Incidental Mutation 'R0970:Smc5'
ID 84045
Institutional Source Beutler Lab
Gene Symbol Smc5
Ensembl Gene ENSMUSG00000024943
Gene Name structural maintenance of chromosomes 5
Synonyms Smc5l1
MMRRC Submission 039099-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0970 (G1)
Quality Score 225
Status Validated
Chromosome 19
Chromosomal Location 23183815-23251261 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 23216362 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 489 (I489F)
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: I489F

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000084837
Gene: ENSMUSG00000024943
AA Change: I489F

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: I489F

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
Predicted Effect possibly damaging
Transcript: ENSMUST00000226111
AA Change: I413F

PolyPhen 2 Score 0.824 (Sensitivity: 0.84; Specificity: 0.93)
Meta Mutation Damage Score 0.3377 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.8%
  • 10x: 97.3%
  • 20x: 95.2%
Validation Efficiency 98% (40/41)
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: 39 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A3galt2 T C 4: 128,661,364 (GRCm39) S307P probably damaging Het
Amdhd2 C T 17: 24,375,544 (GRCm39) probably null Het
Ano1 A T 7: 144,149,308 (GRCm39) M851K probably benign Het
Arid3b A T 9: 57,740,834 (GRCm39) probably benign Het
Arpp21 A G 9: 111,965,516 (GRCm39) probably benign Het
Atxn7l3 C G 11: 102,183,261 (GRCm39) probably benign Het
C87436 G A 6: 86,424,310 (GRCm39) V281M probably damaging Het
Cep70 A G 9: 99,157,652 (GRCm39) K184E possibly damaging Het
Clcn7 T C 17: 25,370,208 (GRCm39) probably null Het
Col1a2 G A 6: 4,518,822 (GRCm39) probably benign Het
Col4a2 A G 8: 11,465,438 (GRCm39) T383A probably benign Het
Commd5 A T 15: 76,784,885 (GRCm39) probably null Het
Cyp4b1 G A 4: 115,492,833 (GRCm39) A292V probably benign Het
Dthd1 T C 5: 63,045,324 (GRCm39) L696P probably damaging Het
Dync1h1 G A 12: 110,602,943 (GRCm39) E2195K probably benign Het
Eepd1 A G 9: 25,514,722 (GRCm39) R510G probably damaging Het
Eno3 T C 11: 70,551,628 (GRCm39) I196T probably damaging Het
Eva1a A G 6: 82,069,084 (GRCm39) E137G probably damaging Het
Gapvd1 T A 2: 34,620,625 (GRCm39) probably null Het
Ggnbp2 T C 11: 84,753,138 (GRCm39) M34V possibly damaging Het
Gpihbp1 G A 15: 75,469,795 (GRCm39) S170N probably benign Het
Kdm3b T C 18: 34,942,092 (GRCm39) S528P probably damaging Het
Lrrk2 A T 15: 91,613,372 (GRCm39) Q832L probably benign Het
Nav2 C A 7: 49,233,901 (GRCm39) P1861Q probably damaging Het
Or52n5 A C 7: 104,588,284 (GRCm39) M184L probably benign Het
Piezo1 A T 8: 123,213,549 (GRCm39) I1782N possibly damaging Het
Pikfyve T A 1: 65,304,983 (GRCm39) S1757T probably damaging Het
Plxnb1 G T 9: 108,932,331 (GRCm39) W523C probably damaging Het
Pmm2 G T 16: 8,460,640 (GRCm39) L31F probably damaging Het
Ppm1f T C 16: 16,721,457 (GRCm39) probably null Het
Prss16 T C 13: 22,189,287 (GRCm39) Y34C probably damaging Het
Slc10a2 C G 8: 5,155,115 (GRCm39) E23D probably benign Het
Snx2 T C 18: 53,343,762 (GRCm39) probably benign Het
Stradb C T 1: 59,016,219 (GRCm39) L3F possibly damaging Het
Tnxb C G 17: 34,917,917 (GRCm39) P2277A possibly damaging Het
Tpm2 T A 4: 43,515,968 (GRCm39) I270F probably benign Het
Ugt2b38 T G 5: 87,560,232 (GRCm39) N361H probably damaging Het
Urb1 A T 16: 90,566,335 (GRCm39) L1484Q possibly damaging Het
Xylt1 G A 7: 117,233,963 (GRCm39) V497I 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
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
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'- GAAACTGCAACCCCATGAAGGAGAA -3'
(R):5'- TGAGTCCCAGTGAGATGCTTGGAAAT -3'

Sequencing Primer
(F):5'- CCCCATGAAGGAGAAAAGCAG -3'
(R):5'- gcacacgtctttaatcccag -3'
Posted On 2013-11-08