About   Help   FAQ
Smchd1 Gene Detail
Summary
  • Symbol
    Smchd1
  • Name
    SMC hinge domain containing 1
  • Synonyms
    4931400A14Rik, mKIAA0650, MommeD1
  • Feature Type
    protein coding gene
  • IDs
    MGI:1921605
    NCBI Gene: 74355
  • Alliance
    gene page
  • Transcription Start Sites
    8 TSS
Location &
Maps
more
  • Sequence Map
    Chr17:71651484-71782338 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 17, 41.87 cM
  • Mapping Data
    3 experiments
Strain
Comparison
more
  • SNPs within 2kb
    4063 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1921605
 protein coding gene Chr17:71651484-71782361 (-)
129S1/SvImJ MGP_129S1SvImJ_G0024007
 protein coding gene Chr17:73785398-73929541 (-)
A/J MGP_AJ_G0023965
 protein coding gene Chr17:71552377-71689701 (-)
AKR/J MGP_AKRJ_G0023934
 protein coding gene Chr17:72525147-72656269 (-)
BALB/cJ MGP_BALBcJ_G0023966
 protein coding gene Chr17:71453248-71586165 (-)
C3H/HeJ MGP_C3HHeJ_G0023730
 protein coding gene Chr17:73480859-73612882 (-)
C57BL/6NJ MGP_C57BL6NJ_G0024412
 protein coding gene Chr17:76484118-76625773 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0021857
 protein coding gene Chr17:67320041-67443898 (-)
CAST/EiJ MGP_CASTEiJ_G0023211
 protein coding gene Chr17:73913136-74046607 (-)
CBA/J MGP_CBAJ_G0023705
 protein coding gene Chr17:79660741-79820141 (-)
DBA/2J MGP_DBA2J_G0023834
 protein coding gene Chr17:70216572-70346923 (-)
FVB/NJ MGP_FVBNJ_G0023800
 protein coding gene Chr17:69690153-69815459 (-)
LP/J MGP_LPJ_G0023916
 protein coding gene Chr17:74536633-74666729 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0023828
 protein coding gene Chr17:79535127-79669686 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0024456
 protein coding gene Chr17:73039536-73182646 (-)
PWK/PhJ MGP_PWKPhJ_G0022957
 protein coding gene Chr17:69528442-69658178 (-)
SPRET/EiJ MGP_SPRETEiJ_G0022768
 protein coding gene Chr17:69748377-69874839 (-)
WSB/EiJ MGP_WSBEiJ_G0023278
 protein coding gene Chr17:73856511-73989989 (-)



Homology
more
  • Human Ortholog
    SMCHD1, structural maintenance of chromosomes flexible hinge domain containing 1
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SMCHD1, structural maintenance of chromosomes flexible hinge domain containing 1
  • Synonyms
    BAMS, FSHD2
  • Links
    NCBI Gene ID: 23347
    UniProt: A6NHR9

  • Chr Location
    18p11.32; chr18:2655726-2805017 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with human SMCHD1 associations

Human Disease Mouse Models
      
IDs
Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    12 phenotypes from 3 alleles in 4 genetic backgrounds
    1 phenotype from multigenic genotypes
    28 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Females homozygous for an ENU-induced allele die at midgestation showing placental defects and hypomethylation at X-linked genes that are normally subject to X-inactivation, whereas homozygous males are viable. Females homozygous for a gene trap allele die before E13.5, whereas males remain healthy.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    47
  • GO References
    13
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    797
  • Tissues
    27
  • cDNA Data
    170
  • Literature Summary
    8
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000024054 Ensembl Gene Model | MGI Sequence Detail 130855 C57BL/6J ±  kb
    transcript ENSMUST00000127430 Ensembl | MGI Sequence Detail 7052 Not Applicable  
    polypeptide ENSMUSP00000121835 Ensembl | MGI Sequence Detail 2007 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      3 Sequences
    • Protein Ontology
      PR:000030591 structural maintenance of chromosomes flexible hinge domain-containing protein 1
      (term hierarchy)
    • PDB
      6N64
    • EC
      3.6.1.-
    • InterPro Domains
      IPR036890 Histidine kinase/HSP90-like ATPase superfamily
      IPR010935 SMCs flexible hinge
      IPR036277 SMCs flexible hinge superfamily
      IPR038892 Structural maintenance of chromosomes flexible hinge domain-containing protein 1
    • GlyGen
      Q6P5D8 2 sites, 1 O-linked glycan (1 site)
    Molecular
    Reagents
    less
    • All nucleic 172
      cDNA 170
      Primer pair 2

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGI:2147087, MGI:3586534
    References
    more
    • Summaries
      All 67
      Developmental Gene Expression 8
      Gene Ontology 13
      Phenotypes 28
    • Earliest
      J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
    • Latest
      J:363283 Engal E, et al., DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis. Sci Adv. 2024 May 31;10(22):eadn7732
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
    Citing These Resources
    Funding Information
    Warranty Disclaimer, Privacy Notice, Licensing, & Copyright
    Send questions and comments to User Support.     		last database update
    03/18/2025
    MGI 6.24     		The Jackson Laboratory