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	9126
Gene name	Structural maintenance of chromosomes 3
Gene symbol	SMC3
Synonyms (NCBI Gene)	BAMBMHCDLS3CSPG6HCAPSMC3L1
Chromosome	10
Chromosome location	10q25.2
Summary	This gene belongs to the SMC3 subfamily of SMC proteins. The encoded protein occurs in certain cell types as either an intracellular, nuclear protein or a secreted protein. The nuclear form, known as structural maintenance of chromosomes 3, is a component

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SNP ID	Visualize variation	Clinical significance	Consequence
rs587784425	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs587784427	G>C	Likely-pathogenic	Coding sequence variant, missense variant
rs587784429	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs727503775	TACAGGAACTT>-	Pathogenic	Coding sequence variant, intron variant, splice acceptor variant
rs748876063	C>G,T	Likely-pathogenic	Coding sequence variant, synonymous variant, missense variant
rs776056911	T>C,G	Likely-pathogenic	Coding sequence variant, missense variant
rs779885552	A>C,G	Likely-pathogenic	Coding sequence variant, missense variant
rs797044861	A>C	Pathogenic	Coding sequence variant, missense variant
rs797045070	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs797045996	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs797045997	->GAA	Likely-pathogenic	Inframe insertion, coding sequence variant
rs863223279	AGA>-	Pathogenic	Coding sequence variant, inframe deletion
rs863225258	T>C	Pathogenic	Coding sequence variant, missense variant
rs863225259	ACT>-	Pathogenic	Coding sequence variant, inframe deletion
rs863225260	G>A	Pathogenic	Coding sequence variant, missense variant
rs863225261	G>C	Pathogenic	Coding sequence variant, missense variant
rs866273473	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs869312672	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs886041239	A>G	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs901512521	C>A,G,T	Likely-pathogenic	Missense variant, coding sequence variant
rs1057521663	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1064793598	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1064796790	G>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1131691432	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1564792181	GCT>-	Likely-pathogenic	Inframe deletion, coding sequence variant
rs1564794233	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1564796294	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1590556378	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1590556722	AGAA>-	Pathogenic	Frameshift variant, coding sequence variant
rs1590567950	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1590571077	AAA>-	Likely-pathogenic	Inframe deletion, coding sequence variant
rs1590572104	G>T	Likely-pathogenic	Missense variant, coding sequence variant

108

Show/Hide all (108)

miRTarBase ID	miRNA	Experiments	Reference
MIRT019626	hsa-miR-340-5p	Sequencing	20371350
MIRT026077	hsa-miR-196a-5p	Sequencing	20371350
MIRT049364	hsa-miR-92a-3p	CLASH	23622248
MIRT041357	hsa-miR-193b-3p	CLASH	23622248
MIRT040180	hsa-miR-615-3p	CLASH	23622248
MIRT448453	hsa-miR-4668-3p	PAR-CLIP	22100165
MIRT055334	hsa-miR-3163	PAR-CLIP	22100165
MIRT448452	hsa-miR-4762-5p	PAR-CLIP	22100165
MIRT448451	hsa-miR-4427	PAR-CLIP	22100165
MIRT448450	hsa-miR-5187-3p	PAR-CLIP	22100165
MIRT448449	hsa-miR-4680-3p	PAR-CLIP	22100165
MIRT448448	hsa-miR-27b-5p	PAR-CLIP	22100165
MIRT448447	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT176641	hsa-miR-382-5p	PAR-CLIP	22100165
MIRT448461	hsa-miR-7844-5p	PAR-CLIP	22100165
MIRT448460	hsa-miR-10a-3p	PAR-CLIP	22100165
MIRT448459	hsa-miR-4700-3p	PAR-CLIP	22100165
MIRT448458	hsa-miR-302a-5p	PAR-CLIP	22100165
MIRT176645	hsa-miR-3613-5p	PAR-CLIP	22100165
MIRT448457	hsa-miR-520d-5p	PAR-CLIP	22100165
MIRT448456	hsa-miR-524-5p	PAR-CLIP	22100165
MIRT448455	hsa-let-7c-3p	PAR-CLIP	22100165
MIRT176639	hsa-let-7a-2-3p	PAR-CLIP	22100165
MIRT176640	hsa-let-7g-3p	PAR-CLIP	22100165
MIRT448454	hsa-miR-493-5p	PAR-CLIP	22100165
MIRT448453	hsa-miR-4668-3p	PAR-CLIP	22100165
MIRT055334	hsa-miR-3163	PAR-CLIP	22100165
MIRT448452	hsa-miR-4762-5p	PAR-CLIP	22100165
MIRT448451	hsa-miR-4427	PAR-CLIP	22100165
MIRT448450	hsa-miR-5187-3p	PAR-CLIP	22100165
MIRT448449	hsa-miR-4680-3p	PAR-CLIP	22100165
MIRT448448	hsa-miR-27b-5p	PAR-CLIP	22100165
MIRT448447	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT735352	hsa-miR-4720-3p	Luciferase reporter assayWestern blottingIn situ hybridization	32314520
MIRT448453	hsa-miR-4668-3p	PAR-CLIP	22100165
MIRT055334	hsa-miR-3163	PAR-CLIP	22100165
MIRT448452	hsa-miR-4762-5p	PAR-CLIP	22100165
MIRT448451	hsa-miR-4427	PAR-CLIP	22100165
MIRT448450	hsa-miR-5187-3p	PAR-CLIP	22100165
MIRT448449	hsa-miR-4680-3p	PAR-CLIP	22100165
MIRT448448	hsa-miR-27b-5p	PAR-CLIP	22100165
MIRT448447	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT176641	hsa-miR-382-5p	PAR-CLIP	22100165
MIRT448461	hsa-miR-7844-5p	PAR-CLIP	22100165
MIRT448460	hsa-miR-10a-3p	PAR-CLIP	22100165
MIRT448459	hsa-miR-4700-3p	PAR-CLIP	22100165
MIRT448458	hsa-miR-302a-5p	PAR-CLIP	22100165
MIRT176645	hsa-miR-3613-5p	PAR-CLIP	22100165
MIRT448457	hsa-miR-520d-5p	PAR-CLIP	22100165
MIRT448456	hsa-miR-524-5p	PAR-CLIP	22100165
MIRT448455	hsa-let-7c-3p	PAR-CLIP	22100165
MIRT176639	hsa-let-7a-2-3p	PAR-CLIP	22100165
MIRT176640	hsa-let-7g-3p	PAR-CLIP	22100165
MIRT448454	hsa-miR-493-5p	PAR-CLIP	22100165
MIRT448453	hsa-miR-4668-3p	PAR-CLIP	22100165
MIRT055334	hsa-miR-3163	PAR-CLIP	22100165
MIRT448452	hsa-miR-4762-5p	PAR-CLIP	22100165
MIRT448451	hsa-miR-4427	PAR-CLIP	22100165
MIRT448450	hsa-miR-5187-3p	PAR-CLIP	22100165
MIRT448449	hsa-miR-4680-3p	PAR-CLIP	22100165
MIRT448448	hsa-miR-27b-5p	PAR-CLIP	22100165
MIRT448447	hsa-miR-526b-5p	PAR-CLIP	22100165
MIRT1372399	hsa-miR-1343	CLIP-seq
MIRT1372400	hsa-miR-4464	CLIP-seq
MIRT1372401	hsa-miR-4748	CLIP-seq
MIRT1372402	hsa-miR-513a-3p	CLIP-seq
MIRT1372403	hsa-miR-582-5p	CLIP-seq
MIRT2110605	hsa-miR-1279	CLIP-seq
MIRT2110606	hsa-miR-150	CLIP-seq
MIRT2110607	hsa-miR-382	CLIP-seq
MIRT2110608	hsa-miR-4712-3p	CLIP-seq
MIRT2110609	hsa-miR-4713-5p	CLIP-seq
MIRT2110610	hsa-miR-532-3p	CLIP-seq
MIRT2110611	hsa-miR-580	CLIP-seq
MIRT2110605	hsa-miR-1279	CLIP-seq
MIRT2110606	hsa-miR-150	CLIP-seq
MIRT2334010	hsa-miR-196a	CLIP-seq
MIRT2334011	hsa-miR-196b	CLIP-seq
MIRT2334012	hsa-miR-3927	CLIP-seq
MIRT2110609	hsa-miR-4713-5p	CLIP-seq
MIRT2110610	hsa-miR-532-3p	CLIP-seq
MIRT2628209	hsa-miR-1264	CLIP-seq
MIRT2628210	hsa-miR-1272	CLIP-seq
MIRT2628211	hsa-miR-1322	CLIP-seq
MIRT1372399	hsa-miR-1343	CLIP-seq
MIRT2628212	hsa-miR-3187-3p	CLIP-seq
MIRT2628213	hsa-miR-323-3p	CLIP-seq
MIRT2628214	hsa-miR-340	CLIP-seq
MIRT2628215	hsa-miR-3926	CLIP-seq
MIRT2628216	hsa-miR-4435	CLIP-seq
MIRT1372400	hsa-miR-4464	CLIP-seq
MIRT2628217	hsa-miR-4701-5p	CLIP-seq
MIRT2110608	hsa-miR-4712-3p	CLIP-seq
MIRT1372401	hsa-miR-4748	CLIP-seq
MIRT2628218	hsa-miR-4759	CLIP-seq
MIRT2628219	hsa-miR-4766-5p	CLIP-seq
MIRT2628220	hsa-miR-4797-5p	CLIP-seq
MIRT1372402	hsa-miR-513a-3p	CLIP-seq
MIRT2628221	hsa-miR-548s	CLIP-seq
MIRT2628222	hsa-miR-570	CLIP-seq
MIRT1372403	hsa-miR-582-5p	CLIP-seq
MIRT2628223	hsa-miR-588	CLIP-seq
MIRT2628210	hsa-miR-1272	CLIP-seq
MIRT2628211	hsa-miR-1322	CLIP-seq
MIRT2628213	hsa-miR-323-3p	CLIP-seq
MIRT2628214	hsa-miR-340	CLIP-seq
MIRT2628218	hsa-miR-4759	CLIP-seq
MIRT2628220	hsa-miR-4797-5p	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000278	Process	Mitotic cell cycle	TAS	9506951
GO:0000775	Component	Chromosome, centromeric region	IEA
GO:0000775	Component	Chromosome, centromeric region	TAS
GO:0000785	Component	Chromatin	IDA	16682347, 19907496
GO:0000800	Component	Lateral element	IEA
GO:0000987	Function	Cis-regulatory region sequence-specific DNA binding	IEA
GO:0003682	Function	Chromatin binding	IEA
GO:0003690	Function	Double-stranded DNA binding	IBA
GO:0003777	Function	Microtubule motor activity	NAS	11590136
GO:0005515	Function	Protein binding	IPI	9506951, 9789013, 11590136, 11983169, 15656913, 15737063, 15837422, 15855230, 16682347, 16802858, 17105772, 17112726, 17113138, 17349791, 17962804, 18235444, 18832153, 19629043, 19907496, 20818333, 22293751, 22540012, 22628566, 22885700, 23242214, 24299456, 24981860, 26496610, 28514
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	32409525
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:0006275	Process	Regulation of DNA replication	IMP	19907496
GO:0006281	Process	DNA repair	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0007062	Process	Sister chromatid cohesion	IMP	15917200
GO:0007062	Process	Sister chromatid cohesion	NAS	11590136
GO:0007064	Process	Mitotic sister chromatid cohesion	IBA
GO:0008278	Component	Cohesin complex	IDA	9789013, 11590136, 22628566
GO:0008278	Component	Cohesin complex	IEA
GO:0008278	Component	Cohesin complex	NAS	9506951
GO:0016363	Component	Nuclear matrix	IDA	11590136
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0019827	Process	Stem cell population maintenance	IEA
GO:0030892	Component	Mitotic cohesin complex	IBA
GO:0030892	Component	Mitotic cohesin complex	IPI	23242214
GO:0030892	Component	Mitotic cohesin complex	ISS
GO:0030893	Component	Meiotic cohesin complex	IDA	21242291
GO:0030893	Component	Meiotic cohesin complex	IEA
GO:0030893	Component	Meiotic cohesin complex	NAS	32409525
GO:0031981	Component	Nuclear lumen	IEA
GO:0034087	Process	Establishment of mitotic sister chromatid cohesion	NAS	32409525
GO:0034089	Process	Establishment of meiotic sister chromatid cohesion	NAS	32409525
GO:0036033	Function	Mediator complex binding	IEA
GO:0046982	Function	Protein heterodimerization activity	IPI	11590136
GO:0048487	Function	Beta-tubulin binding	IDA	11590136
GO:0051276	Process	Chromosome organization	IEA
GO:0051301	Process	Cell division	IEA
GO:0051321	Process	Meiotic cell cycle	IDA
GO:0051321	Process	Meiotic cell cycle	IEA
GO:0051321	Process	Meiotic cell cycle	IEA
GO:0070840	Function	Dynein complex binding	IDA	11590136
GO:0090307	Process	Mitotic spindle assembly	IMP	11590136
GO:0097431	Component	Mitotic spindle pole	IDA	11590136

MIM	HGNC	e!Ensembl
606062	2468	ENSG00000108055

Q9UQE7

Protein name

Structural maintenance of chromosomes protein 3 (SMC protein 3) (SMC-3) (Basement membrane-associated chondroitin proteoglycan) (Bamacan) (Chondroitin sulfate proteoglycan 6) (Chromosome-associated polypeptide) (hCAP)

Protein function

Central component of cohesin, a complex required for chromosome cohesion during the cell cycle. The cohesin complex may form a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissoc

PDB

6WG3 , 6WG4 , 6WG6 , 6WGE , 7W1M , 8P0A , 8PQ5 , 8ROH , 8ROI , 8ROJ , 8ROK , 8ROL

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02463	SMC_N	2 → 1197	RecF/RecN/SMC N terminal domain	Domain
PF06470	SMC_hinge	529 → 643	SMC proteins Flexible Hinge Domain	Domain

Sequence

MYIKQVIIQGFRSYRDQTIVDPFSSKHNVIVGRNGSGKSNFFYAIQFVLSDEFSHLRPEQ
RLALLHEGTGPRVISAFVEIIFDNSDNRLPIDKEEVSLRRVIGAKKDQYFLDKKMVTKND
VMNLLESAGFSRSNPYYIVKQGKINQMATAPDSQRLKLLREVAGTRVYDERKEESISLMK
ETEGKREKINELLKYIEERLHTLEEEKEELAQYQKWDKMRRALEYTIYNQELNETRAKLD
ELSAKRETSGEKSRQLRDAQQDARDKMEDIERQVRELKTKISAMKEEKEQLSAERQEQIK
QRTKLELKAKDLQDELAGNSEQRKRLLKERQKLLEKIEEKQKELAETEPKFNSVKEKEER
GIARLAQATQERTDLYAKQGRGSQFTSKEERDKWIKKELKSLDQAINDKKRQIAAIHKDL
EDTEANKEKNLEQYNKLDQDLNEVKARVEELDRKYYEVKNKKDELQSERNYLWREENAEQ
QALAAKREDLEKKQQLLRAATGKAILNGIDSINKVLDHFRRKGINQHVQNGYHGIVMNNF
ECEPAFYTCVEVTAGNRLFYHIVDSDEVSTKILMEFNKMNLPGEVTFLPLNKLDVRDTAY
PETNDAIPMISKLRYNPRFDKAFKHVFGKTLICRSMEVSTQLARAFTMDCITLEGDQVSH
RGALTGGYYDTRKSRLELQKDVRKAEEELGELEAKLNENLRRNIERINNEIDQLMNQMQQ
IETQQRKFKASRDSILSEMKMLKEKRQQSEKTFMPKQRSLQSLEASLHAMESTRESLKAE
LGTDLLSQLSLEDQKRVDALNDEIRQLQQENRQLLNERIKLEGIITRVETYLNENLRKRL
DQVEQELNELRETEGGTVLTATTSELEAINKRVKDTMARSEDLDNSIDKTEAGIKELQKS
MERWKNMEKEHMDAINHDTKELEKMTNRQGMLLKKKEECMKKIRELGSLPQEAFEKYQTL
SLKQLFRKLEQCNTELKKYSHVNKKALDQFVNFSEQKEKLIKRQEELDRGYKSIMELMNV
LELRKYEAIQLTFKQVSKNFSEVFQKLVPGGKATLVMKKGDVEGSQSQDEGEGSGESERG
SGSQSSVPSVDQFTGVGIRVSFTGKQGEMREMQQLSGGQKSLVALALIFAIQKCDPAPFY
LFDEIDQALDAQHRKAVSDMIMELAVHAQFITTTFRPELLESADKFYGVKFRNKVSHIDV
ITAEMAKDFVEDDTTHG

Sequence length

1217

Interactions

View interactions

	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

428

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Cornelia de Lange syndrome 1	Likely pathogenic	rs1861180589	RCV001270789
Cornelia de Lange syndrome 3	Likely pathogenic; Pathogenic	rs2134740210, rs1861180567, rs2134754195, rs2134750930, rs2134735614, rs2134745322, rs587784429, rs587784425, rs587784427, rs727503775, rs2493144025, rs863223279, rs797044861, rs2493117603, rs797045070 View all (28 more)	RCV001378873 RCV001810308 RCV001771800 RCV001775408 RCV002221949 RCV002246733 RCV000147600 RCV000147580 RCV000147586 RCV000157051 RCV002512473 RCV000004894 RCV000201868 RCV002824105 RCV000191131 RCV000192327 RCV000201864 RCV000201849 RCV000201866 RCV000201859 RCV000209912 RCV003149157 RCV002051833 RCV003322674 RCV003485953 RCV003502812 RCV003504562 RCV003503176 RCV003611782 RCV003612862 RCV003613047 RCV003984930 RCV003992005 RCV000503251 RCV000680264 RCV000680265 RCV000705877 RCV000768435 RCV000809857 RCV000988450 RCV001027668 RCV001072116 RCV006249733 RCV001267657
De Lange syndrome	Likely pathogenic	rs869312672, rs748876063, rs1590572104	RCV004017489 RCV000857247 RCV000857235
Intellectual disability	Likely pathogenic; Pathogenic	rs886041239	RCV000721938
See cases	Likely pathogenic	rs2134745289	RCV001420318
SMC3-related disorder	Pathogenic; Likely pathogenic	rs2493114413, rs2493128583	RCV003408471 RCV003391479
Wiedemann-Steiner syndrome	Pathogenic	rs727503775	RCV000157051

Show/Hide Unknown Diseases (16)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign; Likely benign	rs80087872, rs7094685, rs79912955, rs201281088	RCV005915260 RCV005919388 RCV005888232 RCV005888236
Autism spectrum disorder	Uncertain significance	rs760111391	RCV001291379
Cervical cancer	Benign; Likely benign	rs7094685, rs79912955	RCV005919389 RCV005888234
Cholangiocarcinoma	Benign	rs79110044, rs7911129	RCV005922957 RCV005923477
Colon adenocarcinoma	Likely benign	rs768587428	RCV005869963
Familial cancer of breast	Likely benign	rs768587428	RCV005869962
Gastric cancer	Benign	rs7094685	RCV005919390
Lung cancer	Benign; Uncertain significance	rs79110044, rs373545953	RCV005922958 RCV005930353
Malignant lymphoma, large B-cell, diffuse	Benign	rs79110044	RCV005922956
Malignant tumor of esophagus	Benign; Likely benign; Uncertain significance	rs79912955, rs745657228	RCV005888233 RCV005931340
Neurodevelopmental abnormality	Likely benign	rs1861074510	RCV001264677
Neurodevelopmental disorder	Uncertain significance	rs2493113288	RCV003389211
Ovarian serous cystadenocarcinoma	Benign	rs80087872, rs7094685	RCV005915261 RCV005919391
Thymoma	Benign	rs7911129	RCV005923476
Uterine carcinosarcoma	Benign	rs7094685	RCV005919392
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs80087872, rs7094685, rs79912955	RCV005915262 RCV005919393 RCV005888235

Show/Hide Text Mining Associations (26)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Aneuploidy	Associate	23455720
Ataxia	Associate	25655089
Bone Diseases	Associate	33397451
Carcinoma Hepatocellular	Stimulate	36281130
Carcinoma Hepatocellular	Associate	37204480
De Lange Syndrome	Associate	17273969, 18996922, 19052029, 19701948, 20358602, 20448023, 22241092, 22857006, 22885700, 23106691, 24756084, 24918291, 25125236, 25574841, 25652421 View all (8 more)
Depression Postpartum	Associate	25655089
Dermatitis Atopic	Associate	33289509
Down Syndrome	Associate	35587378, 35838049
Fractures Bone	Associate	33397451
Growth Disorders	Associate	25655089
Heart Defects Congenital	Associate	22965847, 25655089
Intellectual Disability	Associate	17273969
Leukemia	Associate	23733339, 25095896
Leukemia Megakaryoblastic Acute	Associate	35838049
Leukemia Myeloid Acute	Associate	24335498, 36727396
Mental Retardation X Linked Nonsyndromic	Associate	17273969
Myeloproliferative Disorders	Associate	35838049
Neoplasms	Associate	25006131, 33460400, 36281130
Orofacial Cleft 1	Associate	37350193
Polycystic Ovary Syndrome	Associate	26308735
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	22237025, 27022003, 27470916
Purpura Thrombocytopenic Idiopathic	Associate	33222560
Roberts Syndrome	Associate	34989322
Sarcoma	Associate	33460400
Urinary Bladder Neoplasms	Associate	37542643

SMC3 (structural maintenance of chromosomes 3)