Mutagenetix > Incidental Mutation

Incidental Mutation 'R6258:Smc3'

506515

Institutional Source

Beutler Lab

Gene Symbol

Smc3

Ensembl Gene

ENSMUSG00000024974

Gene Name

structural maintenance of chromosomes 3

Synonyms

Cspg6, Bamacan, Mmip1, SmcD

MMRRC Submission

044375-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6258 (G1)

Quality Score

153.008

Status

Validated

Chromosome

Chromosomal Location

53588827-53634262 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to A at 53616162 bp (GRCm39)

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: 99.7%
10x: 98.5%
20x: 95.7%

Validation Efficiency

99% (74/75)

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
Adamtsl3	T	C	7: 82,178,191 (GRCm39)		probably null	Het
Alms1	A	T	6: 85,605,717 (GRCm39)	K2456*	probably null	Het
Alppl2	A	T	1: 87,016,184 (GRCm39)	M225K	probably damaging	Het
AU041133	A	G	10: 81,986,992 (GRCm39)	E215G	probably damaging	Het
Carmil3	T	A	14: 55,737,889 (GRCm39)	L815Q	probably damaging	Het
Casr	A	G	16: 36,337,971 (GRCm39)	C60R	probably damaging	Het
Cdc7	A	G	5: 107,117,093 (GRCm39)	K84E	probably damaging	Het
Cdc73	G	A	1: 143,567,211 (GRCm39)	T104I	probably benign	Het
Clcc1	G	A	3: 108,580,624 (GRCm39)	V313I	possibly damaging	Het
Cntn3	A	G	6: 102,254,178 (GRCm39)		probably null	Het
Crocc2	A	G	1: 93,141,360 (GRCm39)	K1171R	possibly damaging	Het
Ctsa	T	C	2: 164,676,281 (GRCm39)	V86A	probably damaging	Het
Cyp2s1	ACAGCAGCAGCAGCAGCAGCAGCAG	ACAGCAGCAGCAGCAGCAGCAG	7: 25,515,867 (GRCm39)		probably benign	Het
Dab1	C	T	4: 104,588,948 (GRCm39)	A524V	probably benign	Het
Dnah17	C	A	11: 118,017,148 (GRCm39)	W197C	probably damaging	Het
Dnah17	A	T	11: 118,017,150 (GRCm39)	W197R	probably damaging	Het
Dnah17	C	T	11: 118,017,149 (GRCm39)	W197*	probably null	Het
Egflam	T	A	15: 7,263,773 (GRCm39)	T726S	probably damaging	Het
Eml2	T	G	7: 18,913,289 (GRCm39)		probably null	Het
Ercc6	T	A	14: 32,279,813 (GRCm39)	D609E	probably benign	Het
Erg	C	A	16: 95,181,100 (GRCm39)	R147L	probably damaging	Het
Faiml	T	C	9: 99,114,513 (GRCm39)	I125M	possibly damaging	Het
Fbxo41	A	T	6: 85,455,537 (GRCm39)	L549H	probably damaging	Het
Fbxw2	A	T	2: 34,702,825 (GRCm39)		probably null	Het
Fgd6	T	A	10: 93,880,161 (GRCm39)	N338K	probably benign	Het
Gaa	C	A	11: 119,171,997 (GRCm39)	A700D	probably benign	Het
Gm32742	T	A	9: 51,068,862 (GRCm39)	I200F	probably damaging	Het
Gm4924	T	G	10: 82,213,307 (GRCm39)		probably benign	Het
Gm8369	G	A	19: 11,488,973 (GRCm39)	A87T	possibly damaging	Het
H2-M10.1	T	A	17: 36,634,994 (GRCm39)	I304F	unknown	Het
Ighv5-8	A	G	12: 113,618,611 (GRCm39)	T9A	possibly damaging	Het
Itgb4	C	T	11: 115,874,983 (GRCm39)	R447W	probably benign	Het
Jakmip1	G	T	5: 37,299,104 (GRCm39)	E775*	probably null	Het
Klhl40	T	C	9: 121,607,026 (GRCm39)	F62S	probably damaging	Het
Krtcap3	A	T	5: 31,409,572 (GRCm39)	R84W	probably damaging	Het
Lgr6	C	T	1: 134,921,748 (GRCm39)	A199T	probably damaging	Het
Lins1	T	C	7: 66,360,496 (GRCm39)		probably null	Het
Magi3	A	G	3: 103,996,912 (GRCm39)	L211P	probably damaging	Het
Map2k5	T	A	9: 63,124,647 (GRCm39)	I359F	probably benign	Het
Map4k5	C	A	12: 69,878,336 (GRCm39)	R355L	probably benign	Het
Mef2c	T	A	13: 83,801,057 (GRCm39)	D252E	probably damaging	Het
Methig1	T	C	15: 100,251,422 (GRCm39)	V111A	possibly damaging	Het
Mical3	A	T	6: 120,985,991 (GRCm39)	L150Q	probably damaging	Het
Nf1	A	T	11: 79,456,581 (GRCm39)		probably null	Het
Nisch	T	A	14: 30,899,085 (GRCm39)		probably benign	Het
Or4f15	C	T	2: 111,814,396 (GRCm39)	V8I	probably benign	Het
Or5p61	T	C	7: 107,758,181 (GRCm39)	N300D	probably damaging	Het
Pcdhb12	T	C	18: 37,569,892 (GRCm39)	V346A	probably benign	Het
Pde7b	T	C	10: 20,316,546 (GRCm39)	D168G	possibly damaging	Het
Pdzrn4	A	T	15: 92,655,562 (GRCm39)	E485V	probably damaging	Het
Pla2g4a	A	G	1: 149,733,238 (GRCm39)	S504P	probably benign	Het
Plin2	G	T	4: 86,575,526 (GRCm39)	A341D	probably damaging	Het
Psma8	A	G	18: 14,854,324 (GRCm39)	D68G	probably damaging	Het
Rcor3	G	A	1: 191,808,559 (GRCm39)	H207Y	probably benign	Het
Rptn	C	G	3: 93,305,437 (GRCm39)	H923Q	possibly damaging	Het
Ryr3	A	G	2: 112,490,449 (GRCm39)	F3795S	probably damaging	Het
Samm50	C	G	15: 84,084,512 (GRCm39)	P150A	probably damaging	Het
Samm50	C	A	15: 84,084,513 (GRCm39)	P150H	probably damaging	Het
Slc28a2b	A	T	2: 122,353,963 (GRCm39)	I530F	probably damaging	Het
Slc6a18	A	T	13: 73,818,164 (GRCm39)	C284*	probably null	Het
Snrnp200	G	A	2: 127,060,343 (GRCm39)	G529D	possibly damaging	Het
Sord	T	A	2: 122,089,613 (GRCm39)		probably null	Het
Spdl1	T	A	11: 34,710,713 (GRCm39)	N345I	probably damaging	Het
Sucnr1	T	C	3: 59,993,778 (GRCm39)	L102P	probably damaging	Het
Tbc1d9	T	C	8: 83,937,145 (GRCm39)	W76R	probably damaging	Het
Tcerg1	T	A	18: 42,686,530 (GRCm39)	Y696N	probably damaging	Het
Thsd7b	A	G	1: 129,595,655 (GRCm39)	T492A	probably benign	Het
Trdmt1	T	A	2: 13,524,870 (GRCm39)	Q195L	probably benign	Het
Ubr3	A	G	2: 69,813,208 (GRCm39)		probably null	Het
Ung	A	T	5: 114,275,361 (GRCm39)	Y250F	probably benign	Het
Vezf1	A	G	11: 87,972,326 (GRCm39)	N229S	probably damaging	Het
Wdfy3	C	T	5: 102,020,831 (GRCm39)	R2491Q	possibly damaging	Het
Wdr97	C	A	15: 76,239,895 (GRCm39)	S277*	probably null	Het
Zfp1007	T	C	5: 109,824,433 (GRCm39)	H339R	probably benign	Het
Zfp709	TCGACG	TCG	8: 72,644,552 (GRCm39)		probably benign	Het
Zscan4-ps1	C	A	7: 10,799,829 (GRCm39)	E353D	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
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
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'- TGAGCACAAGGATTCGAGTTTTCAG -3'
(R):5'- TCCAGTTCTTCAACTCGAGC -3'

Sequencing Primer
(F):5'- GGCCTCTCACTGCTTATAGAAAGAG -3'
(R):5'- CAACTCGAGCTTTGACTTCATTGAG -3'

Posted On

2018-03-15