Mutagenetix > Incidental Mutation

Incidental Mutation 'R6169:Smc3'

490350

Institutional Source

Beutler Lab

Gene Symbol

Smc3

Ensembl Gene

ENSMUSG00000024974

Gene Name

structural maintenance of chromosomes 3

Synonyms

Cspg6, Bamacan, Mmip1, SmcD

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6169 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

53588827-53634262 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 53622517 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 697 (N697K)

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 benign
Transcript: ENSMUST00000025930
AA Change: N697K

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000025930
Gene: ENSMUSG00000024974
AA Change: N697K

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000157053

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.5%

Validation Efficiency

94% (67/71)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930556J24Rik	C	A	11: 3,888,005 (GRCm39)	C127F	unknown	Het
9930111J21Rik2	A	T	11: 48,910,088 (GRCm39)		probably null	Het
Adamts16	A	T	13: 70,918,393 (GRCm39)	L676*	probably null	Het
Adgrv1	A	T	13: 81,567,378 (GRCm39)	V5265E	probably benign	Het
Afg3l2	G	T	18: 67,554,329 (GRCm39)	L458M	probably damaging	Het
Akap6	T	A	12: 53,189,141 (GRCm39)	M2185K	probably benign	Het
Ankfy1	G	A	11: 72,645,285 (GRCm39)	C788Y	probably benign	Het
Ankrd50	A	G	3: 38,509,988 (GRCm39)	V793A	probably damaging	Het
Arid2	T	A	15: 96,266,558 (GRCm39)	N535K	probably benign	Het
Atrnl1	A	G	19: 57,630,895 (GRCm39)	T221A	probably benign	Het
Bbof1	C	T	12: 84,473,588 (GRCm39)	T306I	probably benign	Het
Cabs1	C	T	5: 88,127,613 (GRCm39)	T88I	possibly damaging	Het
Ccdc60	C	A	5: 116,275,131 (GRCm39)	A351S	probably benign	Het
Cetn3	A	C	13: 81,940,097 (GRCm39)	R44S	probably damaging	Het
Cluap1	A	G	16: 3,746,425 (GRCm39)	K262R	possibly damaging	Het
Cnrip1	G	A	11: 17,004,731 (GRCm39)	V94I	probably null	Het
Cog6	A	T	3: 52,914,722 (GRCm39)	S245T	probably benign	Het
Disp2	T	A	2: 118,622,031 (GRCm39)	V921D	probably damaging	Het
Entrep2	G	A	7: 64,409,147 (GRCm39)	P416S	probably benign	Het
Ep400	T	C	5: 110,889,863 (GRCm39)	K504E	possibly damaging	Het
Fbn1	T	A	2: 125,177,409 (GRCm39)		probably null	Het
Fyb2	T	C	4: 104,857,713 (GRCm39)	V630A	probably benign	Het
Gm43218	T	A	6: 70,217,606 (GRCm39)	Y50F	probably benign	Het
Gm5431	T	C	11: 48,779,402 (GRCm39)	T507A	probably benign	Het
Gucy2e	G	T	11: 69,126,930 (GRCm39)	A181E	probably benign	Het
Hrnr	C	G	3: 93,233,062 (GRCm39)	S1100*	probably null	Het
Htt	T	C	5: 35,064,817 (GRCm39)	V3010A	probably damaging	Het
Ighv1-11	T	C	12: 114,575,918 (GRCm39)	Y99C	probably damaging	Het
Ighv1-12	T	C	12: 114,579,577 (GRCm39)	K25E	possibly damaging	Het
Il6ra	A	G	3: 89,778,598 (GRCm39)	F417S	probably benign	Het
Itgb4	T	C	11: 115,885,102 (GRCm39)	S994P	probably damaging	Het
Itgbl1	G	A	14: 123,897,790 (GRCm39)	A24T	probably benign	Het
Itpr1	T	C	6: 108,346,077 (GRCm39)	F127L	probably damaging	Het
Itprid2	T	G	2: 79,475,406 (GRCm39)	I455R	probably damaging	Het
Krt86	A	G	15: 101,374,170 (GRCm39)	Y243C	probably damaging	Het
Lnx1	A	T	5: 74,838,230 (GRCm39)	W11R	probably damaging	Het
Mast4	A	G	13: 102,923,929 (GRCm39)	L302P	probably damaging	Het
Mettl3	A	G	14: 52,536,214 (GRCm39)	V210A	possibly damaging	Het
Mllt1	T	C	17: 57,206,822 (GRCm39)	T341A	probably benign	Het
Obscn	T	C	11: 58,891,325 (GRCm39)	E7069G	unknown	Het
Or1e27-ps1	A	T	11: 73,556,160 (GRCm39)	T242S	possibly damaging	Het
Or52b4	T	C	7: 102,184,479 (GRCm39)	I175T	probably benign	Het
Osgep	A	G	14: 51,157,209 (GRCm39)	V11A	possibly damaging	Het
Oxld1	G	A	11: 120,347,675 (GRCm39)	A174V	possibly damaging	Het
Pibf1	A	T	14: 99,350,443 (GRCm39)	E197V	probably null	Het
Pkn1	G	A	8: 84,407,835 (GRCm39)	Q425*	probably null	Het
Pramel22	T	C	4: 143,380,685 (GRCm39)	Y446C	probably benign	Het
Prss35	T	C	9: 86,637,491 (GRCm39)	I87T	probably benign	Het
Psmc3	T	C	2: 90,888,184 (GRCm39)	F304S	probably damaging	Het
Psmd11	T	A	11: 80,351,539 (GRCm39)	M254K	probably damaging	Het
Ralgapa2	T	C	2: 146,292,385 (GRCm39)	Y218C	probably damaging	Het
Sec23b	C	T	2: 144,428,894 (GRCm39)	R701C	probably damaging	Het
Slc22a21	A	G	11: 53,848,913 (GRCm39)	S280P	probably damaging	Het
Slc39a12	T	C	2: 14,405,044 (GRCm39)	I212T	possibly damaging	Het
Slc7a12	T	C	3: 14,562,388 (GRCm39)	V255A	probably damaging	Het
Snai1	C	A	2: 167,380,831 (GRCm39)	P108Q	probably benign	Het
Stim2	T	G	5: 54,276,021 (GRCm39)	L732R	probably damaging	Het
Syde1	A	G	10: 78,421,938 (GRCm39)	L597S	probably damaging	Het
Tcte1	T	A	17: 45,845,996 (GRCm39)	M200K	probably benign	Het
Tenm2	T	A	11: 36,030,517 (GRCm39)	T761S	probably damaging	Het
Thoc2l	T	A	5: 104,666,262 (GRCm39)	N261K	probably benign	Het
Tlr2	C	A	3: 83,745,455 (GRCm39)	E209D	probably benign	Het
Tpp2	T	C	1: 44,022,739 (GRCm39)	L33P	probably damaging	Het
Trmt1l	C	A	1: 151,304,704 (GRCm39)		probably benign	Het
Unc45a	A	C	7: 79,978,511 (GRCm39)	S646A	possibly damaging	Het
Usp37	A	T	1: 74,534,910 (GRCm39)	I12N	probably damaging	Het
Vmn2r81	T	C	10: 79,104,382 (GRCm39)	V335A	probably benign	Het
Wwc2	A	T	8: 48,311,878 (GRCm39)	S762T	unknown	Het
Yeats2	A	G	16: 20,038,417 (GRCm39)	K129E	probably damaging	Het
Zscan4-ps2	T	C	7: 11,251,558 (GRCm39)	V198A	probably benign	Het

Other mutations in Smc3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01017:Smc3	APN	19	53,617,758 (GRCm39)	missense	probably damaging	0.99
IGL01300:Smc3	APN	19	53,630,283 (GRCm39)	splice site	probably benign
IGL02136:Smc3	APN	19	53,624,147 (GRCm39)	missense	probably benign	0.02
IGL02216:Smc3	APN	19	53,610,275 (GRCm39)	missense	probably damaging	1.00
IGL02473:Smc3	APN	19	53,624,879 (GRCm39)	missense	probably benign	0.06
IGL02797:Smc3	APN	19	53,627,189 (GRCm39)	missense	probably benign	0.03
IGL02959:Smc3	APN	19	53,611,988 (GRCm39)	missense	probably benign	0.00
IGL03343:Smc3	APN	19	53,602,273 (GRCm39)	missense	probably damaging	1.00
Bits	UTSW	19	53,611,649 (GRCm39)	critical splice donor site	probably null
Pieces	UTSW	19	53,617,802 (GRCm39)	missense	probably damaging	0.99
Smithereens	UTSW	19	53,630,362 (GRCm39)	missense	probably damaging	1.00
R0081:Smc3	UTSW	19	53,589,993 (GRCm39)	splice site	probably benign
R0940:Smc3	UTSW	19	53,629,340 (GRCm39)	missense	probably benign	0.10
R1248:Smc3	UTSW	19	53,622,509 (GRCm39)	missense	probably benign	0.01
R1661:Smc3	UTSW	19	53,613,496 (GRCm39)	missense	probably benign	0.08
R1779:Smc3	UTSW	19	53,627,800 (GRCm39)	missense	probably benign	0.02
R2046:Smc3	UTSW	19	53,627,845 (GRCm39)	missense	probably benign	0.00
R2073:Smc3	UTSW	19	53,619,964 (GRCm39)	missense	probably benign	0.08
R2074:Smc3	UTSW	19	53,619,964 (GRCm39)	missense	probably benign	0.08
R3077:Smc3	UTSW	19	53,616,322 (GRCm39)	missense	probably benign	0.16
R4962:Smc3	UTSW	19	53,619,948 (GRCm39)	missense	probably damaging	0.99
R5684:Smc3	UTSW	19	53,629,235 (GRCm39)	missense	probably benign	0.00
R6020:Smc3	UTSW	19	53,613,594 (GRCm39)	critical splice donor site	probably null
R6221:Smc3	UTSW	19	53,630,362 (GRCm39)	missense	probably damaging	1.00
R6258:Smc3	UTSW	19	53,616,162 (GRCm39)	splice site	probably null
R6960:Smc3	UTSW	19	53,617,802 (GRCm39)	missense	probably damaging	0.99
R7048:Smc3	UTSW	19	53,617,682 (GRCm39)	missense	probably benign	0.01
R7148:Smc3	UTSW	19	53,630,326 (GRCm39)	missense	possibly damaging	0.93
R7157:Smc3	UTSW	19	53,630,329 (GRCm39)	missense	probably damaging	1.00
R7805:Smc3	UTSW	19	53,629,390 (GRCm39)	missense	probably benign	0.26
R7968:Smc3	UTSW	19	53,611,649 (GRCm39)	critical splice donor site	probably null
R8066:Smc3	UTSW	19	53,603,576 (GRCm39)	missense	probably damaging	1.00
R8202:Smc3	UTSW	19	53,617,123 (GRCm39)	missense	possibly damaging	0.94
R8472:Smc3	UTSW	19	53,617,142 (GRCm39)	missense	probably benign	0.02
R8683:Smc3	UTSW	19	53,629,616 (GRCm39)	missense	possibly damaging	0.50
R8827:Smc3	UTSW	19	53,611,085 (GRCm39)	missense	probably benign	0.01
R9072:Smc3	UTSW	19	53,617,200 (GRCm39)	missense	probably benign	0.00
R9073:Smc3	UTSW	19	53,617,200 (GRCm39)	missense	probably benign	0.00
R9355:Smc3	UTSW	19	53,622,544 (GRCm39)	critical splice donor site	probably null
R9428:Smc3	UTSW	19	53,617,150 (GRCm39)	missense	possibly damaging	0.48
X0026:Smc3	UTSW	19	53,613,551 (GRCm39)	missense	probably benign	0.13

Predicted Primers

PCR Primer
(F):5'- ACTCATTGAATGGAGGCTGG -3'
(R):5'- CAAAGCATGCACTAGTACTGTCTAC -3'

Sequencing Primer
(F):5'- GCTGGTAAAGAGAACGACTCCTTC -3'
(R):5'- GCATGCACTAGTACTGTCTACTTAAC -3'

Posted On

2017-10-10