Gene Gene information from NCBI Gene database.
Entrez ID 8243
Gene name Structural maintenance of chromosomes 1A
Gene symbol SMC1A
Synonyms (NCBI Gene)
CDLS2DEE85DXS423EEIEE85SB1.8SMC1SMC1L1SMC1alphaSMCB
Chromosome X
Chromosome location Xp11.22
Summary Proper cohesion of sister chromatids is a prerequisite for the correct segregation of chromosomes during cell division. The cohesin multiprotein complex is required for sister chromatid cohesion. This complex is composed partly of two structural maintenan
SNPs SNP information provided by dbSNP.
74
SNP ID Visualize variation Clinical significance Consequence
rs122454122 T>G Pathogenic Coding sequence variant, missense variant
rs122454123 C>T Pathogenic Coding sequence variant, missense variant
rs387906702 A>G Likely-pathogenic, pathogenic Missense variant, coding sequence variant
rs587784403 C>T Pathogenic Missense variant, coding sequence variant
rs587784404 G>T Likely-pathogenic Missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
1298
miRTarBase ID miRNA Experiments Reference
MIRT004469 hsa-let-7e-5p Luciferase reporter assay 15131085
MIRT031051 hsa-miR-21-5p Microarray 18591254
MIRT004469 hsa-let-7e-5p Reporter assay;Other 15131085
MIRT052108 hsa-let-7b-5p CLASH 23622248
MIRT052108 hsa-let-7b-5p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
56
GO ID Ontology Definition Evidence Reference
GO:0000070 Process Mitotic sister chromatid segregation TAS 7757074
GO:0000166 Function Nucleotide binding IEA
GO:0000775 Component Chromosome, centromeric region IEA
GO:0000775 Component Chromosome, centromeric region TAS
GO:0000776 Component Kinetochore IDA 11682612, 12199140
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300040 11111 ENSG00000072501
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q14683
Protein name Structural maintenance of chromosomes protein 1A (SMC protein 1A) (SMC-1-alpha) (SMC-1A) (Sb1.8)
Protein function Involved in chromosome cohesion during cell cycle and in DNA repair. Central component of cohesin complex. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large
PDB 6WG3 , 6WG4 , 6WG6 , 6WGE , 7W1M , 8P0A , 8PQ5 , 8RO6 , 8RO7 , 8RO8 , 8RO9 , 8ROA , 8ROB , 8ROC , 8ROD , 8ROE , 8ROF , 8ROG
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02463 SMC_N 3 1211 RecF/RecN/SMC N terminal domain Domain
PF06470 SMC_hinge 512 629 SMC proteins Flexible Hinge Domain Domain
Sequence
MGFLKLIEIENFKSYKGRQIIGPFQRFTAIIGPNGSGKSNLMDAISFVLGEKTSNLRVKT
LRDLIHGAPVGKPAANRAFVSMVYSEEGAEDRTFARVIVGGSSEYKINNKVVQLHEYSEE
LEKLGILIKARNFLVFQGAVESIAMKNPKERTALFEEISRSGELAQEYDKRKKEMVKAEE
DTQFNYHRKKNIAAERKEAKQEKEEADRYQRLKDEVVRAQVQLQLFKLYHNEVEIEKLNK
ELASKNKEIEKDKKRMDKVEDELKEKKKELGKMMREQQQIEKEIKEKDSELNQKRPQYIK
AKENTSHKIKKLEAAKKSLQNAQKHYKKRKGDMDELEKEMLSVEKARQEFEERMEEESQS
QGRDLTLEENQVKKYHRLKEEASKRAATLAQELEKFNRDQKADQDRLDLEERKKVETEAK
IKQKLREIEENQKRIEKLEEYITTSKQSLEEQKKLEGELTEEVEMAKRRIDEINKELNQV
MEQLGDARIDRQESSRQQRKAEIMESIKRLY
PGSVYGRLIDLCQPTQKKYQIAVTKVLGK
NMDAIIVDSEKTGRDCIQYIKEQRGEPETFLPLDYLEVKPTDEKLRELKGAKLVIDVIRY
EPPHIKKALQYACGNALVCDNVEDARRIA
FGGHQRHKTVALDGTLFQKSGVISGGASDLK
AKARRWDEKAVDKLKEKKERLTEELKEQMKAKRKEAELRQVQSQAHGLQMRLKYSQSDLE
QTKTRHLALNLQEKSKLESELANFGPRINDIKRIIQSREREMKDLKEKMNQVEDEVFEEF
CREIGVRNIREFEEEKVKRQNEIAKKRLEFENQKTRLGIQLDFEKNQLKEDQDKVHMWEQ
TVKKDENEIEKLKKEEQRHMKIIDETMAQLQDLKNQHLAKKSEVNDKNHEMEEIRKKLGG
ANKEMTHLQKEVTAIETKLEQKRSDRHNLLQACKMQDIKLPLSKGTMDDISQEEGSSQGE
DSVSGSQRISSIYAREALIEIDYGDLCEDLKDAQAEEEIKQEMNTLQQKLNEQQSVLQRI
AAPNMKAMEKLESVRDKFQETSDEFEAARKRAKKAKQAFEQIKKERFDRFNACFESVATN
IDEIYKALSRNSSAQAFLGPENPEEPYLDGINYNCVAPGKRFRPMDNLSGGEKTVAALAL
LFAIHSYKPAPFFVLDEIDAALDNTNIGKVANYIKEQSTCNFQAIVISLKEEFYTKAESL
IGVYPEQGDCV
ISKVLTFDLTKYPDANPNPNEQ
Sequence length 1233
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Cell cycle
Oocyte meiosis
  Separation of Sister Chromatids
Establishment of Sister Chromatid Cohesion
Cohesin Loading onto Chromatin
Resolution of Sister Chromatid Cohesion
SUMOylation of DNA damage response and repair proteins
Estrogen-dependent gene expression
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
52
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormality of the nervous system Likely pathogenic rs2146599602 RCV001814493
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital muscular hypertrophy-cerebral syndrome Likely pathogenic; Pathogenic rs2075726992, rs2146582443, rs2146598341, rs2146582701, rs2146592407, rs2146593421, rs2146598241, rs782176647, rs587784422, rs2146605644, rs2146614137, rs2146598316, rs2146604602, rs2075758478, rs2146599562
View all (119 more)
RCV001334531
RCV001379576
RCV001378227
RCV001379710
RCV001380272
View all (132 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cornelia de Lange syndrome 1 Pathogenic rs1057520375 RCV001527652
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Developmental and epileptic encephalopathy, 85, with or without midline brain defects Pathogenic; Likely pathogenic rs2146582701, rs782176647, rs2146582657, rs2146604738, rs2146599562, rs2146599361, rs2146599339, rs2520828047, rs587784416, rs587784409, rs2520960923, rs863225459, rs863225458, rs2520828613, rs2520885035
View all (14 more)
RCV001775171
RCV005050374
RCV001542626
RCV001785350
RCV001843850
View all (24 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Abnormal facial shape Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Acute myeloid leukemia Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATYPICAL RETT SYNDROME GWAS catalog, Orphanet
GWAS catalog, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARCINOMA, ADENOID CYSTIC CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute Promyelocytic Leukemia Promyelocytic Leukemia GENOMICS_ENGLAND_DG 26886259
★☆☆☆☆
Found in Text Mining only
Adenoid Cystic Carcinoma Adenocarcinoma CTD_human_DG 23685749
★☆☆☆☆
Found in Text Mining only
Adenoma Adenoma BEFREE 25080505, 25884313
★☆☆☆☆
Found in Text Mining only
Aicardi Goutieres syndrome Aicardi goutieres syndrome Pubtator 39871364 Associate
★☆☆☆☆
Found in Text Mining only
Anophthalmos with limb anomalies Anophthalmia Pubtator 32193685 Associate
★☆☆☆☆
Found in Text Mining only
Anxiety Anxiety Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only
Ataxia Telangiectasia Ataxia Telangiectasia BEFREE 19147735
★☆☆☆☆
Found in Text Mining only
Ataxia Telangiectasia Ataxia telangiectasia Pubtator 19147735, 25032865 Associate
★☆☆☆☆
Found in Text Mining only
Atrial Septal Defects Atrial Septal Defect HPO_DG
★☆☆☆☆
Found in Text Mining only
Attention deficit hyperactivity disorder Attention Deficit Hyperactivity Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only