GediPNet logo

SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1)

Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
23347
Gene nameGene Name - the full gene name approved by the HGNC.
Structural maintenance of chromosomes flexible hinge domain containing 1
Gene symbolGene Symbol - the official gene symbol approved by the HGNC, which is a short abbreviated form of the gene name.
SMCHD1
SynonymsGene synonyms aliases
BAMS, FSHD2
ChromosomeChromosome number
18
Chromosome locationChromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
18p11.32
SummarySummary of gene provided in NCBI Entrez Gene.
This gene encodes a protein which contains a hinge region domain found in members of the SMC (structural maintenance of chromosomes) protein family. [provided by RefSeq, Dec 2011]
SNPsSNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs58683258 G>A,T Conflicting-interpretations-of-pathogenicity Coding sequence variant, non coding transcript variant, synonymous variant
rs72862973 A>G Conflicting-interpretations-of-pathogenicity, likely-benign Coding sequence variant, non coding transcript variant, synonymous variant
rs76290319 T>A,C Conflicting-interpretations-of-pathogenicity, likely-benign Coding sequence variant, non coding transcript variant, synonymous variant
rs112500113 T>C Conflicting-interpretations-of-pathogenicity Non coding transcript variant, coding sequence variant, synonymous variant
rs144115061 T>C,G Likely-benign, conflicting-interpretations-of-pathogenicity Intron variant, genic downstream transcript variant
miRNAmiRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT003173 hsa-miR-210-3p immunoprecipitaion, Microarray, qRT-PCR 19826008
MIRT021727 hsa-miR-132-3p Microarray 17612493
MIRT021952 hsa-miR-128-3p Microarray 17612493
MIRT025085 hsa-miR-181a-5p Microarray 17612493
MIRT050718 hsa-miR-18a-5p CLASH 23622248
Gene ontology (GO)Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0000781 Component Chromosome, telomeric region IDA 24270157
GO:0001740 Component Barr body IDA 23542155
GO:0003677 Function DNA binding IEA
GO:0005515 Function Protein binding IPI 23542155
GO:0005524 Function ATP binding IEA
Other IDsOther ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM
HGNC
e!Ensembl
Protein
UniProt ID A6NHR9
Protein name Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (SMC hinge domain-containing protein 1) (EC 3.6.1.-)
Protein function Non-canonical member of the structural maintenance of chromosomes (SMC) protein family that plays a key role in epigenetic silencing by regulating chromatin architecture (By similarity). Promotes heterochromatin formation in both autosomes and c
PDB 6MW7
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13589 HATPase_c_3
139 295
Domain
PF06470 SMC_hinge
1719 1847
SMC proteins Flexible Hinge Domain
Domain
Sequence
MAAADGGGPGGASVGTEEDGGGVGHRTVYLFDRREKESELGDRPLQVGERSDYAGFRACV
CQTLGISPEEKFVITTTSRKEITCDNFDETVKDGVTLYLLQSVNQLLLTATKERIDFLPH
YDTLVKSGMYEYYASEGQNPLPFALAELIDNSLSATSRNIGVRRIQIKLLFDETQGKPAV
AVIDNGRGMTSKQLNNWAVYRLSKFTRQGDFESDHSGYVRPVPVPRSLNSDISYFGVGGK
QAVFFVGQSARMISKPADSQDVHELVLSKEDFEKKEKNKEAIYSGYIRNRKPSDS
VHITN
DDERFLHHLIIEEKEKDSFTAVVITGVQPEHIQYLKNYFHLWTRQLAHIYHYYIHGPKGN
EIRTSKEVEPFNNIDIEISMFEKGKVPKIVNLREIQDDMQTLYVNTAADSFEFKAHVEGD
GVVEGIIRYHPFLYDRETYPDDPCFPSKLKDEDDEDDCFILEKAARGKRPIFECFWNGRL
IPYTSVEDFDWCTPPKKRGLAPIECYNRISGALFTNDKFQVSTNKLTFMDLELKLKDKNT
LFTRILNGQEQRMKIDREFALWLKDCHEKYDKQIKFTLFKGVITRPDLPSKKQGPWATYA
AIEWDGKIYKAGQLVKTIKTLPLFYGSIVRFFLYGDHDGEVYATGGEVQIAMEPQALYDE
VRTVPIAKLDRTVAEKAVKKYVEDEMARLPDRLSVTWPEGDELLPNEVRPAGTPIGALRI
EILNKKGEAMQKLPGTSHGGSKKLLVELKVILHSSSGNKEIISHISQHGGKWPYWFKKME
NIQKLGNYTLKLQVVLNESNADTYAGRPLPSKAIKFSVKEGKPEKFSFGLLDLPFRVGVP
FNIPLEFQDEFGHTSQLVTDIQPVLEASGLSLHYEEITKGPNCVIRGVTAKGPVNSCQGK
NYNLKVTLPGLKEDSQILKIRLLPGHPRRLKVKPDSEILVIENGTAFPFQVEVLDESDNI
TAQPKLIVHCKFSGAPNLPVYVVDCSSSGTSILTGSAIQVQNIKKDQTLKARIEIPSCKD
VAPVEKTIKLLPSSHVARLQIFSVEGQKAIQIKHQDEVNWIAGDIMHNLIFQMYDEGERE
INITSALAEKIKVNWTPEINKEHLLQGLLPDVQVPTSVKDMRYCQVSFQDDHVSLESAFT
VRPLPDEPKHLKCEMKGGKTVQMGQELQGEVVIIITDQYGNQIQAFSPSSLSSLSIAGVG
LDSSNLKTTFQENTQSISVRGIKFIPGPPGNKDLCFTWREFSDFIRVQLISGPPAKLLLI
DWPELKESIPVINGRDLQNPIIVQLCDQWDNPAPVQHVKISLTKASNLKLMPSNQQHKTD
EKGRANLGVFSVFAPRGEHTLQVKAIYNKSIIEGPIIKLMILPDPEKPVRLNVKYDKDAS
FLAGGLFTDFMISVISEDDSIIKNINPARISMKMWKLSTSGNRPPANAETFSCNKIKDND
KEDGCFYFRDKVIPNKVGTYCIQFGFMMDKTNILNSEQVIVEVLPNQPVKLVPKIKPPTP
AVSNVRSVASRTLVRDLHLSITDDYDNHTGIDLVGTIIATIKGSNEEDTDTPLFIGKVRT
LEFPFVNGSAEIMSLVLAESSPGRDSTEYFIVFEPRLPLLSRTLEPYILPFMFYNDVKKQ
QQMAALTKEKDQLSQSIVMYKSLFEASQQLLNEMKCQVEEARLKEAQLRNELKIHNIDIP
TTQQVPHIEALLKRKLSEQEELKKKPRRSCTLPNYTKGSGDVLGKIAHLAQIEDDRAAMV
ISWHLASDMDCVVTLTTDAARRIYDETQGRQQVLPLDSIYKKTLPDWKRSLPHFRNGKLY
FKPIGDPVFARDLLTFPDNVEHCETVFGMLLGDTIILDNLDAANHYR
KEVVKITHCPTLL
TRDGDRIRSNGKFGGLQNKAPPMDKLRGMVFGAPVPKQCLILGEQIDLLQQYRSAVCKLD
SVNKDLNSQLEYLRTPDMRKKKQELDEHEKNLKLIEEKLGMTPIRKCNDSLRHSPKVETT
DCPVPPKRMRREATRQNRIITKTDV
Sequence length 2005
Interactions View interactions
Associated diseases
Causal
Disease name Disease term dbSNP ID References
Cataract Cataract rs118203965, rs118203966, rs104893685, rs121908938, rs104894175, rs121909048, rs28937573, rs121909049, rs121909050, rs74315488, rs80358200, rs80358203, rs121434643, rs56141211, rs132630322, rs121917775, rs121917735, rs121917736, rs137853199, rs137853200, rs121917867, rs121917869, rs121913555, rs104893736, rs121909595, rs121909596, rs121909597, rs28931605, rs121909598, rs104893618, rs1695062782, rs74315486, rs74315487, rs74315490, rs74315489, rs745938679, rs1566402656, rs74315439, rs74315441, rs121912973, rs121917823, rs1593332981, rs121917825, rs121917827, rs113994108, rs387906963, rs387906964, rs1240503246, rs387906965, rs387906966, rs750207077, rs387907336, rs387907337, rs387907342, rs140332366, rs397514703, rs398122937, rs398122378, rs398122392, rs398122944, rs137853924, rs398122947, rs397515623, rs397515624, rs397515625, rs397515626, rs398122948, rs587778872, rs398123066, rs587777601, rs370424081, rs786205221, rs786205222, rs864309684, rs864309688, rs864309701, rs864309689, rs864309690, rs864309681, rs864309686, rs864309696, rs864309693, rs864309687, rs864309691, rs864309692, rs864309695, rs864309678, rs864309685, rs864309700, rs864309698, rs864309683, rs864309682, rs864309679, rs111534978, rs864309680, rs864309702, rs864622780, rs756898971, rs869312732, rs775038545, rs878852983, rs1114167312, rs1114167313, rs1114167314, rs1114167315, rs1114167307, rs886041410, rs886041412, rs1057518738, rs1057517926, rs1057518878, rs1057519616, rs12799308, rs1064793935, rs1064797219, rs1085307126, rs1085307127, rs765628635, rs1114167427, rs1114167433, rs1554744860, rs1554743428, rs747093432, rs1411557416, rs1555179713, rs1481963503, rs1555549755, rs1456161420, rs1555547008, rs1555889308, rs1555888762, rs766522434, rs1264025914, rs1553585262, rs1567671947, rs1337897299, rs764945940, rs1307969607, rs949335475, rs1184095219, rs776129797, rs1569203234, rs1567668570, rs749141857, rs764098604, rs1184398243, rs1578956689, rs1568480054, rs1564745688, rs1564722302, rs1564723150, rs1571175950, rs1569602837, rs1576552712, rs1575369255, rs981126461, rs1570403798, rs200557771, rs1477743112, rs1651879427, rs1651881222, rs1651919374, rs2024441691, rs148284531, rs1246080692
Arrhinia with choanal atresia and microphthalmia syndrome Arhinia, choanal atresia, and microphthalmia rs1057519640, rs1057519641, rs1057519642, rs1057519644, rs1057519645, rs1057519646, rs1135402737, rs1135402738, rs1135402739, rs1135402741, rs1135402742, rs1135402743, rs1135402744, rs1135402745 28067909, 29748383, 28067911
Congenital ocular coloboma Congenital ocular coloboma (disorder) rs587778875, rs587777249, rs767611891, rs2091986259, rs2091987023, rs2091988799
Cryptorchidism Cryptorchidism rs121912555, rs104894697, rs104894698, rs398122886 28067909
Unknown
Disease name Disease term dbSNP ID References
Arrhinia Arrhinia
Choanal atresia Choanal Atresia
Congenital coloboma of iris Congenital coloboma of iris
Congenital hypoplasia of penis Congenital hypoplasia of penis

| © 2021, Biomedical Informatics Centre, NIRRH |
ICMR-National Institute for Research in Reproductive Health, Jehangir Merwanji Street, Parel, Mumbai-400012
Tel: +91-22-24192104, Fax No: +91-22-24139412