Incidental Mutation 'R2073:Smc3'
ID 227382
Institutional Source Beutler Lab
Gene Symbol Smc3
Ensembl Gene ENSMUSG00000024974
Gene Name structural maintenance of chromosomes 3
Synonyms Cspg6, Bamacan, Mmip1, SmcD
MMRRC Submission 040078-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2073 (G1)
Quality Score 225
Status Not validated
Chromosome 19
Chromosomal Location 53588827-53634262 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 53619964 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 620 (D620G)
Ref Sequence ENSEMBL: ENSMUSP00000025930 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025930]
AlphaFold Q9CW03
PDB Structure SMC hinge heterodimer (Mouse) [X-RAY DIFFRACTION]
Predicted Effect probably benign
Transcript: ENSMUST00000025930
AA Change: D620G

PolyPhen 2 Score 0.075 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000025930
Gene: ENSMUSG00000024974
AA Change: D620G

DomainStartEndE-ValueType
Pfam:AAA_23 5 359 5.4e-10 PFAM
SMC_hinge 530 643 1.85e-23 SMART
low complexity region 684 711 N/A INTRINSIC
Blast:SMC_hinge 712 804 3e-49 BLAST
low complexity region 805 818 N/A INTRINSIC
Blast:SMC_hinge 819 870 3e-23 BLAST
Blast:INB 898 1174 2e-52 BLAST
PDB:1XEW|Y 1032 1212 6e-30 PDB
SCOP:d1e69a_ 1114 1193 2e-9 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000157053
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.2%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the SMC3 subfamily of SMC proteins. The encoded protein occurs in certain cell types as either an intracellular, nuclear protein or a secreted protein. The nuclear form, known as structural maintenance of chromosomes 3, is a component of the multimeric cohesin complex that holds together sister chromatids during mitosis, enabling proper chromosome segregation. Post-translational modification of the encoded protein by the addition of chondroitin sulfate chains gives rise to the secreted proteoglycan bamacan, an abundant basement membrane protein. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit complete embryonic lethality. Mice heterozygous for this allele exhibit partial postnatal lethality, decreased body weight, abnormal craniofacial morphology, and increased T cell number. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 86 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310057M21Rik T C 7: 130,959,242 (GRCm39) R153G probably benign Het
5730596B20Rik C A 6: 52,155,962 (GRCm39) Y9* probably null Het
Aco1 G A 4: 40,183,605 (GRCm39) G508S probably damaging Het
Acot3 A G 12: 84,100,230 (GRCm39) H2R possibly damaging Het
Adamts13 T A 2: 26,896,326 (GRCm39) C1240S probably damaging Het
Adra1b T C 11: 43,726,698 (GRCm39) N73S probably damaging Het
Aebp2 G A 6: 140,579,420 (GRCm39) S219N probably benign Het
Akap8l C T 17: 32,551,457 (GRCm39) R511H probably damaging Het
Ank T C 15: 27,565,108 (GRCm39) S270P probably benign Het
Ankle1 G A 8: 71,861,973 (GRCm39) R492H possibly damaging Het
Ankub1 G A 3: 57,599,713 (GRCm39) H19Y possibly damaging Het
Anln C A 9: 22,244,464 (GRCm39) W1083L probably benign Het
Apaf1 G T 10: 90,867,556 (GRCm39) S763* probably null Het
Apba3 A G 10: 81,105,128 (GRCm39) T134A probably benign Het
Armh3 A T 19: 45,953,820 (GRCm39) I188K probably damaging Het
Bod1l C T 5: 41,976,532 (GRCm39) S1594N probably benign Het
C7 T C 15: 5,019,910 (GRCm39) M746V probably benign Het
Cdkn2a T A 4: 89,212,730 (GRCm39) I11F possibly damaging Het
Cideb T C 14: 55,992,617 (GRCm39) M100V possibly damaging Het
Cntnap5c T C 17: 58,612,547 (GRCm39) L862P possibly damaging Het
Coch A T 12: 51,649,472 (GRCm39) D261V probably benign Het
Cyp2ab1 A G 16: 20,132,639 (GRCm39) F220L possibly damaging Het
Ddx10 A T 9: 53,151,805 (GRCm39) D73E probably benign Het
Dgkg A G 16: 22,384,067 (GRCm39) F462S probably damaging Het
Dlgap3 C T 4: 127,089,159 (GRCm39) H252Y probably damaging Het
Dmd G C X: 83,356,089 (GRCm39) A2257P probably benign Het
Dnaaf6rt A G 1: 31,262,077 (GRCm39) S20G probably benign Het
Dnai4 G A 4: 102,907,390 (GRCm39) T632M probably damaging Het
Dtnb A G 12: 3,831,273 (GRCm39) T658A probably benign Het
Duox2 T A 2: 122,125,639 (GRCm39) S323C probably damaging Het
Dync1h1 T A 12: 110,581,026 (GRCm39) I251N probably damaging Het
Eml5 A G 12: 98,768,705 (GRCm39) S1457P probably damaging Het
Fam114a1 T A 5: 65,153,247 (GRCm39) probably null Het
Fcho1 A T 8: 72,163,133 (GRCm39) L632Q probably damaging Het
Gm12695 T C 4: 96,612,182 (GRCm39) Y527C possibly damaging Het
Gm16223 T C 5: 42,371,942 (GRCm39) C111R unknown Het
H2-Q4 T A 17: 35,599,378 (GRCm39) S154T possibly damaging Het
Hhat A G 1: 192,409,687 (GRCm39) F125L possibly damaging Het
Ier5l T A 2: 30,363,068 (GRCm39) D319V probably damaging Het
Kif5a T C 10: 127,081,238 (GRCm39) D232G probably damaging Het
M1ap A G 6: 82,958,863 (GRCm39) I165V probably benign Het
Map2k4 A C 11: 65,584,282 (GRCm39) F334V probably damaging Het
Mmp19 G A 10: 128,630,848 (GRCm39) R156H probably damaging Het
Mpped2 T A 2: 106,575,147 (GRCm39) Y77* probably null Het
Nhs T A X: 160,625,717 (GRCm39) H544L probably damaging Het
Nr4a1 C A 15: 101,171,948 (GRCm39) H541N probably damaging Het
Or4a74 A G 2: 89,439,822 (GRCm39) V208A probably benign Het
Or5b122 A T 19: 13,562,965 (GRCm39) Q99L probably damaging Het
Pak6 A C 2: 118,519,332 (GRCm39) N17T probably damaging Het
Pcnt T A 10: 76,216,214 (GRCm39) T2225S possibly damaging Het
Pdzd2 A G 15: 12,385,905 (GRCm39) L955P probably damaging Het
Phf21a A G 2: 92,178,381 (GRCm39) D357G probably damaging Het
Pkhd1l1 G T 15: 44,422,035 (GRCm39) A3102S probably damaging Het
Plch2 A T 4: 155,074,366 (GRCm39) L754Q probably damaging Het
Plekhd1 A G 12: 80,768,066 (GRCm39) N335D probably benign Het
Pole C A 5: 110,473,417 (GRCm39) T1737N probably damaging Het
Potefam1 T C 2: 111,030,763 (GRCm39) E382G probably damaging Het
Pramel6 G A 2: 87,339,088 (GRCm39) S96N probably damaging Het
Prdm14 A C 1: 13,195,954 (GRCm39) Y36D possibly damaging Het
Psg27 T C 7: 18,294,342 (GRCm39) D355G probably damaging Het
Rfc1 A T 5: 65,459,282 (GRCm39) D225E probably damaging Het
Sec16a A G 2: 26,330,251 (GRCm39) I588T probably damaging Het
Setd6 G A 8: 96,443,416 (GRCm39) V60M probably damaging Het
Sgk3 A G 1: 9,961,649 (GRCm39) I432V probably benign Het
Six2 A G 17: 85,994,933 (GRCm39) S150P probably damaging Het
Slc1a6 T C 10: 78,635,964 (GRCm39) V343A possibly damaging Het
Slc43a3 T C 2: 84,774,956 (GRCm39) probably null Het
Smg6 C G 11: 74,821,120 (GRCm39) P464A probably damaging Het
Sox11 T C 12: 27,392,278 (GRCm39) T44A possibly damaging Het
Spata22 A G 11: 73,227,052 (GRCm39) R89G possibly damaging Het
Spmip6 A G 4: 41,507,519 (GRCm39) probably null Het
Stk3 T C 15: 34,959,195 (GRCm39) M256V possibly damaging Het
Syne2 A G 12: 76,062,353 (GRCm39) D4226G possibly damaging Het
Tecpr2 T C 12: 110,934,863 (GRCm39) S1370P possibly damaging Het
Tek A G 4: 94,715,966 (GRCm39) I463V probably benign Het
Trib1 T A 15: 59,526,189 (GRCm39) I253N probably damaging Het
Triobp G T 15: 78,858,095 (GRCm39) G1232V probably damaging Het
Trpm6 G A 19: 18,853,406 (GRCm39) V1809M probably damaging Het
Tsc22d4 A G 5: 137,760,749 (GRCm39) K57E possibly damaging Het
Vmn2r109 T A 17: 20,784,974 (GRCm39) K15N probably benign Het
Wnt9a A G 11: 59,222,055 (GRCm39) N318D probably damaging Het
Wwp1 A G 4: 19,662,181 (GRCm39) V138A possibly damaging Het
Zfp37 A T 4: 62,109,945 (GRCm39) M411K probably damaging Het
Zfp715 T A 7: 42,960,544 (GRCm39) T16S probably benign Het
Zfp932 A G 5: 110,157,684 (GRCm39) T461A possibly damaging Het
Zscan29 A T 2: 120,991,336 (GRCm39) C817* probably null Het
Other mutations in Smc3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01017:Smc3 APN 19 53,617,758 (GRCm39) missense probably damaging 0.99
IGL01300:Smc3 APN 19 53,630,283 (GRCm39) splice site probably benign
IGL02136:Smc3 APN 19 53,624,147 (GRCm39) missense probably benign 0.02
IGL02216:Smc3 APN 19 53,610,275 (GRCm39) missense probably damaging 1.00
IGL02473:Smc3 APN 19 53,624,879 (GRCm39) missense probably benign 0.06
IGL02797:Smc3 APN 19 53,627,189 (GRCm39) missense probably benign 0.03
IGL02959:Smc3 APN 19 53,611,988 (GRCm39) missense probably benign 0.00
IGL03343:Smc3 APN 19 53,602,273 (GRCm39) missense probably damaging 1.00
Bits UTSW 19 53,611,649 (GRCm39) critical splice donor site probably null
Pieces UTSW 19 53,617,802 (GRCm39) missense probably damaging 0.99
Smithereens UTSW 19 53,630,362 (GRCm39) missense probably damaging 1.00
R0081:Smc3 UTSW 19 53,589,993 (GRCm39) splice site probably benign
R0940:Smc3 UTSW 19 53,629,340 (GRCm39) missense probably benign 0.10
R1248:Smc3 UTSW 19 53,622,509 (GRCm39) missense probably benign 0.01
R1661:Smc3 UTSW 19 53,613,496 (GRCm39) missense probably benign 0.08
R1779:Smc3 UTSW 19 53,627,800 (GRCm39) missense probably benign 0.02
R2046:Smc3 UTSW 19 53,627,845 (GRCm39) missense probably benign 0.00
R2074:Smc3 UTSW 19 53,619,964 (GRCm39) missense probably benign 0.08
R3077:Smc3 UTSW 19 53,616,322 (GRCm39) missense probably benign 0.16
R4962:Smc3 UTSW 19 53,619,948 (GRCm39) missense probably damaging 0.99
R5684:Smc3 UTSW 19 53,629,235 (GRCm39) missense probably benign 0.00
R6020:Smc3 UTSW 19 53,613,594 (GRCm39) critical splice donor site probably null
R6169:Smc3 UTSW 19 53,622,517 (GRCm39) missense probably benign 0.02
R6221:Smc3 UTSW 19 53,630,362 (GRCm39) missense probably damaging 1.00
R6258:Smc3 UTSW 19 53,616,162 (GRCm39) splice site probably null
R6960:Smc3 UTSW 19 53,617,802 (GRCm39) missense probably damaging 0.99
R7048:Smc3 UTSW 19 53,617,682 (GRCm39) missense probably benign 0.01
R7148:Smc3 UTSW 19 53,630,326 (GRCm39) missense possibly damaging 0.93
R7157:Smc3 UTSW 19 53,630,329 (GRCm39) missense probably damaging 1.00
R7805:Smc3 UTSW 19 53,629,390 (GRCm39) missense probably benign 0.26
R7968:Smc3 UTSW 19 53,611,649 (GRCm39) critical splice donor site probably null
R8066:Smc3 UTSW 19 53,603,576 (GRCm39) missense probably damaging 1.00
R8202:Smc3 UTSW 19 53,617,123 (GRCm39) missense possibly damaging 0.94
R8472:Smc3 UTSW 19 53,617,142 (GRCm39) missense probably benign 0.02
R8683:Smc3 UTSW 19 53,629,616 (GRCm39) missense possibly damaging 0.50
R8827:Smc3 UTSW 19 53,611,085 (GRCm39) missense probably benign 0.01
R9072:Smc3 UTSW 19 53,617,200 (GRCm39) missense probably benign 0.00
R9073:Smc3 UTSW 19 53,617,200 (GRCm39) missense probably benign 0.00
R9355:Smc3 UTSW 19 53,622,544 (GRCm39) critical splice donor site probably null
R9428:Smc3 UTSW 19 53,617,150 (GRCm39) missense possibly damaging 0.48
X0026:Smc3 UTSW 19 53,613,551 (GRCm39) missense probably benign 0.13
Predicted Primers PCR Primer
(F):5'- GCAGAGGCAGACTTTCCATG -3'
(R):5'- TGTATAGCCCAAGTGACAGATTAC -3'

Sequencing Primer
(F):5'- CAGAGGCAGACTTTCCATGTAGTTC -3'
(R):5'- TAGCCCAAGTGACAGATTACATATC -3'
Posted On 2014-09-17