IUBMB) for SCCPDH Gene

Phenotypes From GWAS Catalog for SCCPDH Gene

Gene Ontology (GO) - Molecular Function for SCCPDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with SCCPDH: view
genes like me logo Genes that share phenotypes with SCCPDH: view

Animal Model Products

CRISPR Products

miRNA for SCCPDH Gene

miRTarBase miRNAs that target SCCPDH

Inhibitory RNA Products

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

Clone Products

No data available for Molecular function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SCCPDH Gene

Localization for SCCPDH Gene

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 SCCPDH gene
Compartment Confidence
extracellular 4
plasma membrane 3
mitochondrion 2
cytosol 2
cytoskeleton 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SCCPDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005634 nucleus HDA 21630459
GO:0005739 mitochondrion IBA 21873635
GO:0005811 lipid droplet IDA,IBA 14741744
GO:0005886 plasma membrane IBA 21873635
genes like me logo Genes that share ontologies with SCCPDH: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for SCCPDH Gene

Pathways & Interactions for SCCPDH Gene

genes like me logo Genes that share pathways with SCCPDH: view

Gene Ontology (GO) - Biological Process for SCCPDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002576 platelet degranulation TAS --
GO:0009247 glycolipid biosynthetic process IBA 21873635
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with SCCPDH: view

No data available for SIGNOR curated interactions for SCCPDH Gene

Drugs & Compounds for SCCPDH Gene

(2) Drugs for SCCPDH Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
NADH Approved Nutra 0
NAD Experimental Pharma Full agonist, Agonist, Activator 0

(1) Additional Compounds for SCCPDH Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
saccharopine
  • epsilon-N-(L-Glutar-2-yl)-L-lysine
  • N-[(S)-5-amino-5-Carboxypentyl]-L-glutamic acid
  • N6-(L-1,3-Dicarboxypropyl)-L-lysine
  • N-[(S)-5-amino-5-Carboxypentyl]-L-glutamate
  • (S)-N-(5-amino-5-Carboxypentyl)-L-glutamic acid
997-68-2
genes like me logo Genes that share compounds with SCCPDH: view

Transcripts for SCCPDH Gene

mRNA/cDNA for SCCPDH Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13a · 13b
SP1: -
SP2:
SP3: - -
SP4: -

Relevant External Links for SCCPDH Gene

GeneLoc Exon Structure for
SCCPDH

Expression for SCCPDH Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCCPDH Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x4.2).

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



Protein tissue co-expression partners for SCCPDH Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCCPDH

SOURCE GeneReport for Unigene cluster for SCCPDH Gene:

Hs.498397

Evidence on tissue expression from TISSUES for SCCPDH Gene

  • Nervous system(4.9)
  • Liver(4.6)
  • Kidney(2)
genes like me logo Genes that share expression patterns with SCCPDH: view

No data available for Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCCPDH Gene

Orthologs for SCCPDH Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SCCPDH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCCPDH 31 30
  • 99.15 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SCCPDH 31 30
  • 89.12 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SCCPDH 31 30
  • 88.34 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Sccpdh 17 31 30
  • 87.8 (n)
rat
(Rattus norvegicus)
Mammalia LOC100910414 30
  • 86.71 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SCCPDH 31
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SCCPDH 31
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCCPDH 31 30
  • 70.35 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCCPDH 31
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sccpdh 30
  • 69.48 (n)
Str.94 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.7722 30
zebrafish
(Danio rerio)
Actinopterygii sccpdha 31 30
  • 63 (n)
OneToMany
sccpdhb 31
  • 59 (a)
OneToMany
SCCPDH (2 of 3) 31
  • 53 (a)
OneToMany
sbcb4 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002652 30
  • 50.72 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG2604 31 30
  • 48.66 (n)
OneToMany
CG5167 31
  • 37 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea F22F7.1 31 30
  • 47.57 (n)
OneToMany
Y50D4B.2 31
  • 34 (a)
OneToMany
F22F7.2 31
  • 33 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G39410 30
  • 48.55 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 44 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU07563 30
  • 43.12 (n)
Species where no ortholog for SCCPDH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SCCPDH Gene

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

Paralogs for SCCPDH Gene

No data available for Paralogs for SCCPDH Gene

Variants for SCCPDH Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCCPDH Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs7779 - p.Gly418Arg

Additional dbSNP identifiers (rs#s) for SCCPDH Gene

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

Variant ID Type Subtype PubMed ID
esv1000885 CNV deletion 20482838
esv1589537 CNV deletion 17803354
esv1933268 CNV deletion 18987734
esv2443936 CNV deletion 19546169
esv2660077 CNV deletion 23128226
esv2667587 CNV deletion 23128226
esv2727518 CNV deletion 23290073
esv2743351 CNV deletion 23290073
esv2762192 CNV gain 21179565
esv3575872 CNV gain 25503493
esv3589489 CNV loss 21293372
nsv1006262 CNV gain 25217958
nsv160725 CNV deletion 16902084
nsv523531 CNV gain 19592680

Variation tolerance for SCCPDH Gene

Residual Variation Intolerance Score: 53% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.50; 55.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCCPDH Gene

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

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

Disorders for SCCPDH Gene

MalaCards: The human disease database

(3) MalaCards diseases for SCCPDH Gene - From: DISEASES

Disorder Aliases PubMed IDs
hyperlysinemia, type i
  • lysine:alpha-ketoglutarate reductase deficiency
l-2-hydroxyglutaric aciduria
  • l2hga
2-hydroxyglutaric aciduria
  • combined d-2- and l-2-hydroxyglutaric aciduria
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SCCPDH

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SCCPDH: view

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

Publications for SCCPDH Gene

  1. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4 54
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 41 54
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 54
  4. 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 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54

Products for SCCPDH Gene

Sources for SCCPDH Gene