Incidental Mutation 'R4816:Smc2'
ID 369779
Institutional Source Beutler Lab
Gene Symbol Smc2
Ensembl Gene ENSMUSG00000028312
Gene Name structural maintenance of chromosomes 2
Synonyms 5730502P04Rik, CAP-E, Fin16, Smc2l1
MMRRC Submission 042434-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.959) question?
Stock # R4816 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 52439243-52488260 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 52451231 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 292 (T292A)
Ref Sequence ENSEMBL: ENSMUSP00000113940 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000102915] [ENSMUST00000117280] [ENSMUST00000142227]
AlphaFold Q8CG48
Predicted Effect probably benign
Transcript: ENSMUST00000102915
AA Change: T292A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000099979
Gene: ENSMUSG00000028312
AA Change: T292A

DomainStartEndE-ValueType
internal_repeat_1 146 174 2.4e-6 PROSPERO
low complexity region 183 207 N/A INTRINSIC
coiled coil region 238 355 N/A INTRINSIC
coiled coil region 400 503 N/A INTRINSIC
SMC_hinge 520 640 3.8e-34 SMART
coiled coil region 676 880 N/A INTRINSIC
coiled coil region 984 1031 N/A INTRINSIC
PDB:4I99|B 1034 1186 3e-15 PDB
SCOP:d1e69a_ 1066 1144 2e-7 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000117280
AA Change: T292A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000113940
Gene: ENSMUSG00000028312
AA Change: T292A

DomainStartEndE-ValueType
Pfam:AAA_21 27 131 3.8e-6 PFAM
internal_repeat_1 146 174 2.4e-6 PROSPERO
low complexity region 183 207 N/A INTRINSIC
coiled coil region 238 355 N/A INTRINSIC
coiled coil region 400 503 N/A INTRINSIC
SMC_hinge 520 640 3.8e-34 SMART
coiled coil region 676 880 N/A INTRINSIC
coiled coil region 984 1031 N/A INTRINSIC
PDB:4I99|B 1034 1186 3e-15 PDB
SCOP:d1e69a_ 1066 1144 2e-7 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131163
Predicted Effect probably benign
Transcript: ENSMUST00000142227
AA Change: T292A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000114228
Gene: ENSMUSG00000028312
AA Change: T292A

DomainStartEndE-ValueType
Pfam:SMC_N 2 351 2.3e-36 PFAM
Pfam:AAA_21 27 131 1.7e-8 PFAM
coiled coil region 400 471 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146787
Meta Mutation Damage Score 0.0591 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.5%
  • 20x: 93.0%
Validation Efficiency 97% (113/116)
MGI Phenotype FUNCTION: The protein encoded by this gene is a component of both condensin I and condensin II complexes, and forms a heterodimer with structural maintenance of chromosome 4 (Smc4). This heterodimer is the catalytic subunit for both condensin complexes, and is involved in several processes, including chromosome condensation during mitosis and meiosis, cohesin removal during mitosis and meiosis, and single-strand break (SSB) repair. Reduced expression of this gene results in chromosome segregation defects during mitosis and meiosis, with a more severe defect observed in embryonic stem cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]
PHENOTYPE: Homozygous null mice die embryonically. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 107 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc8 C A 7: 45,754,131 (GRCm39) A1562S probably benign Het
Adam30 C A 3: 98,070,061 (GRCm39) D631E possibly damaging Het
Adgrv1 T C 13: 81,676,793 (GRCm39) T2013A probably damaging Het
Ark2n A T 18: 77,740,995 (GRCm39) probably null Het
Baiap3 T A 17: 25,466,269 (GRCm39) probably benign Het
Bicra T C 7: 15,722,831 (GRCm39) T229A possibly damaging Het
C1qbp A G 11: 70,873,190 (GRCm39) probably benign Het
C2cd3 C A 7: 100,040,226 (GRCm39) T265K probably benign Het
Cacna1s T A 1: 136,043,007 (GRCm39) I1331K possibly damaging Het
Cdadc1 AGACGGA AGA 14: 59,806,440 (GRCm39) probably null Het
Cdcp2 A G 4: 106,963,969 (GRCm39) Y273C probably damaging Het
Cdh23 A C 10: 60,244,856 (GRCm39) V1013G possibly damaging Het
Celf3 T A 3: 94,386,529 (GRCm39) I39N probably damaging Het
Cep152 A C 2: 125,405,674 (GRCm39) S1619R probably damaging Het
Cfap36 A G 11: 29,195,108 (GRCm39) I42T probably damaging Het
Cfap61 G T 2: 145,985,020 (GRCm39) V955L probably damaging Het
Cit G A 5: 116,046,750 (GRCm39) D388N probably damaging Het
Clca3a2 T C 3: 144,516,613 (GRCm39) M328V probably benign Het
Cntn4 A T 6: 106,527,458 (GRCm39) I447L probably benign Het
Csmd3 T C 15: 47,721,330 (GRCm39) T1538A possibly damaging Het
Cstf1 A G 2: 172,214,905 (GRCm39) K9E probably damaging Het
Dip2c T A 13: 9,625,186 (GRCm39) M560K probably benign Het
Dsg1a A T 18: 20,466,779 (GRCm39) T550S probably benign Het
Dtnb A G 12: 3,799,505 (GRCm39) E460G probably damaging Het
Dus1l GAGGTAAG GAG 11: 120,680,584 (GRCm39) probably benign Het
Efl1 T A 7: 82,320,927 (GRCm39) V120E probably damaging Het
Fbxl13 T C 5: 21,689,001 (GRCm39) Y769C probably benign Het
Fcho2 T C 13: 98,942,874 (GRCm39) Y22C probably damaging Het
Flacc1 G A 1: 58,709,567 (GRCm39) A196V probably benign Het
Gbp3 T C 3: 142,273,335 (GRCm39) V294A probably damaging Het
Gls A G 1: 52,239,104 (GRCm39) probably benign Het
Gm15130 A T 2: 110,965,714 (GRCm39) probably benign Het
Gm6185 A T 1: 161,040,728 (GRCm39) noncoding transcript Het
Gpr171 T A 3: 59,005,517 (GRCm39) H86L probably damaging Het
Gpr179 T C 11: 97,230,074 (GRCm39) T694A probably damaging Het
H2-Aa A T 17: 34,502,794 (GRCm39) V124E probably damaging Het
H2bc13 A G 13: 21,900,135 (GRCm39) M60T probably benign Het
H2-M5 A G 17: 37,300,309 (GRCm39) probably benign Het
Igf2r A T 17: 12,902,984 (GRCm39) N2355K probably damaging Het
Il9r A C 11: 32,142,654 (GRCm39) S295A possibly damaging Het
Ipo9 T C 1: 135,334,288 (GRCm39) T313A probably benign Het
Kalrn C T 16: 34,334,389 (GRCm39) probably benign Het
Lama3 G A 18: 12,610,661 (GRCm39) V1175M possibly damaging Het
Lhpp T A 7: 132,272,104 (GRCm39) C242* probably null Het
Lipe A G 7: 25,079,568 (GRCm39) S1013P probably damaging Het
Lrrc25 C T 8: 71,070,726 (GRCm39) T169I probably benign Het
Lrrc39 T C 3: 116,362,515 (GRCm39) probably null Het
Lrrd1 T A 5: 3,901,126 (GRCm39) L477* probably null Het
Lrriq4 A G 3: 30,714,196 (GRCm39) I515V possibly damaging Het
Magel2 A G 7: 62,030,840 (GRCm39) Y1248C unknown Het
Maml1 G T 11: 50,149,162 (GRCm39) N859K possibly damaging Het
Mdm1 A T 10: 117,982,782 (GRCm39) H139L possibly damaging Het
Mef2d C T 3: 88,075,397 (GRCm39) P420S possibly damaging Het
Mgat4b A G 11: 50,101,848 (GRCm39) K38E probably benign Het
Mtmr4 T C 11: 87,494,923 (GRCm39) V405A probably damaging Het
Naip5 G A 13: 100,356,195 (GRCm39) T1140M probably benign Het
Naip5 T C 13: 100,356,204 (GRCm39) Q1137R probably benign Het
Naip5 G A 13: 100,356,189 (GRCm39) S1142F probably benign Het
Nfe2l3 T C 6: 51,433,604 (GRCm39) S239P probably damaging Het
Nlrp3 A G 11: 59,439,127 (GRCm39) I235V probably benign Het
Nyap2 T A 1: 81,219,028 (GRCm39) L318Q probably damaging Het
Nynrin G A 14: 56,109,458 (GRCm39) V1522M probably damaging Het
Oog3 A G 4: 143,885,731 (GRCm39) L289P probably damaging Het
Or52n20 C T 7: 104,319,942 (GRCm39) P11L probably benign Het
Or5b107 A G 19: 13,142,488 (GRCm39) I37V probably benign Het
Or6c69b T C 10: 129,627,308 (GRCm39) D50G probably damaging Het
Or8b12b T A 9: 37,684,726 (GRCm39) M257K possibly damaging Het
Or9g20 A T 2: 85,630,391 (GRCm39) N74K probably benign Het
Pax6 T C 2: 105,514,129 (GRCm39) probably benign Het
Pbrm1 G A 14: 30,832,405 (GRCm39) R1441K probably benign Het
Pcdha9 C T 18: 37,132,511 (GRCm39) R527W probably damaging Het
Pcdhb17 T C 18: 37,620,450 (GRCm39) S747P probably benign Het
Pcnx3 A C 19: 5,738,023 (GRCm39) probably null Het
Pds5a A T 5: 65,808,632 (GRCm39) V413E probably damaging Het
Phpt1 G T 2: 25,464,332 (GRCm39) probably benign Het
Phykpl A G 11: 51,483,780 (GRCm39) E220G probably benign Het
Pias2 T C 18: 77,193,587 (GRCm39) probably null Het
Pkhd1 T A 1: 20,269,639 (GRCm39) I3302L probably damaging Het
Poli A G 18: 70,655,822 (GRCm39) L241P probably damaging Het
Ppm1h T A 10: 122,515,284 (GRCm39) I65N possibly damaging Het
Ptpn14 T C 1: 189,588,997 (GRCm39) L954P probably damaging Het
Pxk T G 14: 8,136,893 (GRCm38) M138R probably damaging Het
Rasl11b G T 5: 74,359,058 (GRCm39) D188Y probably damaging Het
Rtraf A G 14: 19,872,644 (GRCm39) F59S probably benign Het
Sanbr A C 11: 23,565,243 (GRCm39) I248S possibly damaging Het
Serpinb5 G T 1: 106,800,069 (GRCm39) L86F probably damaging Het
Setdb2 G A 14: 59,651,095 (GRCm39) T412I probably benign Het
Shank2 C A 7: 143,606,043 (GRCm39) N75K probably damaging Het
Shank3 T A 15: 89,427,318 (GRCm39) I791N probably damaging Het
Slc25a13 T A 6: 6,114,274 (GRCm39) M213L possibly damaging Het
Slc25a21 T C 12: 56,760,623 (GRCm39) Y298C probably damaging Het
Slc34a2 A G 5: 53,226,362 (GRCm39) N495S probably damaging Het
Spag9 T C 11: 93,939,425 (GRCm39) probably benign Het
Tas2r113 C T 6: 132,870,745 (GRCm39) P258S probably benign Het
Tbkbp1 T C 11: 97,029,567 (GRCm39) S530G probably benign Het
Tenm2 A G 11: 35,918,117 (GRCm39) V1881A probably damaging Het
Tm9sf1 C T 14: 55,878,606 (GRCm39) R262Q possibly damaging Het
Tmcc3 G T 10: 94,414,646 (GRCm39) G147V possibly damaging Het
Trim38 A T 13: 23,972,264 (GRCm39) E195V probably damaging Het
Try5 T C 6: 41,290,349 (GRCm39) Y45C probably benign Het
Umad1 A C 6: 8,457,462 (GRCm39) probably benign Het
Vmn2r105 T C 17: 20,428,953 (GRCm39) I708V probably benign Het
Zc3h12d A T 10: 7,743,711 (GRCm39) S494C probably damaging Het
Zeb2 A G 2: 44,887,780 (GRCm39) S382P probably damaging Het
Zfc3h1 A G 10: 115,251,599 (GRCm39) S1304G probably benign Het
Zfp287 G T 11: 62,605,074 (GRCm39) T611K probably damaging Het
Zfp534 G A 4: 147,758,743 (GRCm39) T642I possibly damaging Het
Other mutations in Smc2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01322:Smc2 APN 4 52,450,842 (GRCm39) missense probably damaging 1.00
IGL02045:Smc2 APN 4 52,462,914 (GRCm39) missense probably benign 0.01
IGL03013:Smc2 APN 4 52,442,280 (GRCm39) missense probably damaging 1.00
IGL03031:Smc2 APN 4 52,449,638 (GRCm39) missense probably benign 0.35
IGL03246:Smc2 APN 4 52,440,301 (GRCm39) nonsense probably null
Janitor UTSW 4 52,478,448 (GRCm39) missense probably damaging 1.00
R0539:Smc2 UTSW 4 52,458,558 (GRCm39) missense probably benign 0.01
R0782:Smc2 UTSW 4 52,469,799 (GRCm39) missense probably benign 0.30
R1908:Smc2 UTSW 4 52,450,863 (GRCm39) missense probably damaging 0.97
R2054:Smc2 UTSW 4 52,462,948 (GRCm39) missense probably benign 0.00
R2109:Smc2 UTSW 4 52,474,987 (GRCm39) missense probably benign 0.00
R2318:Smc2 UTSW 4 52,446,030 (GRCm39) missense probably damaging 1.00
R2352:Smc2 UTSW 4 52,460,266 (GRCm39) missense probably benign
R3418:Smc2 UTSW 4 52,476,850 (GRCm39) splice site probably benign
R4003:Smc2 UTSW 4 52,462,897 (GRCm39) missense probably damaging 1.00
R4133:Smc2 UTSW 4 52,450,947 (GRCm39) missense probably damaging 0.99
R4299:Smc2 UTSW 4 52,440,238 (GRCm39) utr 5 prime probably benign
R4547:Smc2 UTSW 4 52,467,866 (GRCm39) missense probably benign 0.09
R4787:Smc2 UTSW 4 52,462,927 (GRCm39) missense probably damaging 0.98
R4829:Smc2 UTSW 4 52,449,612 (GRCm39) missense probably damaging 0.98
R4861:Smc2 UTSW 4 52,461,090 (GRCm39) missense probably benign 0.14
R4861:Smc2 UTSW 4 52,461,090 (GRCm39) missense probably benign 0.14
R4951:Smc2 UTSW 4 52,462,926 (GRCm39) missense possibly damaging 0.95
R4963:Smc2 UTSW 4 52,450,826 (GRCm39) missense probably damaging 1.00
R4996:Smc2 UTSW 4 52,461,042 (GRCm39) splice site probably null
R5028:Smc2 UTSW 4 52,458,447 (GRCm39) missense probably damaging 0.96
R5103:Smc2 UTSW 4 52,459,033 (GRCm39) missense probably damaging 1.00
R5159:Smc2 UTSW 4 52,460,181 (GRCm39) missense possibly damaging 0.65
R5387:Smc2 UTSW 4 52,475,096 (GRCm39) missense probably benign 0.16
R5697:Smc2 UTSW 4 52,459,045 (GRCm39) missense probably benign 0.01
R6006:Smc2 UTSW 4 52,459,024 (GRCm39) missense probably benign
R6246:Smc2 UTSW 4 52,460,289 (GRCm39) missense probably damaging 1.00
R6321:Smc2 UTSW 4 52,462,814 (GRCm39) missense probably benign
R6590:Smc2 UTSW 4 52,449,375 (GRCm39) missense probably benign 0.01
R6658:Smc2 UTSW 4 52,451,322 (GRCm39) missense probably benign 0.21
R6690:Smc2 UTSW 4 52,449,375 (GRCm39) missense probably benign 0.01
R7422:Smc2 UTSW 4 52,440,301 (GRCm39) missense probably benign 0.02
R7486:Smc2 UTSW 4 52,462,861 (GRCm39) missense possibly damaging 0.54
R7487:Smc2 UTSW 4 52,478,448 (GRCm39) missense probably damaging 1.00
R7532:Smc2 UTSW 4 52,451,013 (GRCm39) missense probably damaging 1.00
R7556:Smc2 UTSW 4 52,457,379 (GRCm39) missense probably benign 0.03
R7912:Smc2 UTSW 4 52,450,854 (GRCm39) missense probably benign 0.00
R7953:Smc2 UTSW 4 52,470,911 (GRCm39) critical splice donor site probably null
R7979:Smc2 UTSW 4 52,450,857 (GRCm39) missense probably damaging 1.00
R8343:Smc2 UTSW 4 52,450,965 (GRCm39) missense probably benign
R8344:Smc2 UTSW 4 52,449,376 (GRCm39) missense probably benign 0.01
R8495:Smc2 UTSW 4 52,450,992 (GRCm39) missense probably benign 0.00
R8880:Smc2 UTSW 4 52,462,856 (GRCm39) missense probably benign 0.00
R8988:Smc2 UTSW 4 52,475,100 (GRCm39) missense probably benign
R9201:Smc2 UTSW 4 52,446,044 (GRCm39) missense probably damaging 1.00
R9263:Smc2 UTSW 4 52,470,848 (GRCm39) missense possibly damaging 0.89
R9287:Smc2 UTSW 4 52,449,361 (GRCm39) missense probably damaging 1.00
R9534:Smc2 UTSW 4 52,462,870 (GRCm39) missense probably damaging 1.00
RF006:Smc2 UTSW 4 52,442,276 (GRCm39) missense probably benign 0.03
X0065:Smc2 UTSW 4 52,440,370 (GRCm39) missense probably damaging 1.00
Z1176:Smc2 UTSW 4 52,481,682 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AAGGCTCTCAATTGTGAAATCG -3'
(R):5'- CCCCGTAGCTGACATTAAATATGAAC -3'

Sequencing Primer
(F):5'- CTCAATTGTGAAATCGAAGAATTGG -3'
(R):5'- CTTACCTCAGCCATACTGTT -3'
Posted On 2016-02-04