Human Gene SMCHD1 (ENST00000320876.11_6) from GENCODE V47lift37
  Description: structural maintenance of chromosomes flexible hinge domain containing 1 (from RefSeq NM_015295.3)
Gencode Transcript: ENST00000320876.11_6
Gencode Gene: ENSG00000101596.17_14
Transcript (Including UTRs)
   Position: hg19 chr18:2,655,725-2,805,015 Size: 149,291 Total Exon Count: 48 Strand: +
Coding Region
   Position: hg19 chr18:2,656,075-2,802,550 Size: 146,476 Coding Exon Count: 48 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:2,655,725-2,805,015)mRNA (may differ from genome)Protein (2005 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SMHD1_HUMAN
DESCRIPTION: RecName: Full=Structural maintenance of chromosomes flexible hinge domain-containing protein 1;
FUNCTION: Required for maintenance of X inactivation in females and hypermethylation of CpG islands associated with inactive X. Involved in a pathway that mediates the methylation of a subset of CpG islands slowly and requires the de novo methyltransferase DNMT3B (By similarity).
SUBCELLULAR LOCATION: Chromosome (By similarity). Note=Localizes to Barr body (By similarity).
SEQUENCE CAUTION: Sequence=BAB15202.1; Type=Erroneous initiation; Sequence=BC035774; Type=Frameshift; Positions=1730; Sequence=CAH10538.1; Type=Erroneous initiation;

-  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: SMCHD1
Diseases sorted by gene-association score: bosma arhinia microphthalmia syndrome* (1593), fascioscapulohumeral muscular dystrophy 2, digenic* (1300), arhinia choanal atresia microphthalmia* (400), cryptorchidism* (288), pseudovaginal perineoscrotal hypospadias* (283), facioscapulohumeral muscular dystrophy 1* (279), 18p deletion syndrome (18), microphthalmia (10), muscular dystrophy (6)
* = 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: 19.31 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 393.95 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 -204.60350-0.585 Picture PostScript Text
3' UTR -596.302465-0.242 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
IPR003594 - ATPase-like_ATP-bd
IPR010935 - SMC_hinge

Pfam Domains:
PF06470 - SMC proteins Flexible Hinge Domain
PF13589 - Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

SCOP Domains:
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
75553 - Smc hinge domain

ModBase Predicted Comparative 3D Structure on A6NHR9
FrontTopSide
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    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005524 ATP binding
GO:0016887 ATPase activity

Biological Process:
GO:0009048 dosage compensation by inactivation of X chromosome
GO:0043584 nose development
GO:0051276 chromosome organization
GO:0060821 inactivation of X chromosome by DNA methylation

Cellular Component:
GO:0001740 Barr body
GO:0005694 chromosome
GO:0000784 nuclear chromosome, telomeric region


-  Descriptions from all associated GenBank mRNAs
  CR627458 - Homo sapiens mRNA; cDNA DKFZp686O0631 (from clone DKFZp686O0631).
AK126324 - Homo sapiens cDNA FLJ44350 fis, clone TRACH3006228.
AB014550 - Homo sapiens mRNA for KIAA0650 protein, partial cds.
AL080138 - Homo sapiens mRNA; cDNA DKFZp434K063 (from clone DKFZp434K063).
BC006008 - Homo sapiens, clone IMAGE:4285740, mRNA.
AK025646 - Homo sapiens cDNA: FLJ21993 fis, clone HEP06576.
BC035774 - Homo sapiens cDNA clone IMAGE:5580737, containing frame-shift errors.
KJ902330 - Synthetic construct Homo sapiens clone ccsbBroadEn_11724 SMCHD1 gene, encodes complete protein.
JD333428 - Sequence 314452 from Patent EP1572962.
JD541076 - Sequence 522100 from Patent EP1572962.
JD230966 - Sequence 211990 from Patent EP1572962.
JD297151 - Sequence 278175 from Patent EP1572962.
JD566511 - Sequence 547535 from Patent EP1572962.
JD469671 - Sequence 450695 from Patent EP1572962.
JD181956 - Sequence 162980 from Patent EP1572962.
JD509735 - Sequence 490759 from Patent EP1572962.
JD038022 - Sequence 19046 from Patent EP1572962.
JD298651 - Sequence 279675 from Patent EP1572962.
JD491280 - Sequence 472304 from Patent EP1572962.
JD102557 - Sequence 83581 from Patent EP1572962.
JD172182 - Sequence 153206 from Patent EP1572962.
JD309285 - Sequence 290309 from Patent EP1572962.
JD349376 - Sequence 330400 from Patent EP1572962.
JD457333 - Sequence 438357 from Patent EP1572962.
JD341533 - Sequence 322557 from Patent EP1572962.
JD494508 - Sequence 475532 from Patent EP1572962.
JD325235 - Sequence 306259 from Patent EP1572962.
JD426745 - Sequence 407769 from Patent EP1572962.
JD489074 - Sequence 470098 from Patent EP1572962.
JD477004 - Sequence 458028 from Patent EP1572962.
JD398334 - Sequence 379358 from Patent EP1572962.
JD150143 - Sequence 131167 from Patent EP1572962.
JD150144 - Sequence 131168 from Patent EP1572962.
JD068711 - Sequence 49735 from Patent EP1572962.
JD380708 - Sequence 361732 from Patent EP1572962.
JD300195 - Sequence 281219 from Patent EP1572962.
JD557726 - Sequence 538750 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NHR9, ENST00000320876.1, ENST00000320876.10, ENST00000320876.2, ENST00000320876.3, ENST00000320876.4, ENST00000320876.5, ENST00000320876.6, ENST00000320876.7, ENST00000320876.8, ENST00000320876.9, KIAA0650 , NM_015295, O75141, Q6AHX6, Q6ZTQ8, Q9H6Q2, Q9UG39, SMCHD1 , SMHD1_HUMAN, uc317qyr.1, uc317qyr.2
UCSC ID: ENST00000320876.11_6
RefSeq Accession: NM_015295.3
Protein: A6NHR9 (aka SMHD1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SMCHD1:
fsh (Facioscapulohumeral Muscular Dystrophy)

-  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.