Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10274
Gene name	STAG1 cohesin complex component
Gene symbol	STAG1
Synonyms (NCBI Gene)	MRD47SA1SCC3A
Chromosome	3
Chromosome location	3q22.3
Summary	This gene is a member of the SCC3 family and is expressed in the nucleus. It encodes a component of cohesin, a multisubunit protein complex that provides sister chromatid cohesion along the length of a chromosome from DNA replication through prophase and

Show/Hide all (19)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1057519153	T>C	Likely-pathogenic, uncertain-significance	5 prime UTR variant, missense variant, genic upstream transcript variant, non coding transcript variant, coding sequence variant
rs1057524850	C>G	Likely-pathogenic, not-provided	Missense variant, non coding transcript variant, genic upstream transcript variant, coding sequence variant
rs1376334317	C>T	Pathogenic, likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs1471479119	T>C	Likely-pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant
rs1553718528	->A	Pathogenic, likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1553722294	->AAACT	Pathogenic, likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1553722309	T>G	Pathogenic, likely-pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1553727865	A>C	Likely-pathogenic	Non coding transcript variant, missense variant, genic upstream transcript variant, coding sequence variant
rs1553728634	T>G	Likely-pathogenic	Non coding transcript variant, missense variant, genic upstream transcript variant, coding sequence variant
rs1553738686	T>C	Pathogenic, likely-pathogenic	Non coding transcript variant, genic upstream transcript variant, 5 prime UTR variant, missense variant, coding sequence variant
rs1553738694	T>C	Likely-pathogenic	Non coding transcript variant, genic upstream transcript variant, 5 prime UTR variant, missense variant, coding sequence variant
rs1553743217	C>T	Likely-pathogenic	Non coding transcript variant, genic upstream transcript variant, 5 prime UTR variant, missense variant, coding sequence variant
rs1553789166	T>-	Likely-pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant
rs1553801881	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1559791842	TTGA>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1559824939	G>A	Likely-pathogenic	Genic upstream transcript variant, missense variant, non coding transcript variant, coding sequence variant
rs1560062082	->C	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant
rs1576367919	TCTC>-	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs1576656734	A>-	Pathogenic	Non coding transcript variant, coding sequence variant, genic upstream transcript variant, frameshift variant, 5 prime UTR variant

115

Show/Hide all (115)

miRTarBase ID	miRNA	Experiments	Reference
MIRT022070	hsa-miR-128-3p	Microarray	17612493
MIRT029901	hsa-miR-26b-5p	Microarray	19088304
MIRT050227	hsa-miR-25-3p	CLASH	23622248
MIRT049410	hsa-miR-92a-3p	CLASH	23622248
MIRT045515	hsa-miR-149-5p	CLASH	23622248
MIRT618538	hsa-miR-8485	HITS-CLIP	19536157
MIRT618537	hsa-miR-4742-3p	HITS-CLIP	19536157
MIRT618538	hsa-miR-8485	HITS-CLIP	23824327
MIRT618537	hsa-miR-4742-3p	HITS-CLIP	23824327
MIRT625649	hsa-miR-450b-3p	HITS-CLIP	23824327
MIRT625648	hsa-miR-769-3p	HITS-CLIP	23824327
MIRT625647	hsa-miR-6728-5p	HITS-CLIP	23824327
MIRT625646	hsa-miR-5089-5p	HITS-CLIP	23824327
MIRT625645	hsa-miR-6513-5p	HITS-CLIP	23824327
MIRT618538	hsa-miR-8485	HITS-CLIP	23824327
MIRT618537	hsa-miR-4742-3p	HITS-CLIP	23824327
MIRT449483	hsa-miR-132-3p	PAR-CLIP	22100165
MIRT449482	hsa-miR-212-3p	PAR-CLIP	22100165
MIRT449481	hsa-miR-2277-3p	PAR-CLIP	22100165
MIRT726436	hsa-miR-181a-5p	HITS-CLIP	22473208
MIRT726437	hsa-miR-181b-5p	HITS-CLIP	22473208
MIRT726435	hsa-miR-181c-5p	HITS-CLIP	22473208
MIRT726434	hsa-miR-181d-5p	HITS-CLIP	22473208
MIRT618538	hsa-miR-8485	HITS-CLIP	19536157
MIRT618537	hsa-miR-4742-3p	HITS-CLIP	19536157
MIRT618538	hsa-miR-8485	HITS-CLIP	23824327
MIRT618537	hsa-miR-4742-3p	HITS-CLIP	23824327
MIRT625649	hsa-miR-450b-3p	HITS-CLIP	23824327
MIRT625648	hsa-miR-769-3p	HITS-CLIP	23824327
MIRT625647	hsa-miR-6728-5p	HITS-CLIP	23824327
MIRT625646	hsa-miR-5089-5p	HITS-CLIP	23824327
MIRT625645	hsa-miR-6513-5p	HITS-CLIP	23824327
MIRT618538	hsa-miR-8485	HITS-CLIP	23824327
MIRT618537	hsa-miR-4742-3p	HITS-CLIP	23824327
MIRT449483	hsa-miR-132-3p	PAR-CLIP	22100165
MIRT449482	hsa-miR-212-3p	PAR-CLIP	22100165
MIRT449481	hsa-miR-2277-3p	PAR-CLIP	22100165
MIRT1394359	hsa-miR-1207-5p	CLIP-seq
MIRT1394360	hsa-miR-1245b-5p	CLIP-seq
MIRT1394361	hsa-miR-1251	CLIP-seq
MIRT1394362	hsa-miR-1271	CLIP-seq
MIRT1394363	hsa-miR-1273g	CLIP-seq
MIRT1394364	hsa-miR-128	CLIP-seq
MIRT1394365	hsa-miR-132	CLIP-seq
MIRT1394366	hsa-miR-138	CLIP-seq
MIRT1394367	hsa-miR-144	CLIP-seq
MIRT1394368	hsa-miR-147	CLIP-seq
MIRT1394369	hsa-miR-182	CLIP-seq
MIRT1394370	hsa-miR-212	CLIP-seq
MIRT1394371	hsa-miR-27a	CLIP-seq
MIRT1394372	hsa-miR-27b	CLIP-seq
MIRT1394373	hsa-miR-300	CLIP-seq
MIRT1394374	hsa-miR-3120-3p	CLIP-seq
MIRT1394375	hsa-miR-3142	CLIP-seq
MIRT1394376	hsa-miR-3529	CLIP-seq
MIRT1394377	hsa-miR-3650	CLIP-seq
MIRT1394378	hsa-miR-379	CLIP-seq
MIRT1394379	hsa-miR-381	CLIP-seq
MIRT1394380	hsa-miR-3911	CLIP-seq
MIRT1394381	hsa-miR-409-3p	CLIP-seq
MIRT1394382	hsa-miR-4253	CLIP-seq
MIRT1394383	hsa-miR-4307	CLIP-seq
MIRT1394384	hsa-miR-4451	CLIP-seq
MIRT1394385	hsa-miR-4455	CLIP-seq
MIRT1394386	hsa-miR-4650-3p	CLIP-seq
MIRT1394387	hsa-miR-4736	CLIP-seq
MIRT1394388	hsa-miR-4757-5p	CLIP-seq
MIRT1394389	hsa-miR-4761-3p	CLIP-seq
MIRT1394390	hsa-miR-4763-3p	CLIP-seq
MIRT1394391	hsa-miR-545	CLIP-seq
MIRT1394392	hsa-miR-548ac	CLIP-seq
MIRT1394393	hsa-miR-548ae	CLIP-seq
MIRT1394394	hsa-miR-548aj	CLIP-seq
MIRT1394395	hsa-miR-548am	CLIP-seq
MIRT1394396	hsa-miR-548d-3p	CLIP-seq
MIRT1394397	hsa-miR-548x	CLIP-seq
MIRT1394398	hsa-miR-548z	CLIP-seq
MIRT1394399	hsa-miR-568	CLIP-seq
MIRT1394400	hsa-miR-580	CLIP-seq
MIRT1394401	hsa-miR-644	CLIP-seq
MIRT1394402	hsa-miR-888	CLIP-seq
MIRT1394403	hsa-miR-96	CLIP-seq
MIRT2118371	hsa-miR-1197	CLIP-seq
MIRT1394359	hsa-miR-1207-5p	CLIP-seq
MIRT1394362	hsa-miR-1271	CLIP-seq
MIRT1394369	hsa-miR-182	CLIP-seq
MIRT2118372	hsa-miR-1825	CLIP-seq
MIRT2118373	hsa-miR-199a-5p	CLIP-seq
MIRT2118374	hsa-miR-199b-5p	CLIP-seq
MIRT2118375	hsa-miR-3145-5p	CLIP-seq
MIRT2118376	hsa-miR-3692	CLIP-seq
MIRT2118377	hsa-miR-3974	CLIP-seq
MIRT1394382	hsa-miR-4253	CLIP-seq
MIRT2118378	hsa-miR-4268	CLIP-seq
MIRT2118379	hsa-miR-4452	CLIP-seq
MIRT2118380	hsa-miR-4528	CLIP-seq
MIRT2118381	hsa-miR-4680-5p	CLIP-seq
MIRT2118382	hsa-miR-4719	CLIP-seq
MIRT1394387	hsa-miR-4736	CLIP-seq
MIRT1394389	hsa-miR-4761-3p	CLIP-seq
MIRT1394390	hsa-miR-4763-3p	CLIP-seq
MIRT2118383	hsa-miR-599	CLIP-seq
MIRT2118384	hsa-miR-622	CLIP-seq
MIRT1394403	hsa-miR-96	CLIP-seq
MIRT2340476	hsa-miR-181a	CLIP-seq
MIRT2340477	hsa-miR-181b	CLIP-seq
MIRT2340478	hsa-miR-181c	CLIP-seq
MIRT2340479	hsa-miR-181d	CLIP-seq
MIRT2340480	hsa-miR-4262	CLIP-seq
MIRT2340481	hsa-miR-4303	CLIP-seq
MIRT2340482	hsa-miR-4762-3p	CLIP-seq
MIRT2340483	hsa-miR-548t	CLIP-seq
MIRT2340484	hsa-miR-579	CLIP-seq
MIRT2118384	hsa-miR-622	CLIP-seq
MIRT2340485	hsa-miR-668	CLIP-seq

Show/Hide all (29)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000775	Component	Chromosome, centromeric region	IEA
GO:0000775	Component	Chromosome, centromeric region	TAS
GO:0000785	Component	Chromatin	IBA
GO:0000785	Component	Chromatin	IDA	16682347
GO:0000785	Component	Chromatin	IEA
GO:0003682	Function	Chromatin binding	IBA
GO:0003682	Function	Chromatin binding	IEA
GO:0005515	Function	Protein binding	IPI	15855230, 16682347, 17112726, 17113138, 17349791, 17962804, 22885700, 24981860, 26496610, 29867216, 30021884, 35271311
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	32409525
GO:0005634	Component	Nucleus	TAS	9305759
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005694	Component	Chromosome	TAS
GO:0005829	Component	Cytosol	TAS
GO:0005929	Component	Cilium	IDA
GO:0007059	Process	Chromosome segregation	IEA
GO:0007062	Process	Sister chromatid cohesion	IBA
GO:0008278	Component	Cohesin complex	IBA
GO:0008278	Component	Cohesin complex	IDA	11590136, 22628566
GO:0016363	Component	Nuclear matrix	IDA	11590136
GO:0016604	Component	Nuclear body	IDA
GO:0030892	Component	Mitotic cohesin complex	ISS
GO:0034087	Process	Establishment of mitotic sister chromatid cohesion	NAS	32409525
GO:0051301	Process	Cell division	IEA
GO:0090307	Process	Mitotic spindle assembly	IMP	11590136
GO:0097431	Component	Mitotic spindle pole	IDA	11590136

MIM	HGNC	e!Ensembl
604358	11354	ENSG00000118007

Q8WVM7

Protein name

Cohesin subunit SA-1 (SCC3 homolog 1) (Stromal antigen 1)

Protein function

Component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex

PDB

5QSM , 5QSN , 5QSO , 5QSP , 5QSQ , 5QSR , 5QSS , 5QST , 5QSU , 5QSV , 5QSW , 5QSX , 5QSY , 5QSZ , 6QB5 , 6R7O , 6RRC , 6RRK , 6WG3 , 7W1M

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF08514	STAG	160 → 274	STAG domain	Family

Sequence

MITSELPVLQDSTNETTAHSDAGSELEETEVKGKRKRGRPGRPPSTNKKPRKSPGEKSRI
EAGIRGAGRGRANGHPQQNGEGEPVTLFEVVKLGKSAMQSVVDDWIESYKQDRDIALLDL
INFFIQCSGCRGTVRIEMFRNMQNAEIIRKMTEEFDEDSGDYPLTMPGPQWKKFRSNFCE
FIGVLIRQCQYSIIYDEYMMDTVISLLTGLSDSQVRAFRHTSTLAAMKLMTALVNVALNL
SIHQDNTQRQYEAERNKMIGKRANERLELLLQKRKELQENQDEIENMMNSIFKGIFVHRY
RDAIAEIRAICIEEIGVWMKMYSDAFLNDSYLKYVGWTLHDRQGEVRLKCLKALQSLYTN
RELFPKLELFTNRFKDRIVSMTLDKEYDVAVEAIRLVTLILHGSEEALSNEDCENVYHLV
YSAHRPVAVAAGEFLHKKLFSRHDPQAEEALAKRRGRNSPNGNLIRMLVLFFLESELHEH
AAYLVDSLWESSQELLKDWECMTELLLEEPVQGEEAMSDRQESALIELMVCTIRQAAEAH
PPVGRGTGKRVLTAKERKTQIDDRNKLTEHFIITLPMLLSKYSADAEKVANLLQIPQYFD
LEIYSTGRMEKHLDALLKQIKFVVEKHVESDVLEACSKTYSILCSEEYTIQNRVDIARSQ
LIDEFVDRFNHSVEDLLQEGEEADDDDIYNVLSTLKRLTSFHNAHDLTKWDLFGNCYRLL
KTGIEHGAMPEQIVVQALQCSHYSILWQLVKITDGSPSKEDLLVLRKTVKSFLAVCQQCL
SNVNTPVKEQAFMLLCDLLMIFSHQLMTGGREGLQPLVFNPDTGLQSELLSFVMDHVFID
QDEENQSMEGDEEDEANKIEALHKRRNLLAAFSKLIIYDIVDMHAAADIFKHYMKYYNDY
GDIIKETLSKTRQIDKIQCAKTLILSLQQLFNELVQEQGPNLDRTSAHVSGIKELARRFA
LTFGLDQIKTREAVATLHKDGIEFAFKYQNQKGQEYPPPNLAFLEVLSEFSSKLLRQDKK
TVHSYLEKFLTEQMMERREDVWLPLISYRNSLVTGGEDDRMSVNSGSSSSKTSSVRNKKG
RPPLHKKRVEDESLDNTWLNRTDTMIQTPGPLPAPQLTSTVLRENSRPMGDQIQEPESEH
GSEPDFLHNPQMQISWLGQPKLEDLNRKDRTGMNYMKVRTGVRHAVRGLMEEDAEPIFED
VMMSSRSQLEDMNEEFEDTMVIDLPPSRNRRERAELRPDFFDSAAIIEDDSGFGMPMF

Sequence length

1258

Interactions

View interactions

	KEGG		Reactome
	Cell cycle		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

108

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Global developmental delay	Likely pathogenic	rs751263539	RCV001255409
Intellectual disability, autosomal dominant 47	Likely pathogenic; Pathogenic	rs2107905668, rs2107905472, rs2530008022, rs2530398321, rs1435519890, rs2530394997, rs1267304310, rs1240231224, rs1553722309, rs1553738686, rs1376334317, rs1553722294, rs1559791842, rs1559824939, rs1553789166 View all (3 more)	RCV001783820 RCV001809157 RCV002288372 RCV002290068 RCV003147903 RCV003329137 RCV003493272 RCV005628387 RCV000504583 RCV000504586 RCV000504582 RCV000504584 RCV000680240 RCV000680241 RCV000677421 RCV000780762 RCV000987341 RCV001289470
Neurodevelopmental delay	Likely pathogenic	rs2107821352	RCV002274378
Neurodevelopmental disorder	Likely pathogenic	rs2107821339, rs2107831013	RCV001375017 RCV001375009
See cases	Likely pathogenic; Pathogenic	rs2107814279	RCV001420303
STAG1-related disorder	Likely pathogenic; Pathogenic	rs2472740882, rs1057524850, rs1553722309, rs1553738686, rs1376334317, rs1553722294, rs1553727865, rs1553728634, rs1553738694	RCV003326171 RCV004545769 RCV000508343 RCV000506734 RCV000507507 RCV000508254 RCV000506603 RCV000507765 RCV000507228

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Clear cell carcinoma of kidney	Likely benign	rs778261236	RCV005926697
Congenital ocular coloboma	Conflicting classifications of pathogenicity	rs759561079	RCV005626853
Intellectual disability	Uncertain significance	rs1553718528	RCV001260831
Malignant tumor of urinary bladder	Benign	rs143784838	RCV005926640
Premature ovarian insufficiency	Uncertain significance	rs1559855546	RCV000766160
Uterine corpus endometrial carcinoma	Benign	rs143784838	RCV005926641

Show/Hide Text Mining Associations (28)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma	Inhibit	27549371
Adenoma	Inhibit	27549371
Apraxias	Associate	39336775
Attention Deficit Disorder with Hyperactivity	Associate	28296084
Autism Spectrum Disorder	Associate	32127416
Carcinogenesis	Associate	27549371, 29471289
Carcinoma Hepatocellular	Stimulate	36052535
Carcinoma Renal Cell	Associate	17205537
Cognition Disorders	Associate	39336775
Colorectal Neoplasms	Associate	27549371, 29471289
Congenital Abnormalities	Associate	28296084, 32253279, 34440290
De Lange Syndrome	Associate	30158690, 34440290, 38284454
Depressive Disorder	Associate	30718454
Developmental Disabilities	Associate	28296084, 34440290, 39336775
Facial Dysmorphism with Multiple Malformations	Associate	39336775
Hypersensitivity Delayed	Associate	34440290, 39336775
IgA Deficiency	Associate	2892861
Intellectual Disability	Associate	32253279, 34440290, 39336775
Language Development Disorders	Associate	28296084
Leukemia Myeloid Acute	Associate	24335498
Mental Disorders	Associate	39336775
Microcephaly	Associate	28296084
Neoplasms	Associate	28430577, 28691904, 29867216, 32253279, 32467316, 36052535
Neurologic Manifestations	Associate	39336775
Prostatic Neoplasms	Associate	17166409
Speech Disorders	Associate	39336775
Squamous Cell Carcinoma of Head and Neck	Associate	30404566, 32716971
Waardenburg Syndrome	Associate	39336775

STAG1 (STAG1 cohesin complex component)