Incidental Mutation 'R6801:Smc5'
ID 533359
Institutional Source Beutler Lab
Gene Symbol Smc5
Ensembl Gene ENSMUSG00000024943
Gene Name structural maintenance of chromosomes 5
Synonyms Smc5l1
MMRRC Submission 044914-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6801 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 23183815-23251261 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 23192010 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Leucine at position 888 (S888L)
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: S888L

PolyPhen 2 Score 0.337 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000084837
Gene: ENSMUSG00000024943
AA Change: S888L

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: S873L

PolyPhen 2 Score 0.031 (Sensitivity: 0.95; Specificity: 0.82)
Predicted Effect probably benign
Transcript: ENSMUST00000226111
AA Change: S797L

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.7%
  • 20x: 96.8%
Validation Efficiency 100% (49/49)
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam3 T A 8: 25,174,680 (GRCm39) Y695F possibly damaging Het
Arhgap20 A G 9: 51,759,892 (GRCm39) D545G probably damaging Het
Arhgef11 A G 3: 87,643,159 (GRCm39) E1457G possibly damaging Het
Atp2b4 T A 1: 133,655,524 (GRCm39) I747F probably damaging Het
Bche T A 3: 73,609,133 (GRCm39) I98L probably benign Het
C2cd6 TC T 1: 59,133,742 (GRCm39) probably null Het
Ccdc90b A G 7: 92,216,943 (GRCm39) T72A probably benign Het
Chrd A G 16: 20,554,497 (GRCm39) E352G possibly damaging Het
Csmd2 A G 4: 128,277,743 (GRCm39) E953G probably benign Het
Dchs2 T A 3: 83,035,841 (GRCm39) M196K probably benign Het
Ddx10 G A 9: 53,159,207 (GRCm39) Q33* probably null Het
Dennd4b T A 3: 90,176,086 (GRCm39) V201E probably damaging Het
Fbn2 T A 18: 58,246,420 (GRCm39) H494L probably benign Het
Fbxw13 G A 9: 109,023,795 (GRCm39) A83V probably null Het
Fxr1 A G 3: 34,108,452 (GRCm39) D321G possibly damaging Het
Galm A G 17: 80,489,053 (GRCm39) H233R probably benign Het
Gm7298 A G 6: 121,752,768 (GRCm39) T837A probably benign Het
Gmppa C G 1: 75,418,391 (GRCm39) S258C possibly damaging Het
Hk1 T G 10: 62,116,910 (GRCm39) E645A probably damaging Het
Igkv1-132 A G 6: 67,737,324 (GRCm39) T97A probably damaging Het
Kcnc1 T C 7: 46,084,716 (GRCm39) F547L probably damaging Het
Lama5 G A 2: 179,833,455 (GRCm39) P1519L probably damaging Het
Lingo2 T A 4: 35,709,566 (GRCm39) E138V probably damaging Het
Myb T C 10: 21,020,865 (GRCm39) probably null Het
Mybl1 A G 1: 9,753,353 (GRCm39) V243A probably benign Het
Mylk4 C T 13: 32,912,393 (GRCm39) S189N probably benign Het
Or13c7 T A 4: 43,855,206 (GRCm39) L299* probably null Het
Or2y16 A G 11: 49,335,169 (GRCm39) M164V probably benign Het
Or4k77 A T 2: 111,199,394 (GRCm39) Q139L probably benign Het
Or4x12-ps1 A T 2: 89,915,953 (GRCm39) I284N probably damaging Het
Or5w1b A G 2: 87,475,667 (GRCm39) Y267H probably benign Het
Or8g19 A T 9: 39,055,506 (GRCm39) I37F probably benign Het
Oxld1 A T 11: 120,347,650 (GRCm39) D182E probably damaging Het
Phf13 A T 4: 152,076,017 (GRCm39) L295Q probably damaging Het
Prrc2c TTGCTGCTGCTGCTGCTGCTGCTGCTGC TTGCTGCTGCTGCTGCTGCTGCTGC 1: 162,536,630 (GRCm39) probably benign Het
Prss33 A G 17: 24,053,813 (GRCm39) L88P possibly damaging Het
Ralgds A G 2: 28,438,448 (GRCm39) Y596C probably damaging Het
Rftn2 A G 1: 55,233,418 (GRCm39) I379T possibly damaging Het
Rnf214 C T 9: 45,807,403 (GRCm39) E267K probably damaging Het
Rpp14 T C 14: 8,083,717 (GRCm38) probably benign Het
Rpusd2 A G 2: 118,865,876 (GRCm39) Y191C probably damaging Het
Serpinb9c T A 13: 33,341,807 (GRCm39) M1L probably benign Het
Shroom3 A G 5: 93,088,795 (GRCm39) D434G probably damaging Het
Suv39h2 C T 2: 3,465,458 (GRCm39) R299K probably benign Het
Trappc4 A T 9: 44,315,685 (GRCm39) I176N probably damaging Het
Trim12c A T 7: 103,997,337 (GRCm39) V73E probably damaging Het
Vmn2r111 T C 17: 22,778,032 (GRCm39) N549S possibly 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
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'- GCCTAGCTTATTATTACCCAGAGC -3'
(R):5'- TGCCTTAAGGGACTATCCAACATG -3'

Sequencing Primer
(F):5'- AGCTTATTATTACCCAGAGCTCCAG -3'
(R):5'- AGGGACTATCCAACATGTATACATC -3'
Posted On 2018-09-12