Mutagenetix > Incidental Mutation

Incidental Mutation 'R6020:Smc3'

478910

Institutional Source

Beutler Lab

Gene Symbol

Smc3

Ensembl Gene

ENSMUSG00000024974

Gene Name

structural maintenance of chromosomes 3

Synonyms

SmcD, Mmip1, Bamacan, Cspg6

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6020 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

53600398-53645833 bp(+) (GRCm38)

Type of Mutation

critical splice donor site (1 bp from exon)

DNA Base Change (assembly)

G to A at 53625163 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000025930 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025930]

AlphaFold

Q9CW03

PDB Structure

SMC hinge heterodimer (Mouse) [X-RAY DIFFRACTION]

Predicted Effect

probably null
Transcript: ENSMUST00000025930

SMART Domains

Protein: ENSMUSP00000025930
Gene: ENSMUSG00000024974

Domain	Start	End	E-Value	Type
Pfam:AAA_23	5	359	5.4e-10	PFAM
SMC_hinge	530	643	1.85e-23	SMART
low complexity region	684	711	N/A	INTRINSIC
Blast:SMC_hinge	712	804	3e-49	BLAST
low complexity region	805	818	N/A	INTRINSIC
Blast:SMC_hinge	819	870	3e-23	BLAST
Blast:INB	898	1174	2e-52	BLAST
PDB:1XEW\|Y	1032	1212	6e-30	PDB
SCOP:d1e69a_	1114	1193	2e-9	SMART

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.8%
20x: 93.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] 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 of the multimeric cohesin complex that holds together sister chromatids during mitosis, enabling proper chromosome segregation. Post-translational modification of the encoded protein by the addition of chondroitin sulfate chains gives rise to the secreted proteoglycan bamacan, an abundant basement membrane protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit complete embryonic lethality. Mice heterozygous for this allele exhibit partial postnatal lethality, decreased body weight, abnormal craniofacial morphology, and increased T cell number. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	C	A	11: 110,145,613	V557F	possibly damaging	Het
Abi3	A	T	11: 95,842,025	L41*	probably null	Het
Actn1	C	A	12: 80,174,455		probably null	Het
Adamts15	G	T	9: 30,902,062	R936S	probably benign	Het
Angel2	T	C	1: 190,932,871	S22P	probably benign	Het
Ank2	T	G	3: 126,946,821		probably benign	Het
Astn1	A	G	1: 158,509,993	D423G	probably damaging	Het
Casp9	A	G	4: 141,796,538	D78G	probably damaging	Het
Cbr4	A	G	8: 61,487,853	D2G	probably benign	Het
Ccdc8	T	A	7: 16,996,581	L665H	probably damaging	Het
Cdh23	T	A	10: 60,331,326	N1847I	probably damaging	Het
Cnst	T	C	1: 179,609,875	W335R	probably benign	Het
Ddr2	T	A	1: 170,005,102	I130F	probably benign	Het
Dnah2	C	T	11: 69,500,839	A677T	probably benign	Het
Dzip3	C	A	16: 48,951,842	W488L	probably damaging	Het
Ephb3	T	G	16: 21,222,013	I637S	probably damaging	Het
Etv3	A	G	3: 87,529,364	D142G	probably benign	Het
Fabp5	C	T	3: 10,016,089	T126I	probably benign	Het
Fam13b	A	C	18: 34,494,774	Y125D	probably damaging	Het
Fsip2	C	A	2: 82,992,127	P6068Q	probably damaging	Het
Gm11232	A	G	4: 71,756,668	F199S	possibly damaging	Het
Gm340	G	A	19: 41,583,547	G247D	possibly damaging	Het
Gm5493	A	G	17: 22,748,061	K57E	probably benign	Het
Gm7334	A	G	17: 50,699,237	M184V	probably benign	Het
Gm9894	T	C	13: 67,763,835		noncoding transcript	Het
Gpd2	T	A	2: 57,364,513	N674K	probably benign	Het
H2-M10.6	A	G	17: 36,813,067	Y141C	probably damaging	Het
Heatr5a	C	T	12: 51,884,327	E1796K	probably benign	Het
Hexim2	A	G	11: 103,138,292	T57A	probably benign	Het
Hrg	A	T	16: 22,954,518	N134Y	probably damaging	Het
Hsd17b12	T	C	2: 94,033,977	T262A	probably damaging	Het
Irak3	G	T	10: 120,143,137	P470T	probably damaging	Het
Itgbl1	A	T	14: 123,846,565	D285V	probably damaging	Het
Kcp	A	T	6: 29,502,864	V164E	probably benign	Het
Klhdc7b	T	A	15: 89,388,386	M1157K	probably damaging	Het
Mdc1	G	A	17: 35,848,633	G635D	probably benign	Het
Mdc1	A	G	17: 35,857,572	K1690R	probably benign	Het
Mpp3	A	T	11: 102,018,539		probably benign	Het
Ncor2	G	T	5: 125,020,011	H2285N	probably benign	Het
Neb	T	A	2: 52,257,827	T2727S	probably benign	Het
Nkx6-2	T	C	7: 139,581,567	D234G	possibly damaging	Het
Nlrp9c	T	C	7: 26,384,725	I476M	probably benign	Het
Nrsn1	T	G	13: 25,253,372	Q191P	probably damaging	Het
Olfr116	A	T	17: 37,623,967	S223T	possibly damaging	Het
Olfr390	C	T	11: 73,787,552	L205F	probably benign	Het
Olfr610	T	A	7: 103,506,799	H49L	probably benign	Het
Patl1	T	G	19: 11,937,354	L623R	probably damaging	Het
Pdc	T	C	1: 150,333,366	I200T	probably benign	Het
Pdzk1	A	G	3: 96,868,426	D370G	probably benign	Het
Pglyrp3	A	T	3: 92,031,534	I339F	probably damaging	Het
Plxnb1	T	C	9: 109,116,611	V2070A	probably damaging	Het
Poln	G	A	5: 34,109,431	R461C	probably damaging	Het
Prl2b1	C	A	13: 27,383,508	V218L	probably damaging	Het
Pygl	T	C	12: 70,216,654	D55G	probably damaging	Het
Rif1	C	G	2: 52,095,844	L614V	probably damaging	Het
Rnd2	C	T	11: 101,468,999	L57F	probably damaging	Het
RP24-351P7.8	T	C	7: 11,610,301	F62S	probably damaging	Het
Rsrp1	T	C	4: 134,924,381	F152S	probably damaging	Het
Sim2	T	C	16: 94,097,251	S115P	probably damaging	Het
Slc17a1	T	A	13: 23,875,610	I108K	possibly damaging	Het
Slc30a8	A	G	15: 52,325,658	D223G	probably damaging	Het
Slc39a4	A	T	15: 76,616,142	N69K	probably benign	Het
Slc51a	T	G	16: 32,479,766	T58P	probably damaging	Het
Slc7a14	T	C	3: 31,224,112	H448R	probably benign	Het
Sox6	A	T	7: 115,486,628	D659E	probably damaging	Het
Stard9	GCCC	GCC	2: 120,693,715		probably null	Het
Tsr1	C	T	11: 74,900,293		probably null	Het
Ttc12	T	C	9: 49,443,122	K565E	probably damaging	Het
Ube4b	A	T	4: 149,368,311	V386E	probably benign	Het
Ush2a	T	A	1: 188,728,096		probably null	Het
Usp5	C	A	6: 124,817,613		probably benign	Het
Vmn1r216	T	C	13: 23,099,935	F263L	probably benign	Het
Vmn2r88	T	A	14: 51,418,149	L606*	probably null	Het
Wee2	T	A	6: 40,449,620		probably null	Het
Zfhx3	T	C	8: 108,792,527	Y94H	probably damaging	Het
Zfp385c	G	A	11: 100,632,768	P120L	probably benign	Het

Other mutations in Smc3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01017:Smc3	APN	19	53629327	missense	probably damaging	0.99
IGL01300:Smc3	APN	19	53641852	splice site	probably benign
IGL02136:Smc3	APN	19	53635716	missense	probably benign	0.02
IGL02216:Smc3	APN	19	53621844	missense	probably damaging	1.00
IGL02473:Smc3	APN	19	53636448	missense	probably benign	0.06
IGL02797:Smc3	APN	19	53638758	missense	probably benign	0.03
IGL02959:Smc3	APN	19	53623557	missense	probably benign	0.00
IGL03343:Smc3	APN	19	53613842	missense	probably damaging	1.00
Bits	UTSW	19	53623218	critical splice donor site	probably null
Pieces	UTSW	19	53629371	missense	probably damaging	0.99
Smithereens	UTSW	19	53641931	missense	probably damaging	1.00
R0081:Smc3	UTSW	19	53601562	splice site	probably benign
R0940:Smc3	UTSW	19	53640909	missense	probably benign	0.10
R1248:Smc3	UTSW	19	53634078	missense	probably benign	0.01
R1661:Smc3	UTSW	19	53625065	missense	probably benign	0.08
R1779:Smc3	UTSW	19	53639369	missense	probably benign	0.02
R2046:Smc3	UTSW	19	53639414	missense	probably benign	0.00
R2073:Smc3	UTSW	19	53631533	missense	probably benign	0.08
R2074:Smc3	UTSW	19	53631533	missense	probably benign	0.08
R3077:Smc3	UTSW	19	53627891	missense	probably benign	0.16
R4962:Smc3	UTSW	19	53631517	missense	probably damaging	0.99
R5684:Smc3	UTSW	19	53640804	missense	probably benign	0.00
R6169:Smc3	UTSW	19	53634086	missense	probably benign	0.02
R6221:Smc3	UTSW	19	53641931	missense	probably damaging	1.00
R6258:Smc3	UTSW	19	53627731	splice site	probably null
R6960:Smc3	UTSW	19	53629371	missense	probably damaging	0.99
R7048:Smc3	UTSW	19	53629251	missense	probably benign	0.01
R7148:Smc3	UTSW	19	53641895	missense	possibly damaging	0.93
R7157:Smc3	UTSW	19	53641898	missense	probably damaging	1.00
R7805:Smc3	UTSW	19	53640959	missense	probably benign	0.26
R7968:Smc3	UTSW	19	53623218	critical splice donor site	probably null
R8066:Smc3	UTSW	19	53615145	missense	probably damaging	1.00
R8202:Smc3	UTSW	19	53628692	missense	possibly damaging	0.94
R8472:Smc3	UTSW	19	53628711	missense	probably benign	0.02
R8683:Smc3	UTSW	19	53641185	missense	possibly damaging	0.50
R8827:Smc3	UTSW	19	53622654	missense	probably benign	0.01
R9072:Smc3	UTSW	19	53628769	missense	probably benign	0.00
R9073:Smc3	UTSW	19	53628769	missense	probably benign	0.00
R9355:Smc3	UTSW	19	53634113	critical splice donor site	probably null
R9428:Smc3	UTSW	19	53628719	missense	possibly damaging	0.48
X0026:Smc3	UTSW	19	53625120	missense	probably benign	0.13

Predicted Primers

PCR Primer
(F):5'- TCGAGGAAGCCAGTTTACG -3'
(R):5'- CATTTTAAGAACAGCATGGTGGAG -3'

Sequencing Primer
(F):5'- GGAAGCCAGTTTACGTCAAAAG -3'
(R):5'- CCTGGTCTATACAGTAAGTTCCAGG -3'

Posted On

2017-06-26