Incidental Mutation 'RF006:Smc2'
ID 602811
Institutional Source Beutler Lab
Gene Symbol Smc2
Ensembl Gene ENSMUSG00000028312
Gene Name structural maintenance of chromosomes 2
Synonyms 5730502P04Rik, CAP-E, Fin16, Smc2l1
Accession Numbers
Essential gene? Probably essential (E-score: 0.959) question?
Stock # RF006 (G1)
Quality Score 225.009
Status Validated
Chromosome 4
Chromosomal Location 52439243-52488260 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 52442276 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 64 (D64E)
Ref Sequence ENSEMBL: ENSMUSP00000099979 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000102915] [ENSMUST00000117280] [ENSMUST00000142227]
AlphaFold Q8CG48
PDB Structure Crystal Structure of the Mouse Condensin Hinge Domain [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000102915
AA Change: D64E

PolyPhen 2 Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000099979
Gene: ENSMUSG00000028312
AA Change: D64E

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: D64E

PolyPhen 2 Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000113940
Gene: ENSMUSG00000028312
AA Change: D64E

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 probably benign
Transcript: ENSMUST00000142227
AA Change: D64E

PolyPhen 2 Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000114228
Gene: ENSMUSG00000028312
AA Change: D64E

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
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.7%
  • 10x: 99.3%
  • 20x: 98.5%
Validation Efficiency 97% (36/37)
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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acbd7 GTT GT 2: 3,341,736 (GRCm39) probably null Het
Acp7 A T 7: 28,314,204 (GRCm39) N330K possibly damaging Het
Adam25 A T 8: 41,208,834 (GRCm39) H700L probably benign Het
Alg9 GGGTGG GGGTGGTGG 9: 50,686,717 (GRCm39) probably benign Het
Atp8b3 A T 10: 80,362,070 (GRCm39) V689E probably benign Het
Atxn2l A G 7: 126,095,063 (GRCm39) V533A probably benign Het
Catsperb G A 12: 101,542,238 (GRCm39) probably null Het
Ccdc121 C T 5: 31,644,894 (GRCm39) Q216* probably null Het
Ccdc13 T C 9: 121,643,273 (GRCm39) K376R probably damaging Het
Ccdc170 C CCAA 10: 4,511,030 (GRCm39) probably benign Het
Cdh9 G C 15: 16,855,916 (GRCm39) R652P probably damaging Het
Cenpf A C 1: 189,389,583 (GRCm39) C1416W probably damaging Het
Chga GCA GCATCA 12: 102,527,671 (GRCm39) probably benign Het
Cyb5r4 TGTGACAGACACACTGCCCAGGGAAG TGTGACAGACACACTGCCCAGGGAAGTGACAGACACACTGCCCAGGGAAG 9: 86,922,478 (GRCm39) probably benign Het
Cyb5r4 CCCAGGGA CCCAGGGATGTGAGAGACACGCTGGCCAGGGA 9: 86,922,494 (GRCm39) probably benign Het
Dennd3 T C 15: 73,419,441 (GRCm39) I744T probably damaging Het
Dnah1 C T 14: 31,029,832 (GRCm39) R491Q probably benign Het
Eif4a2 A T 16: 22,929,028 (GRCm39) M188L possibly damaging Het
Esf1 CTCCTCTTC CTC 2: 140,006,294 (GRCm39) probably benign Het
Fat3 T C 9: 15,909,913 (GRCm39) I2030V probably benign Het
Gab3 CTT CTTTTT X: 74,043,633 (GRCm39) probably benign Het
Gins4 A T 8: 23,717,183 (GRCm39) V195E possibly damaging Het
Gm17402 TCCTCCTCC TCCTCCTCCCCCTCCTCC 3: 67,272,892 (GRCm39) probably benign Het
Gm17604 CTCTCTTTC CTC X: 163,786,814 (GRCm39) probably null Het
Gm8369 GTGTGT GTGTGTTTGTGT 19: 11,489,128 (GRCm39) probably benign Het
Gnpnat1 T A 14: 45,620,900 (GRCm39) probably null Het
Inpp4a A C 1: 37,427,908 (GRCm39) N651T possibly damaging Het
Ireb2 T C 9: 54,788,768 (GRCm39) F81L possibly damaging Het
Kcnh3 T A 15: 99,137,809 (GRCm39) probably null Het
Kmt2b CTCCTC CTCCTCATCCTC 7: 30,285,802 (GRCm39) probably benign Het
Kmt2c TG TGCTGTGG 5: 25,520,770 (GRCm39) probably benign Het
Myt1 T C 2: 181,439,566 (GRCm39) S405P probably damaging Het
Net1 T C 13: 3,937,406 (GRCm39) T245A probably benign Het
Nkx2-1 T C 12: 56,580,332 (GRCm39) T203A probably damaging Het
Oas3 T C 5: 120,912,165 (GRCm39) E75G probably damaging Het
Pappa T A 4: 65,242,110 (GRCm39) D1491E probably benign Het
Pkhd1l1 C A 15: 44,366,634 (GRCm39) T704K probably benign Het
Pkhd1l1 TT TTTTTTTTTGT 15: 44,421,903 (GRCm39) probably benign Het
Plscr1l1 A T 9: 92,234,702 (GRCm39) I146F possibly damaging Het
Ppp1r8 TCTCTCAC TC 4: 132,557,928 (GRCm39) probably benign Het
Ppp2r3c T A 12: 55,340,600 (GRCm39) I157F probably benign Het
Pramel34 A T 5: 93,784,562 (GRCm39) C301S probably benign Het
Rspo4 C T 2: 151,709,797 (GRCm39) probably null Het
Rtn4 T C 11: 29,656,919 (GRCm39) S358P possibly damaging Het
Siglecg T A 7: 43,058,288 (GRCm39) Y58* probably null Het
Slc4a1 C T 11: 102,247,542 (GRCm39) probably null Het
Slc9b1 CGAAGGAACCAGAAAGGAAGGAACCAGAAAGGAAGGAACCAGAAAGGAAGGAACCAGAAAGGAAGGAACCAGAAAGGAAGG CGAAGGAACCAGAAAGGAAGGAACCAGAAAGGAAGGAACCAGAAAGGAAGG 3: 135,063,303 (GRCm39) probably benign Het
Spaca1 CTCGC CTCGCTATCGC 4: 34,049,853 (GRCm39) probably benign Het
Srrm2 A G 17: 24,031,562 (GRCm39) S236G unknown Het
Sry GCTGCTGGTGGTGGTCATGGAACTGCTGCTTCTGCTGGTGGTGGTCATGGAACTGCTGCTTCTGCTGGTGGTGGTCATGGAACTGCTGCTTCTGCTG GCTGCTGGTGGTGGTCATGGAACTGCTGCTTCTGCTGGTGGTGGTCATGGAACTGCTGCTTCTGCTG Y: 2,662,638 (GRCm39) probably benign Het
Strn TGCTCCCTTACCCCAGTC TGCTCCCTTACCCCAGTCCGTGCTCCCTTACCCCAGTCCGAGCTCCCTTACCCCAGTC 17: 78,984,700 (GRCm39) probably null Het
Tfeb CAG CAGGAG 17: 48,097,038 (GRCm39) probably benign Het
Tktl2 A T 8: 66,965,504 (GRCm39) E354V probably benign Het
Tpte A G 8: 22,796,959 (GRCm39) T94A probably benign Het
Usp40 A C 1: 87,894,917 (GRCm39) S868A possibly damaging Het
Vmn2r24 G A 6: 123,783,378 (GRCm39) C526Y probably damaging Het
Vmn2r58 CAAAATGATGTAGCACTT C 7: 41,486,383 (GRCm39) probably null 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
R4816:Smc2 UTSW 4 52,451,231 (GRCm39) missense probably benign 0.00
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
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'- CTTGCTGACGGATGTGGC -3'
(R):5'- CCACTGCTGTATCATAGTGCAGT -3'

Sequencing Primer
(F):5'- GGCTGCCTGTTTTTACTTAACGTAAC -3'
(R):5'- TTACCAAGCTGCACTGTGG -3'
Posted On 2019-12-04