Incidental Mutation 'R8473:Smc5'
ID 657141
Institutional Source Beutler Lab
Gene Symbol Smc5
Ensembl Gene ENSMUSG00000024943
Gene Name structural maintenance of chromosomes 5
Synonyms Smc5l1
MMRRC Submission 067917-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8473 (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 23221446 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Aspartic acid at position 361 (V361D)
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: V361D

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000084837
Gene: ENSMUSG00000024943
AA Change: V361D

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: V361D

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)
Predicted Effect probably benign
Transcript: ENSMUST00000226111
AA Change: V285D

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
Meta Mutation Damage Score 0.0846 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.4%
Validation Efficiency 100% (33/33)
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: 34 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930583I09Rik T C 17: 65,141,513 (GRCm39) D30G unknown Het
Acad12 T C 5: 121,745,538 (GRCm39) D251G probably damaging Het
Adamts15 T A 9: 30,816,085 (GRCm39) T625S probably damaging Het
Atg13 A T 2: 91,518,993 (GRCm39) L151M probably damaging Het
Atp5f1a T C 18: 77,867,625 (GRCm39) F250L probably damaging Het
Blnk T C 19: 40,940,854 (GRCm39) E183G possibly damaging Het
Csf3 T C 11: 98,592,928 (GRCm39) L97P probably damaging Het
Derl2 A G 11: 70,910,035 (GRCm39) Y10H probably damaging Het
Dgkb A G 12: 38,234,939 (GRCm39) N435D probably damaging Het
Dpy19l2 C A 9: 24,492,526 (GRCm39) V691L probably benign Het
Exoc5 T C 14: 49,256,860 (GRCm39) S509G probably null Het
Fancg A G 4: 43,004,963 (GRCm39) I410T probably damaging Het
Fsip2 G A 2: 82,777,336 (GRCm39) G121D probably damaging Het
Gfm1 T C 3: 67,361,051 (GRCm39) S458P possibly damaging Het
Gm6882 A T 7: 21,161,440 (GRCm39) Y143N probably damaging Het
Grm5 T A 7: 87,252,278 (GRCm39) M176K probably damaging Het
Herc6 T A 6: 57,624,099 (GRCm39) V623D probably damaging Het
Hmcn1 G T 1: 150,479,551 (GRCm39) P4638T possibly damaging Het
Il27ra A G 8: 84,768,735 (GRCm39) Y62H probably benign Het
Kcnh8 A T 17: 53,285,320 (GRCm39) S1097C probably benign Het
Kif19a T G 11: 114,678,377 (GRCm39) S677A probably damaging Het
Lrrc37 T C 11: 103,434,266 (GRCm39) T792A unknown Het
Or8d4 T C 9: 40,038,506 (GRCm39) I250M probably benign Het
Pcdhgb7 T A 18: 37,886,852 (GRCm39) V674D probably benign Het
Pik3r6 A G 11: 68,417,207 (GRCm39) S50G probably benign Het
Ptpn12 T C 5: 21,203,357 (GRCm39) T474A probably benign Het
Rbbp6 T C 7: 122,600,421 (GRCm39) probably benign Het
Scaper T C 9: 55,458,131 (GRCm39) Y880C probably damaging Het
Stag1 T A 9: 100,762,840 (GRCm39) H480Q probably damaging Het
Tdpoz2 T C 3: 93,559,153 (GRCm39) E273G probably damaging Het
Tdpoz3 T A 3: 93,733,870 (GRCm39) W182R possibly damaging Het
Tmx4 T C 2: 134,451,444 (GRCm39) T170A probably benign Het
Vmn1r59 A T 7: 5,457,064 (GRCm39) M232K possibly damaging Het
Wdr20rt A G 12: 65,273,380 (GRCm39) D180G 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
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
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'- TATCAATGATCTCGCCTTCACATA -3'
(R):5'- GACCCAGCCCCAGGTTTC -3'

Sequencing Primer
(F):5'- ACATAAGGCTTTCTCCTCCTG -3'
(R):5'- TCCAATAGCTGACTGTGAGC -3'
Posted On 2021-01-18