Human Gene HSPD1 (ENST00000388968.8_7) from GENCODE V47lift37
  Description: heat shock protein family D (Hsp60) member 1, transcript variant 1 (from RefSeq NM_002156.5)
Gencode Transcript: ENST00000388968.8_7
Gencode Gene: ENSG00000144381.18_16
Transcript (Including UTRs)
   Position: hg19 chr2:198,351,308-198,364,564 Size: 13,257 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr2:198,351,770-198,363,572 Size: 11,803 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:198,351,308-198,364,564)mRNA (may differ from genome)Protein (573 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CH60_HUMAN
DESCRIPTION: RecName: Full=60 kDa heat shock protein, mitochondrial; AltName: Full=60 kDa chaperonin; AltName: Full=Chaperonin 60; Short=CPN60; AltName: Full=Heat shock protein 60; Short=HSP-60; Short=Hsp60; AltName: Full=HuCHA60; AltName: Full=Mitochondrial matrix protein P1; AltName: Full=P60 lymphocyte protein; Flags: Precursor;
FUNCTION: Implicated in mitochondrial protein import and macromolecular assembly. May facilitate the correct folding of imported proteins. May also prevent misfolding and promote the refolding and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix.
SUBUNIT: Interacts with HRAS (By similarity). Interacts with HBV protein X and HTLV-1 protein p40tax. Interacts with ATAD3A.
INTERACTION: P38398:BRCA1; NbExp=2; IntAct=EBI-352528, EBI-349905; P49789:FHIT; NbExp=5; IntAct=EBI-352528, EBI-741760;
SUBCELLULAR LOCATION: Mitochondrion matrix.
DISEASE: Defects in HSPD1 are a cause of spastic paraplegia autosomal dominant type 13 (SPG13) [MIM:605280]. Spastic paraplegia is a degenerative spinal cord disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs.
DISEASE: Defects in HSPD1 are the cause of leukodystrophy hypomyelinating type 4 (HLD4) [MIM:612233]; also called mitochondrial HSP60 chaperonopathy or MitCHAP-60 disease. HLD4 is a severe autosomal recessive hypomyelinating leukodystrophy. Clinically characterized by infantile-onset rotary nystagmus, progressive spastic paraplegia, neurologic regression, motor impairment, profound mental retardation. Death usually occurrs within the first two decades of life.
SIMILARITY: Belongs to the chaperonin (HSP60) family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/HSPD1";
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/HSPD1ID40888ch2q33.html";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: HSPD1
Diseases sorted by gene-association score: leukodystrophy, hypomyelinating, 4* (1686), spastic paraplegia 13, autosomal dominant* (1596), spastic paraplegia 13* (550), chlamydia (33), reactive arthritis (26), vulvovaginitis (21), salpingitis (20), mycobacterium fortuitum (18), opportunistic bacterial infectious disease (17), sennetsu fever (16), paraplegia (15), hypomyelinating leukodystrophy (15), urethritis (14), mycobacterium gordonae (13), inflammatory bowel disease 27 (13), nocardiosis (12), tuberculosis (11), chancroid (11), carrion's disease (11), bartonellosis (11), mixed connective tissue disease (11), connective tissue disease (10), endocarditis (10), leukodystrophy (10), oral lichen planus (9), tic disorder (9), far eastern spotted fever (9), pelvic inflammatory disease (8), kawasaki disease (8), cat-scratch disease (8), whipple disease (8), hereditary spastic paraplegia (8), lyme disease (7), rheumatoid arthritis, systemic juvenile (7), arteriosclerosis (7), human granulocytic anaplasmosis (7), cervicitis (7), mesenteric lymphadenitis (6), lymphoma, malt, somatic (6), fallopian tube disease (6), primary bacterial infectious disease (5), cutaneous anthrax (5), ehrlichiosis (5), squamous cell papilloma (5), behcet syndrome (5), alpha/beta t-cell lymphopenia with gamma/delta t-cell expansion, severe cytomegalovirus infection, and autoimmunity (5), corneal dystrophy, subepithelial mucinous (4), periodontal disease (4), holoprosencephaly 3 (4), diabetes mellitus, insulin-dependent (4), sudden infant death syndrome (4), mitochondrial disorders (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 308.67 RPKM in Adrenal Gland
Total median expression: 3507.37 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -9.9061-0.162 Picture PostScript Text
3' UTR -101.60462-0.220 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR018370 - Chaperonin_Cpn60_CS
IPR001844 - Chaprnin_Cpn60
IPR002423 - Cpn60/TCP-1

Pfam Domains:
PF00118 - TCP-1/cpn60 chaperonin family

SCOP Domains:
48592 - GroEL equatorial domain-like
100934 - Heat shock protein 70kD (HSP70), C-terminal subdomain
52029 - GroEL apical domain-like
54849 - GroEL-intermediate domain like

ModBase Predicted Comparative 3D Structure on P10809
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0001530 lipopolysaccharide binding
GO:0002039 p53 binding
GO:0003688 DNA replication origin binding
GO:0003697 single-stranded DNA binding
GO:0003723 RNA binding
GO:0003725 double-stranded RNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008035 high-density lipoprotein particle binding
GO:0016787 hydrolase activity
GO:0016887 ATPase activity
GO:0019899 enzyme binding
GO:0031625 ubiquitin protein ligase binding
GO:0034185 apolipoprotein binding
GO:0034186 apolipoprotein A-I binding
GO:0044183 protein binding involved in protein folding
GO:0051082 unfolded protein binding
GO:0051087 chaperone binding

Biological Process:
GO:0002368 B cell cytokine production
GO:0002755 MyD88-dependent toll-like receptor signaling pathway
GO:0002842 positive regulation of T cell mediated immune response to tumor cell
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006457 protein folding
GO:0006458 'de novo' protein folding
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0006986 response to unfolded protein
GO:0008637 apoptotic mitochondrial changes
GO:0009409 response to cold
GO:0016032 viral process
GO:0032727 positive regulation of interferon-alpha production
GO:0032729 positive regulation of interferon-gamma production
GO:0032733 positive regulation of interleukin-10 production
GO:0032735 positive regulation of interleukin-12 production
GO:0032755 positive regulation of interleukin-6 production
GO:0042026 protein refolding
GO:0042100 B cell proliferation
GO:0042110 T cell activation
GO:0042113 B cell activation
GO:0043032 positive regulation of macrophage activation
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0045041 protein import into mitochondrial intermembrane space
GO:0048291 isotype switching to IgG isotypes
GO:0050821 protein stabilization
GO:0050870 positive regulation of T cell activation
GO:0051131 chaperone-mediated protein complex assembly
GO:0051604 protein maturation
GO:0051702 interaction with symbiont
GO:0061077 chaperone-mediated protein folding
GO:0044406 adhesion of symbiont to host

Cellular Component:
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005769 early endosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005905 clathrin-coated pit
GO:0009986 cell surface
GO:0016020 membrane
GO:0030135 coated vesicle
GO:0030141 secretory granule
GO:0032991 macromolecular complex
GO:0046696 lipopolysaccharide receptor complex
GO:0070062 extracellular exosome
GO:0019907 cyclin-dependent protein kinase activating kinase holoenzyme complex


-  Descriptions from all associated GenBank mRNAs
  BC047350 - Homo sapiens heat shock 60kDa protein 1 (chaperonin), mRNA (cDNA clone IMAGE:4214709).
BC067082 - Homo sapiens heat shock 60kDa protein 1 (chaperonin), mRNA (cDNA clone MGC:71259 IMAGE:4025725), complete cds.
BC073746 - Homo sapiens heat shock 60kDa protein 1 (chaperonin), mRNA (cDNA clone MGC:88749 IMAGE:6372068), complete cds.
BC003030 - Homo sapiens heat shock 60kDa protein 1 (chaperonin), mRNA (cDNA clone MGC:4335 IMAGE:2821157), complete cds.
GQ900893 - Homo sapiens clone HEL-T-5 epididymis secretory sperm binding protein mRNA, complete cds.
BC002676 - Homo sapiens heat shock 60kDa protein 1 (chaperonin), mRNA (cDNA clone MGC:4084 IMAGE:3609039), complete cds.
BX647145 - Homo sapiens mRNA; cDNA DKFZp779D1616 (from clone DKFZp779D1616).
LP895419 - Sequence 283 from Patent EP3253886.
M22382 - Human mitochondrial matrix protein P1 (nuclear encoded) mRNA, complete cds.
M34664 - Human chaperonin (HSP60) mRNA, complete cds.
JD304804 - Sequence 285828 from Patent EP1572962.
AK298844 - Homo sapiens cDNA FLJ51046 complete cds, highly similar to 60 kDa heat shock protein, mitochondrial precursor.
JD490114 - Sequence 471138 from Patent EP1572962.
JD111151 - Sequence 92175 from Patent EP1572962.
JD440678 - Sequence 421702 from Patent EP1572962.
JD041970 - Sequence 22994 from Patent EP1572962.
JD236605 - Sequence 217629 from Patent EP1572962.
JD236604 - Sequence 217628 from Patent EP1572962.
AK298632 - Homo sapiens cDNA FLJ54373 complete cds, highly similar to 60 kDa heat shock protein, mitochondrial precursor.
JD555435 - Sequence 536459 from Patent EP1572962.
JD403684 - Sequence 384708 from Patent EP1572962.
AK297305 - Homo sapiens cDNA FLJ54912 complete cds, highly similar to 60 kDa heat shock protein, mitochondrial precursor.
JD090857 - Sequence 71881 from Patent EP1572962.
KJ905788 - Synthetic construct Homo sapiens clone ccsbBroadEn_15458 HSPD1 gene, encodes complete protein.
EU719626 - Homo sapiens mitochondrial heat shock 60kD protein 1 variant 1 (HSPD1) mRNA, complete cds, alternatively spliced; nuclear gene for mitochondrial product.
AK312240 - Homo sapiens cDNA, FLJ92534, highly similar to Homo sapiens heat shock 60kDa protein 1 (chaperonin) (HSPD1), mRNA.
DQ893414 - Synthetic construct clone IMAGE:100006044; FLH199495.01X; RZPDo839E0382D heat shock 60kDa protein 1 (chaperonin) (HSPD1) gene, encodes complete protein.
KJ891406 - Synthetic construct Homo sapiens clone ccsbBroadEn_00800 HSPD1 gene, encodes complete protein.
KJ897020 - Synthetic construct Homo sapiens clone ccsbBroadEn_06414 HSPD1 gene, encodes complete protein.
KR709877 - Synthetic construct Homo sapiens clone CCSBHm_00007062 HSPD1 (HSPD1) mRNA, encodes complete protein.
KR709878 - Synthetic construct Homo sapiens clone CCSBHm_00007063 HSPD1 (HSPD1) mRNA, encodes complete protein.
KR709879 - Synthetic construct Homo sapiens clone CCSBHm_00007064 HSPD1 (HSPD1) mRNA, encodes complete protein.
DQ896771 - Synthetic construct Homo sapiens clone IMAGE:100011231; FLH199401.01L; RZPDo839E0381D heat shock 60kDa protein 1 (chaperonin) (HSPD1) gene, encodes complete protein.
AB527645 - Synthetic construct DNA, clone: pF1KB5558, Homo sapiens HSPD1 gene for heat shock 60kDa protein 1, without stop codon, in Flexi system.
KU178139 - Homo sapiens heat shock 60kDa protein 1 isoform 1 (HSPD1) mRNA, partial cds.
KU178140 - Homo sapiens heat shock 60kDa protein 1 isoform 2 (HSPD1) mRNA, complete cds, alternatively spliced.
KU178141 - Homo sapiens heat shock 60kDa protein 1 isoform 4 (HSPD1) mRNA, complete cds, alternatively spliced.
JD314982 - Sequence 296006 from Patent EP1572962.
JD168484 - Sequence 149508 from Patent EP1572962.
AK298368 - Homo sapiens cDNA FLJ51028 complete cds, highly similar to 60 kDa heat shock protein, mitochondrial precursor.
JD560035 - Sequence 541059 from Patent EP1572962.
LF355963 - JP 2014500723-A/163466: Polycomb-Associated Non-Coding RNAs.
CU678108 - Synthetic construct Homo sapiens gateway clone IMAGE:100017412 5' read HSPD1 mRNA.
JD023501 - Sequence 4525 from Patent EP1572962.
JD033173 - Sequence 14197 from Patent EP1572962.
CU678338 - Synthetic construct Homo sapiens gateway clone IMAGE:100020338 5' read HSPD1 mRNA.
LF355966 - JP 2014500723-A/163469: Polycomb-Associated Non-Coding RNAs.
AK301276 - Homo sapiens cDNA FLJ52281 complete cds, highly similar to 60 kDa heat shock protein, mitochondrial precursor.
MA591540 - JP 2018138019-A/163466: Polycomb-Associated Non-Coding RNAs.
MA591543 - JP 2018138019-A/163469: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P10809 (Reactome details) participates in the following event(s):

R-HSA-1268022 TOMM40 complex translocates proteins from the cytosol to the mitochondrial intermembrane space
R-HSA-1299480 Precursor proteins enter TIMM23 PAM
R-HSA-1299475 TIMM23 PAM translocates proteins from the mitochndrial intermebrane space to the mitochondrial matrix
R-HSA-1299478 MPP cleaves targeting peptide (presequence) of matrix precursors
R-HSA-8869496 TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation
R-HSA-1268020 Mitochondrial protein import
R-HSA-8864260 Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors
R-HSA-392499 Metabolism of proteins
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5M6, B7Z712, CH60_HUMAN, ENST00000388968.1, ENST00000388968.2, ENST00000388968.3, ENST00000388968.4, ENST00000388968.5, ENST00000388968.6, ENST00000388968.7, HSP60, NM_002156, P10809, Q38L19, Q9UCR6, uc318tbo.1, uc318tbo.2
UCSC ID: ENST00000388968.8_7
RefSeq Accession: NM_002156.5
Protein: P10809 (aka CH60_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene HSPD1:
hsp (Hereditary Spastic Paraplegia Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.