Mutagenetix > Incidental Mutation

Incidental Mutation 'R7048:Smc3'

547464

Institutional Source

Beutler Lab

Gene Symbol

Smc3

Ensembl Gene

ENSMUSG00000024974

Gene Name

structural maintenance of chromosomes 3

Synonyms

Cspg6, Bamacan, Mmip1, SmcD

MMRRC Submission

045146-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7048 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

53588827-53634262 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 53617682 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 560 (Y560H)

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: Y560H

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000025930
Gene: ENSMUSG00000024974
AA Change: Y560H

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

97% (66/68)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrl2	T	C	3: 148,552,565 (GRCm39)	D629G	probably damaging	Het
Akap11	T	A	14: 78,749,954 (GRCm39)	Q811L		Het
Ank2	T	A	3: 126,819,267 (GRCm39)	Q468L	probably benign	Het
Ano3	A	T	2: 110,513,116 (GRCm39)	Y626*	probably null	Het
Ap1m1	A	G	8: 73,003,642 (GRCm39)	N114S	probably damaging	Het
Asb3	T	A	11: 31,051,121 (GRCm39)	I525N	probably damaging	Het
Atg4a-ps	A	G	3: 103,552,672 (GRCm39)	I223T	probably damaging	Het
B3gnt7	T	C	1: 86,233,308 (GRCm39)	Y68H	probably benign	Het
Bbs5	T	C	2: 69,484,705 (GRCm39)	I125T	probably benign	Het
Cd180	A	G	13: 102,841,431 (GRCm39)	N159S	probably damaging	Het
Cd37	T	C	7: 44,887,888 (GRCm39)		probably benign	Het
Cdk14	T	A	5: 5,143,005 (GRCm39)	Q242L	probably damaging	Het
Clcn1	T	C	6: 42,284,477 (GRCm39)	V605A	probably damaging	Het
Cped1	G	A	6: 22,119,469 (GRCm39)	M309I	probably benign	Het
Cyp2r1	A	T	7: 114,151,971 (GRCm39)	Y120N	probably damaging	Het
Ddx3y	A	T	Y: 1,279,491 (GRCm39)	S124R	probably benign	Het
Dlec1	A	T	9: 118,972,472 (GRCm39)		probably null	Het
Dnah17	T	C	11: 117,936,944 (GRCm39)	E3420G	possibly damaging	Het
Dnajc13	C	T	9: 104,080,613 (GRCm39)		probably null	Het
Dusp23	A	T	1: 172,459,253 (GRCm39)	Y136*	probably null	Het
Eif4b	A	G	15: 102,001,571 (GRCm39)		probably benign	Het
F13a1	A	G	13: 37,082,117 (GRCm39)	V529A	probably benign	Het
Fhl2	A	G	1: 43,162,808 (GRCm39)	Y236H	probably damaging	Het
Gm826	C	T	2: 160,169,026 (GRCm39)	W94*	probably null	Het
Gpsm2	C	T	3: 108,610,361 (GRCm39)	R33H	probably damaging	Het
Hmcn1	T	C	1: 150,475,404 (GRCm39)		probably null	Het
Ifit1bl2	T	C	19: 34,596,551 (GRCm39)	D355G	probably benign	Het
Itga8	A	G	2: 12,115,895 (GRCm39)	V77A	probably damaging	Het
Kcmf1	C	T	6: 72,826,450 (GRCm39)	R40K	probably damaging	Het
Kdm7a	T	C	6: 39,145,982 (GRCm39)	E315G	probably damaging	Het
Kmt2b	C	T	7: 30,268,731 (GRCm39)	G2666D	probably damaging	Het
Lrrtm1	A	G	6: 77,221,152 (GRCm39)	N203S	probably damaging	Het
Mdn1	A	G	4: 32,767,969 (GRCm39)	N5301D	probably benign	Het
Mest	T	G	6: 30,742,723 (GRCm39)	H108Q	probably damaging	Het
Mettl25b	A	G	3: 87,837,167 (GRCm39)	I36T	probably damaging	Het
Moxd1	C	A	10: 24,157,374 (GRCm39)	D335E	probably damaging	Het
Ncf2	A	C	1: 152,683,921 (GRCm39)	N47H	probably benign	Het
Npc1	A	G	18: 12,337,822 (GRCm39)		probably null	Het
Or14j2	A	T	17: 37,886,114 (GRCm39)	S67T	probably damaging	Het
Pcid2	A	G	8: 13,128,243 (GRCm39)	V386A	probably benign	Het
Phactr2	T	A	10: 13,121,168 (GRCm39)	T444S	probably benign	Het
Plekha7	T	C	7: 115,747,559 (GRCm39)	N710D	probably benign	Het
Ppp1r16b	C	T	2: 158,599,174 (GRCm39)	T382I	probably benign	Het
Pramel15	T	C	4: 144,103,754 (GRCm39)	D124G	probably benign	Het
Ptprz1	A	T	6: 22,961,622 (GRCm39)	Y111F	probably benign	Het
Rbbp8	A	G	18: 11,865,277 (GRCm39)	E722G	possibly damaging	Het
Rimbp3	A	G	16: 17,028,190 (GRCm39)	D538G	probably benign	Het
Rims1	A	G	1: 22,511,901 (GRCm39)	S551P	probably damaging	Het
Rsrc1	A	G	3: 67,088,164 (GRCm39)	D166G	probably damaging	Het
Selenon	T	C	4: 134,270,154 (GRCm39)	N350S	probably benign	Het
Sh3gl2	T	A	4: 85,295,802 (GRCm39)	L168H	probably damaging	Het
Syce1	C	T	7: 140,359,281 (GRCm39)	D147N	possibly damaging	Het
Syt10	A	C	15: 89,675,008 (GRCm39)	V446G	probably damaging	Het
Taar1	T	C	10: 23,796,722 (GRCm39)	L140P	probably benign	Het
Tfpi2	C	A	6: 3,968,032 (GRCm39)	C36F	probably damaging	Het
Thoc5	G	A	11: 4,876,237 (GRCm39)		probably null	Het
Tnrc6c	T	A	11: 117,612,800 (GRCm39)	N319K	probably benign	Het
Trhr2	C	T	8: 123,085,418 (GRCm39)	D189N	probably damaging	Het
Trim42	A	T	9: 97,245,474 (GRCm39)	F442Y	probably damaging	Het
Ubap2	G	A	4: 41,196,033 (GRCm39)	T949I	possibly damaging	Het
Ugt1a8	T	C	1: 88,016,024 (GRCm39)	F146L	probably benign	Het
Vmn2r80	C	A	10: 79,030,153 (GRCm39)	Q660K	probably damaging	Het
Vstm2b	C	T	7: 40,578,800 (GRCm39)	T258I	possibly damaging	Het
Washc2	T	C	6: 116,197,544 (GRCm39)	L259P	possibly damaging	Het
Zscan18	A	T	7: 12,508,671 (GRCm39)		probably benign	Het
Zzef1	T	G	11: 72,757,525 (GRCm39)	Y1193*	probably null	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
R6169:Smc3	UTSW	19	53,622,517 (GRCm39)	missense	probably benign	0.02
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
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'- GTTTCACAGTTCAGAAACCAGAAC -3'
(R):5'- ATGTGTGTTTACCTTACAGACCAC -3'

Sequencing Primer
(F):5'- GAAACCAGAACTTTACCCTTTGG -3'
(R):5'- CCAGCACATATTAAGCAGATGTC -3'

Posted On

2019-05-13