Incidental Mutation 'R6175:Smc5'
ID 487734
Institutional Source Beutler Lab
Gene Symbol Smc5
Ensembl Gene ENSMUSG00000024943
Gene Name structural maintenance of chromosomes 5
Synonyms Smc5l1
MMRRC Submission 044317-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6175 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 23183815-23251261 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 23191534 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Leucine at position 875 (V875L)
Ref Sequence ENSEMBL: ENSMUSP00000153364 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000087556] [ENSMUST00000223934] [ENSMUST00000226111]
AlphaFold Q8CG46
Predicted Effect probably benign
Transcript: ENSMUST00000087556
AA Change: V889L

PolyPhen 2 Score 0.431 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000084837
Gene: ENSMUSG00000024943
AA Change: V889L

DomainStartEndE-ValueType
Pfam:SMC_N 52 1057 9.2e-19 PFAM
Pfam:AAA_23 55 456 1.2e-9 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000223934
AA Change: V875L

PolyPhen 2 Score 0.595 (Sensitivity: 0.87; Specificity: 0.91)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224008
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224441
Predicted Effect probably benign
Transcript: ENSMUST00000226111
AA Change: V799L

PolyPhen 2 Score 0.225 (Sensitivity: 0.91; Specificity: 0.88)
Meta Mutation Damage Score 0.1712 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.7%
  • 20x: 93.2%
Validation Efficiency 97% (85/88)
MGI Phenotype PHENOTYPE: Homozygous knockout in embryonic stem cells causes abnormal mitosis, increased apoptosis and a shift from pluripotency to differentiation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 88 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610008E11Rik T C 10: 78,902,448 (GRCm39) K623E probably damaging Het
A530064D06Rik T A 17: 48,460,016 (GRCm39) S227C possibly damaging Het
Adam30 A T 3: 98,070,266 (GRCm39) I700F probably damaging Het
Adam5 A T 8: 25,276,167 (GRCm39) M500K probably benign Het
Adgb A T 10: 10,274,687 (GRCm39) S755T possibly damaging Het
Adgrv1 C T 13: 81,534,124 (GRCm39) G5819D probably damaging Het
Ank3 T A 10: 69,763,557 (GRCm39) Y17N probably damaging Het
Ano2 A T 6: 125,969,918 (GRCm39) M745L probably benign Het
Arap2 A G 5: 62,872,074 (GRCm39) probably null Het
Atg2a A T 19: 6,291,759 (GRCm39) probably benign Het
AU021092 G T 16: 5,038,312 (GRCm39) probably null Het
Bbs1 A T 19: 4,940,749 (GRCm39) L578Q probably damaging Het
Brd9 A T 13: 74,108,433 (GRCm39) E589D probably damaging Het
Calr4 A G 4: 109,101,442 (GRCm39) D108G probably benign Het
Ccdc82 A G 9: 13,272,798 (GRCm39) D429G probably damaging Het
Cdh22 G T 2: 164,988,550 (GRCm39) N268K probably damaging Het
Ceacam12 G A 7: 17,801,312 (GRCm39) G97D probably damaging Het
Clcn1 A G 6: 42,291,096 (GRCm39) D990G probably damaging Het
Cyp2c40 T C 19: 39,801,004 (GRCm39) T84A probably benign Het
Dnah7a G A 1: 53,472,181 (GRCm39) P3529S probably damaging Het
Dnah8 G A 17: 30,967,542 (GRCm39) D2585N probably benign Het
Efna3 GAGCAGCAGCAGCAGCAGCAGC GAGCAGCAGCAGCAGCAGC 3: 89,230,105 (GRCm39) probably benign Het
Ehd2 G A 7: 15,697,389 (GRCm39) Q4* probably null Het
Eml5 A G 12: 98,760,715 (GRCm39) V1726A possibly damaging Het
Esam A G 9: 37,439,544 (GRCm39) T10A probably benign Het
Fbxl6 A G 15: 76,422,633 (GRCm39) L95P probably benign Het
Fbxw18 T A 9: 109,505,947 (GRCm39) L441F probably damaging Het
Fbxw4 A G 19: 45,624,766 (GRCm39) S73P probably benign Het
Fndc1 T A 17: 7,991,479 (GRCm39) H739L unknown Het
Foxp1 G A 6: 98,943,037 (GRCm39) T237I probably damaging Het
Greb1 A T 12: 16,724,771 (GRCm39) I1801N probably damaging Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Hoxa13 G T 6: 52,236,908 (GRCm39) N281K probably damaging Het
Hspg2 A G 4: 137,296,829 (GRCm39) T4328A probably damaging Het
Htr2a C G 14: 74,882,474 (GRCm39) Y153* probably null Het
Iglv1 C A 16: 18,903,844 (GRCm39) A92S probably damaging Het
Itih1 A G 14: 30,653,152 (GRCm39) S759P probably damaging Het
Kctd1 G T 18: 15,102,688 (GRCm39) S831* probably null Het
Kif20a T A 18: 34,761,199 (GRCm39) S265T probably damaging Het
Kif22 T A 7: 126,630,228 (GRCm39) E436V possibly damaging Het
Kif27 A G 13: 58,459,051 (GRCm39) W927R probably damaging Het
Lcorl G A 5: 45,933,832 (GRCm39) P66L probably damaging Het
Lct A G 1: 128,255,451 (GRCm39) L197P probably damaging Het
Lefty1 T C 1: 180,762,714 (GRCm39) S14P unknown Het
Lnp1 A G 16: 56,737,855 (GRCm39) S78P possibly damaging Het
Map3k19 A T 1: 127,750,569 (GRCm39) H927Q probably benign Het
Meiosin C A 7: 18,834,814 (GRCm39) probably benign Het
Mta3 A G 17: 84,099,222 (GRCm39) T430A probably benign Het
Muc2 G T 7: 141,282,875 (GRCm39) C627F probably damaging Het
Myh13 A G 11: 67,245,588 (GRCm39) D1076G probably benign Het
Nck2 T A 1: 43,572,729 (GRCm39) M1K probably null Het
Nipal1 A G 5: 72,820,898 (GRCm39) N131S probably damaging Het
Nlrp9c T C 7: 26,077,426 (GRCm39) probably null Het
Nr2f2 A G 7: 70,007,946 (GRCm39) S179P probably damaging Het
Or1j16 A G 2: 36,530,063 (GRCm39) D4G probably benign Het
Or1j21 A T 2: 36,683,980 (GRCm39) H244L probably damaging Het
Or9g19 A T 2: 85,600,652 (GRCm39) N169I probably benign Het
Oxt G T 2: 130,418,163 (GRCm39) probably benign Het
Pank2 T A 2: 131,122,181 (GRCm39) Y235* probably null Het
Pear1 A G 3: 87,659,440 (GRCm39) L798P possibly damaging Het
Pex14 T C 4: 149,046,156 (GRCm39) H258R probably benign Het
Pmpcb A G 5: 21,962,031 (GRCm39) I487V probably benign Het
Ppie T C 4: 123,031,362 (GRCm39) E44G probably benign Het
Ppp1r9a A T 6: 4,905,639 (GRCm39) R65* probably null Het
Ralgapb T C 2: 158,288,075 (GRCm39) S371P probably damaging Het
Ros1 T C 10: 51,977,881 (GRCm39) H1455R probably benign Het
Sacs C A 14: 61,450,275 (GRCm39) T4107K possibly damaging Het
Sec24a G A 11: 51,622,718 (GRCm39) T386M probably damaging Het
Slc10a4 A T 5: 73,169,593 (GRCm39) Y207F possibly damaging Het
Slc30a10 T C 1: 185,187,508 (GRCm39) L83P probably damaging Het
Slc38a9 T A 13: 112,840,093 (GRCm39) L324* probably null Het
Slc7a9 A T 7: 35,165,277 (GRCm39) Q474L probably damaging Het
Snap91 T C 9: 86,707,053 (GRCm39) R246G probably damaging Het
Sned1 A G 1: 93,203,196 (GRCm39) probably null Het
Spink14 G A 18: 44,164,938 (GRCm39) G85E probably benign Het
Srsf11 C T 3: 157,728,981 (GRCm39) probably benign Het
St13 A G 15: 81,283,506 (GRCm39) probably null Het
Stk10 A G 11: 32,553,761 (GRCm39) M593V possibly damaging Het
Tafa1 A G 6: 96,092,721 (GRCm39) H35R probably benign Het
Tex21 C A 12: 76,245,707 (GRCm39) A530S probably benign Het
Tln2 T A 9: 67,131,363 (GRCm39) K1394N probably damaging Het
Trhr2 C A 8: 123,084,118 (GRCm39) R294L probably damaging Het
Unc79 A T 12: 103,149,708 (GRCm39) I2408F probably damaging Het
Wdr24 T C 17: 26,045,552 (GRCm39) L429P probably damaging Het
Wwp2 T A 8: 108,210,039 (GRCm39) I139N possibly damaging Het
Zfp111 G A 7: 23,897,554 (GRCm39) R686C unknown Het
Zfp268 A T 4: 145,350,811 (GRCm39) probably benign Het
Zyg11a A G 4: 108,046,878 (GRCm39) V532A probably benign Het
Other mutations in Smc5
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00569:Smc5 APN 19 23,213,329 (GRCm39) missense probably damaging 1.00
IGL01070:Smc5 APN 19 23,208,965 (GRCm39) missense possibly damaging 0.86
IGL01315:Smc5 APN 19 23,208,968 (GRCm39) missense probably benign
IGL01879:Smc5 APN 19 23,205,548 (GRCm39) missense probably damaging 0.97
IGL01902:Smc5 APN 19 23,237,132 (GRCm39) missense possibly damaging 0.85
IGL02016:Smc5 APN 19 23,251,076 (GRCm39) missense probably benign 0.00
IGL02186:Smc5 APN 19 23,209,223 (GRCm39) missense probably damaging 1.00
IGL02383:Smc5 APN 19 23,191,996 (GRCm39) splice site probably benign
IGL02447:Smc5 APN 19 23,234,856 (GRCm39) missense probably benign 0.01
IGL02534:Smc5 APN 19 23,205,536 (GRCm39) critical splice donor site probably null
IGL02834:Smc5 APN 19 23,234,968 (GRCm39) missense probably benign 0.30
IGL03290:Smc5 APN 19 23,251,022 (GRCm39) missense probably benign 0.19
R0722:Smc5 UTSW 19 23,186,291 (GRCm39) missense probably damaging 0.99
R0893:Smc5 UTSW 19 23,241,017 (GRCm39) missense possibly damaging 0.67
R0970:Smc5 UTSW 19 23,216,362 (GRCm39) missense probably damaging 1.00
R1281:Smc5 UTSW 19 23,213,247 (GRCm39) missense probably benign
R1368:Smc5 UTSW 19 23,187,807 (GRCm39) missense probably damaging 1.00
R2092:Smc5 UTSW 19 23,216,263 (GRCm39) missense probably benign
R3721:Smc5 UTSW 19 23,187,856 (GRCm39) missense probably benign 0.21
R4382:Smc5 UTSW 19 23,246,210 (GRCm39) missense probably benign 0.39
R4735:Smc5 UTSW 19 23,220,069 (GRCm39) missense probably benign
R4936:Smc5 UTSW 19 23,211,367 (GRCm39) missense probably damaging 1.00
R5306:Smc5 UTSW 19 23,237,009 (GRCm39) critical splice donor site probably null
R5754:Smc5 UTSW 19 23,221,467 (GRCm39) missense possibly damaging 0.92
R6313:Smc5 UTSW 19 23,186,312 (GRCm39) nonsense probably null
R6527:Smc5 UTSW 19 23,205,554 (GRCm39) missense probably benign 0.00
R6611:Smc5 UTSW 19 23,206,283 (GRCm39) missense probably benign 0.13
R6750:Smc5 UTSW 19 23,220,004 (GRCm39) missense probably damaging 1.00
R6801:Smc5 UTSW 19 23,192,010 (GRCm39) missense probably benign 0.34
R6821:Smc5 UTSW 19 23,220,151 (GRCm39) missense probably benign 0.20
R7002:Smc5 UTSW 19 23,209,247 (GRCm39) missense probably benign 0.00
R7198:Smc5 UTSW 19 23,237,064 (GRCm39) nonsense probably null
R7386:Smc5 UTSW 19 23,192,539 (GRCm39) missense possibly damaging 0.59
R7439:Smc5 UTSW 19 23,220,064 (GRCm39) missense probably damaging 0.97
R7596:Smc5 UTSW 19 23,191,533 (GRCm39) missense probably damaging 0.99
R7666:Smc5 UTSW 19 23,206,381 (GRCm39) missense probably benign 0.15
R7760:Smc5 UTSW 19 23,213,254 (GRCm39) missense probably benign 0.01
R7990:Smc5 UTSW 19 23,213,246 (GRCm39) missense probably benign 0.01
R8255:Smc5 UTSW 19 23,186,290 (GRCm39) missense
R8359:Smc5 UTSW 19 23,211,443 (GRCm39) missense possibly damaging 0.49
R8473:Smc5 UTSW 19 23,221,446 (GRCm39) missense probably benign 0.02
R8711:Smc5 UTSW 19 23,243,058 (GRCm39) missense probably damaging 0.98
R8815:Smc5 UTSW 19 23,221,422 (GRCm39) missense probably damaging 1.00
R8885:Smc5 UTSW 19 23,191,234 (GRCm39) missense probably damaging 0.99
R8940:Smc5 UTSW 19 23,237,126 (GRCm39) missense probably benign 0.00
R9642:Smc5 UTSW 19 23,238,752 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- TCCACTCTGATATAAGACTTCACAC -3'
(R):5'- ACTTGAAGTACAGCAGTGTGC -3'

Sequencing Primer
(F):5'- GAAAAACACTTTTCGTCTCAGGAG -3'
(R):5'- CAGTGGCATTTTTAGCCAG -3'
Posted On 2017-10-10