Incidental Mutation 'R7990:Smc5'
ID 651708
Institutional Source Beutler Lab
Gene Symbol Smc5
Ensembl Gene ENSMUSG00000024943
Gene Name structural maintenance of chromosomes 5
Synonyms Smc5l1
MMRRC Submission 046031-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7990 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 23183815-23251261 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 23213246 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 555 (N555K)
Ref Sequence ENSEMBL: ENSMUSP00000084837 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000087556] [ENSMUST00000223934] [ENSMUST00000226111]
AlphaFold Q8CG46
Predicted Effect probably benign
Transcript: ENSMUST00000087556
AA Change: N555K

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000084837
Gene: ENSMUSG00000024943
AA Change: N555K

DomainStartEndE-ValueType
Pfam:SMC_N 52 1057 9.2e-19 PFAM
Pfam:AAA_23 55 456 1.2e-9 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000223934
AA Change: N555K

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
Predicted Effect probably benign
Transcript: ENSMUST00000226111
AA Change: N479K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 100% (50/50)
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: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933434E20Rik G A 3: 89,970,549 (GRCm39) V28I probably damaging Het
Abcd4 G T 12: 84,651,162 (GRCm39) probably null Het
Alg2 T C 4: 47,472,308 (GRCm39) T167A probably damaging Het
Asap1 T C 15: 64,044,586 (GRCm39) probably null Het
Atad5 T A 11: 80,024,079 (GRCm39) C1730* probably null Het
Atp8b1 T C 18: 64,671,748 (GRCm39) T1092A possibly damaging Het
C130050O18Rik A G 5: 139,400,672 (GRCm39) T242A probably benign Het
Ccdc88c A G 12: 100,934,244 (GRCm39) V211A probably damaging Het
Ccnl1 A G 3: 65,854,314 (GRCm39) S436P possibly damaging Het
Cgnl1 T C 9: 71,632,547 (GRCm39) E268G probably damaging Het
Clca4b T G 3: 144,634,103 (GRCm39) D104A probably damaging Het
Col6a3 T G 1: 90,709,577 (GRCm39) K2480T unknown Het
Cryba1 T C 11: 77,614,411 (GRCm39) T21A possibly damaging Het
Csn1s1 C T 5: 87,827,912 (GRCm39) A259V possibly damaging Het
Dap3 A C 3: 88,835,814 (GRCm39) Y206* probably null Het
Etnppl T C 3: 130,424,308 (GRCm39) I360T possibly damaging Het
Gal3st3 A T 19: 5,352,617 (GRCm39) M15L probably benign Het
Gdf5 A G 2: 155,783,749 (GRCm39) V401A probably damaging Het
Gm1110 A G 9: 26,792,137 (GRCm39) S628P possibly damaging Het
Gm9493 A T 19: 23,597,397 (GRCm39) I98F possibly damaging Het
Grin2a T C 16: 9,397,040 (GRCm39) K1016E possibly damaging Het
Hdac9 T C 12: 34,265,452 (GRCm39) N850D probably benign Het
Itsn2 C A 12: 4,685,629 (GRCm39) L466I unknown Het
Jkampl T C 6: 73,446,528 (GRCm39) Y7C probably damaging Het
Kcnj16 C A 11: 110,915,886 (GRCm39) R183S probably damaging Het
Kcnk2 A C 1: 188,942,102 (GRCm39) L389R probably damaging Het
Kdm4c A C 4: 74,309,685 (GRCm39) K949N probably damaging Het
Kif3b G A 2: 153,159,383 (GRCm39) E395K probably benign Het
Ldlrad1 G A 4: 107,066,688 (GRCm39) A8T probably benign Het
Map3k1 A T 13: 111,892,696 (GRCm39) M853K probably benign Het
Metap1 T G 3: 138,186,526 (GRCm39) T68P probably benign Het
Mfsd11 T C 11: 116,750,323 (GRCm39) V114A possibly damaging Het
Mroh1 G A 15: 76,336,475 (GRCm39) R1566H probably damaging Het
Msh4 A T 3: 153,602,529 (GRCm39) M233K probably damaging Het
Ncor1 T G 11: 62,240,321 (GRCm39) probably null Het
Npl A T 1: 153,413,230 (GRCm39) V29D possibly damaging Het
Or1e29 C T 11: 73,667,497 (GRCm39) V219I probably benign Het
Osmr T C 15: 6,881,948 (GRCm39) I65M possibly damaging Het
Rabepk C T 2: 34,670,720 (GRCm39) V247I probably benign Het
Rere C T 4: 150,699,327 (GRCm39) P804S unknown Het
Rpgrip1 A T 14: 52,366,975 (GRCm39) Y265F possibly damaging Het
Slc10a1 T C 12: 81,000,554 (GRCm39) D315G probably benign Het
Spata17 T A 1: 186,872,592 (GRCm39) H26L unknown Het
Sphkap C T 1: 83,245,066 (GRCm39) D1518N probably damaging Het
Sult2a6 A T 7: 13,959,795 (GRCm39) M246K possibly damaging Het
Tmx2 A G 2: 84,506,480 (GRCm39) F71L probably damaging Het
Ush2a T A 1: 188,274,996 (GRCm39) L1823Q probably benign Het
Virma T A 4: 11,513,983 (GRCm39) D612E probably benign Het
Wdfy4 A T 14: 32,819,752 (GRCm39) L1484Q Het
Zan A G 5: 137,391,352 (GRCm39) S4711P unknown Het
Zdhhc1 A G 8: 106,203,001 (GRCm39) probably null Het
Zfp971 C T 2: 177,675,361 (GRCm39) T320I probably damaging 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
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
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'- CTGTTCCACAATTTGAAAGATCACC -3'
(R):5'- AATTTCTGACCACCCTAGCAATTCC -3'

Sequencing Primer
(F):5'- TGAAACATGAACATGCTACATGAC -3'
(R):5'- CCTAGCAATTCCAGTAGCAATATGG -3'
Posted On 2020-09-15