Incidental Mutation 'R4936:Smc5'
ID 380421
Institutional Source Beutler Lab
Gene Symbol Smc5
Ensembl Gene ENSMUSG00000024943
Gene Name structural maintenance of chromosomes 5
Synonyms Smc5l1
MMRRC Submission 042536-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4936 (G1)
Quality Score 225
Status Not validated
Chromosome 19
Chromosomal Location 23183815-23251261 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 23211367 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 589 (V589A)
Ref Sequence ENSEMBL: ENSMUSP00000153364 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000087556] [ENSMUST00000223934] [ENSMUST00000226111]
AlphaFold Q8CG46
Predicted Effect probably damaging
Transcript: ENSMUST00000087556
AA Change: V589A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000084837
Gene: ENSMUSG00000024943
AA Change: V589A

DomainStartEndE-ValueType
Pfam:SMC_N 52 1057 9.2e-19 PFAM
Pfam:AAA_23 55 456 1.2e-9 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000223934
AA Change: V589A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
Predicted Effect possibly damaging
Transcript: ENSMUST00000226111
AA Change: V513A

PolyPhen 2 Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 98.0%
  • 10x: 95.0%
  • 20x: 87.5%
Validation Efficiency
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: 84 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2300002M23Rik T A 17: 35,879,212 (GRCm39) F183L possibly damaging Het
4930590J08Rik T A 6: 91,921,245 (GRCm39) M775K probably damaging Het
Actn1 T G 12: 80,219,772 (GRCm39) I700L probably benign Het
Adam5 T C 8: 25,276,287 (GRCm39) Y460C probably damaging Het
Akna C T 4: 63,313,502 (GRCm39) G207E probably damaging Het
Ank2 T A 3: 126,748,688 (GRCm39) H527L possibly damaging Het
Anks1 C A 17: 28,207,779 (GRCm39) N383K probably damaging Het
Apba3 C T 10: 81,105,204 (GRCm39) probably null Het
Atp9b C A 18: 80,779,308 (GRCm39) V1121F possibly damaging Het
Bsn T C 9: 107,988,960 (GRCm39) Y2264C probably damaging Het
Bst1 A G 5: 43,997,799 (GRCm39) D266G probably damaging Het
Cep55 A G 19: 38,060,202 (GRCm39) probably null Het
Ces4a G A 8: 105,864,729 (GRCm39) G69S probably damaging Het
Ckb T C 12: 111,637,664 (GRCm39) K156E probably benign Het
Cln3 T A 7: 126,174,393 (GRCm39) H315L probably damaging Het
Cnot6l A G 5: 96,227,796 (GRCm39) F479S probably damaging Het
Col1a1 A G 11: 94,837,958 (GRCm39) D826G unknown Het
Cyp27a1 T C 1: 74,774,564 (GRCm39) V194A probably benign Het
Dis3l2 C T 1: 86,971,890 (GRCm39) P643S probably benign Het
Dpf3 T C 12: 83,378,740 (GRCm39) D108G probably damaging Het
Eif2b4 C T 5: 31,350,241 (GRCm39) G27D probably benign Het
Eif4a1 T G 11: 69,563,251 (GRCm39) probably benign Het
Espl1 A T 15: 102,213,372 (GRCm39) D566V probably damaging Het
Ext2 T A 2: 93,644,024 (GRCm39) R86* probably null Het
Fasn A T 11: 120,706,911 (GRCm39) F914I probably damaging Het
Fbf1 A G 11: 116,043,378 (GRCm39) L477P probably benign Het
Fsd1 A T 17: 56,303,452 (GRCm39) K441N possibly damaging Het
Fsip2 T A 2: 82,815,384 (GRCm39) S3706T probably benign Het
Gabra5 A T 7: 57,058,547 (GRCm39) N400K probably benign Het
Gimap8 G T 6: 48,633,068 (GRCm39) G296W probably damaging Het
Gli2 A G 1: 118,763,870 (GRCm39) V1427A probably benign Het
Gm7334 A T 17: 51,005,855 (GRCm39) Y47F probably damaging Het
Gm8674 T G 13: 50,054,791 (GRCm39) noncoding transcript Het
Gmeb2 G T 2: 180,896,039 (GRCm39) T377K probably benign Het
Gp9 T A 6: 87,756,229 (GRCm39) D81E probably benign Het
Il5ra T A 6: 106,715,123 (GRCm39) I212F possibly damaging Het
Klhl18 G T 9: 110,258,029 (GRCm39) N470K possibly damaging Het
Lfng G T 5: 140,598,150 (GRCm39) probably null Het
Lpo A G 11: 87,701,166 (GRCm39) I430T probably benign Het
Lrrc31 C T 3: 30,743,417 (GRCm39) D183N probably damaging Het
Meis2 T C 2: 115,694,893 (GRCm39) T410A probably benign Het
Myo6 A G 9: 80,214,963 (GRCm39) D1232G probably damaging Het
Ncapd2 C T 6: 125,146,803 (GRCm39) R1261H probably benign Het
Nfkb1 C T 3: 135,319,743 (GRCm39) V251M probably damaging Het
Nmbr C A 10: 14,642,730 (GRCm39) H96Q probably damaging Het
Nop14 C T 5: 34,809,737 (GRCm39) R256H probably damaging Het
Nqo2 T A 13: 34,165,501 (GRCm39) Y133N probably damaging Het
Or1f12 T C 13: 21,721,357 (GRCm39) I273V probably benign Het
Or5w20 A G 2: 87,727,157 (GRCm39) I213V probably benign Het
Pbld2 C A 10: 62,888,017 (GRCm39) S168R probably damaging Het
Pcdhb7 G T 18: 37,475,202 (GRCm39) G113* probably null Het
Pcdhb7 G T 18: 37,475,203 (GRCm39) G113V probably damaging Het
Pdgfra A T 5: 75,355,687 (GRCm39) T1066S probably damaging Het
Prdm8 A T 5: 98,332,881 (GRCm39) probably null Het
Prdm8 G T 5: 98,332,882 (GRCm39) probably null Het
Prkg1 T C 19: 30,563,775 (GRCm39) Y479C probably benign Het
Pudp T C 18: 50,701,539 (GRCm39) T65A probably benign Het
Rbbp6 C T 7: 122,598,926 (GRCm39) probably benign Het
Rcc1 C G 4: 132,063,046 (GRCm39) V187L probably damaging Het
Rims2 T A 15: 39,301,124 (GRCm39) M285K probably damaging Het
Rtkn2 T C 10: 67,877,745 (GRCm39) *602Q probably null Het
Rxfp3 T G 15: 11,036,866 (GRCm39) S169R probably damaging Het
Sardh T C 2: 27,118,253 (GRCm39) probably null Het
Slc24a2 A T 4: 87,145,584 (GRCm39) F157I probably damaging Het
Slc25a20 T C 9: 108,559,191 (GRCm39) Y186H probably damaging Het
Slc25a24 A G 3: 109,070,864 (GRCm39) R408G probably damaging Het
Slc44a5 T G 3: 153,959,353 (GRCm39) I348S probably damaging Het
Slc8a2 A T 7: 15,868,100 (GRCm39) K111* probably null Het
Thbd A T 2: 148,249,655 (GRCm39) I71N probably damaging Het
Thsd7b T C 1: 129,605,882 (GRCm39) M541T probably benign Het
Tie1 T A 4: 118,341,968 (GRCm39) silent Het
Tln1 A G 4: 43,547,522 (GRCm39) F813S possibly damaging Het
Tnrc18 A T 5: 142,751,732 (GRCm39) L1191* probably null Het
Tubb2a A C 13: 34,259,240 (GRCm39) Y183* probably null Het
Ubr4 T A 4: 139,123,877 (GRCm39) V343E probably damaging Het
Vmn2r93 A T 17: 18,524,327 (GRCm39) D107V possibly damaging Het
Vwa5a T G 9: 38,647,494 (GRCm39) S624R probably benign Het
Wwox G A 8: 115,433,098 (GRCm39) V255I probably benign Het
Wwp1 T C 4: 19,638,804 (GRCm39) K546E probably damaging Het
Xirp2 T A 2: 67,340,163 (GRCm39) F801L possibly damaging Het
Zfp407 T C 18: 84,577,589 (GRCm39) I1175V probably benign Het
Zfp646 T A 7: 127,480,933 (GRCm39) C1037S possibly damaging Het
Zfp786 A T 6: 47,798,202 (GRCm39) C245* probably null Het
Zfp827 T C 8: 79,787,812 (GRCm39) V326A 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
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
R6175:Smc5 UTSW 19 23,191,534 (GRCm39) missense possibly damaging 0.60
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'- GCATCCAGGCATTACGATTTTAG -3'
(R):5'- TGTCAACATTCAGGTTGTATGCC -3'

Sequencing Primer
(F):5'- CCAGGCATTACGATTTTAGCTTTAC -3'
(R):5'- GGAAAAAGTCTCCTACTGGTCTG -3'
Posted On 2016-04-15