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

SmcD, Mmip1, Bamacan, Cspg6

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R6169 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

53600398-53645833 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 53634086 bp (GRCm38)

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: 3,938,005	C127F	unknown	Het
9930111J21Rik2	A	T	11: 49,019,261		probably null	Het
Adamts16	A	T	13: 70,770,274	L676*	probably null	Het
Adgrv1	A	T	13: 81,419,259	V5265E	probably benign	Het
Afg3l2	G	T	18: 67,421,259	L458M	probably damaging	Het
Akap6	T	A	12: 53,142,358	M2185K	probably benign	Het
Ankfy1	G	A	11: 72,754,459	C788Y	probably benign	Het
Ankrd50	A	G	3: 38,455,839	V793A	probably damaging	Het
Arid2	T	A	15: 96,368,677	N535K	probably benign	Het
Atrnl1	A	G	19: 57,642,463	T221A	probably benign	Het
Bbof1	C	T	12: 84,426,814	T306I	probably benign	Het
BC005561	T	A	5: 104,518,396	N261K	probably benign	Het
Cabs1	C	T	5: 87,979,754	T88I	possibly damaging	Het
Ccdc60	C	A	5: 116,137,072	A351S	probably benign	Het
Cetn3	A	C	13: 81,791,978	R44S	probably damaging	Het
Cluap1	A	G	16: 3,928,561	K262R	possibly damaging	Het
Cnrip1	G	A	11: 17,054,731	V94I	probably null	Het
Cog6	A	T	3: 53,007,301	S245T	probably benign	Het
Disp2	T	A	2: 118,791,550	V921D	probably damaging	Het
Ep400	T	C	5: 110,741,997	K504E	possibly damaging	Het
Fam189a1	G	A	7: 64,759,399	P416S	probably benign	Het
Fbn1	T	A	2: 125,335,489		probably null	Het
Fyb2	T	C	4: 105,000,516	V630A	probably benign	Het
Gm13088	T	C	4: 143,654,115	Y446C	probably benign	Het
Gm43218	T	A	6: 70,240,622	Y50F	probably benign	Het
Gm5431	T	C	11: 48,888,575	T507A	probably benign	Het
Gucy2e	G	T	11: 69,236,104	A181E	probably benign	Het
Hrnr	C	G	3: 93,325,755	S1100*	probably null	Het
Htt	T	C	5: 34,907,473	V3010A	probably damaging	Het
Ighv1-11	T	C	12: 114,612,298	Y99C	probably damaging	Het
Ighv1-12	T	C	12: 114,615,957	K25E	possibly damaging	Het
Il6ra	A	G	3: 89,871,291	F417S	probably benign	Het
Itgb4	T	C	11: 115,994,276	S994P	probably damaging	Het
Itgbl1	G	A	14: 123,660,378	A24T	probably benign	Het
Itpr1	T	C	6: 108,369,116	F127L	probably damaging	Het
Krt86	A	G	15: 101,476,289	Y243C	probably damaging	Het
Lnx1	A	T	5: 74,677,569	W11R	probably damaging	Het
Mast4	A	G	13: 102,787,421	L302P	probably damaging	Het
Mettl3	A	G	14: 52,298,757	V210A	possibly damaging	Het
Mllt1	T	C	17: 56,899,822	T341A	probably benign	Het
Obscn	T	C	11: 59,000,499	E7069G	unknown	Het
Olfr387-ps1	A	T	11: 73,665,334	T242S	possibly damaging	Het
Olfr547	T	C	7: 102,535,272	I175T	probably benign	Het
Osgep	A	G	14: 50,919,752	V11A	possibly damaging	Het
Oxld1	G	A	11: 120,456,849	A174V	possibly damaging	Het
Pibf1	A	T	14: 99,113,007	E197V	probably null	Het
Pkn1	G	A	8: 83,681,206	Q425*	probably null	Het
Prss35	T	C	9: 86,755,438	I87T	probably benign	Het
Psmc3	T	C	2: 91,057,839	F304S	probably damaging	Het
Psmd11	T	A	11: 80,460,713	M254K	probably damaging	Het
Ralgapa2	T	C	2: 146,450,465	Y218C	probably damaging	Het
Sec23b	C	T	2: 144,586,974	R701C	probably damaging	Het
Slc22a21	A	G	11: 53,958,087	S280P	probably damaging	Het
Slc39a12	T	C	2: 14,400,233	I212T	possibly damaging	Het
Slc7a12	T	C	3: 14,497,328	V255A	probably damaging	Het
Snai1	C	A	2: 167,538,911	P108Q	probably benign	Het
Ssfa2	T	G	2: 79,645,062	I455R	probably damaging	Het
Stim2	T	G	5: 54,118,679	L732R	probably damaging	Het
Syde1	A	G	10: 78,586,104	L597S	probably damaging	Het
Tcte1	T	A	17: 45,535,070	M200K	probably benign	Het
Tenm2	T	A	11: 36,139,690	T761S	probably damaging	Het
Tlr2	C	A	3: 83,838,148	E209D	probably benign	Het
Tpp2	T	C	1: 43,983,579	L33P	probably damaging	Het
Trmt1l	C	A	1: 151,428,953		probably benign	Het
Unc45a	A	C	7: 80,328,763	S646A	possibly damaging	Het
Usp37	A	T	1: 74,495,751	I12N	probably damaging	Het
Vmn2r81	T	C	10: 79,268,548	V335A	probably benign	Het
Wwc2	A	T	8: 47,858,843	S762T	unknown	Het
Yeats2	A	G	16: 20,219,667	K129E	probably damaging	Het
Zscan4-ps2	T	C	7: 11,517,631	V198A	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
R6020:Smc3	UTSW	19	53625163	critical splice donor site	probably null
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'- ACTCATTGAATGGAGGCTGG -3'
(R):5'- CAAAGCATGCACTAGTACTGTCTAC -3'

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

Posted On

2017-10-10