Incidental Mutation 'R6960:Smc3'
ID 541733
Institutional Source Beutler Lab
Gene Symbol Smc3
Ensembl Gene ENSMUSG00000024974
Gene Name structural maintenance of chromosomes 3
Synonyms Cspg6, Bamacan, Mmip1, SmcD
MMRRC Submission 045070-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6960 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 53588827-53634262 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 53617802 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 600 (Y600H)
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 damaging
Transcript: ENSMUST00000025930
AA Change: Y600H

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000025930
Gene: ENSMUSG00000024974
AA Change: Y600H

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
Meta Mutation Damage Score 0.3041 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.3%
  • 20x: 97.6%
Validation Efficiency 98% (50/51)
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: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca1 T C 4: 53,072,924 (GRCm39) D1170G probably benign Het
Ak7 A T 12: 105,676,503 (GRCm39) T68S probably benign Het
Arhgap12 A T 18: 6,111,901 (GRCm39) N26K probably damaging Het
B3galt1 A T 2: 67,949,033 (GRCm39) E249D probably damaging Het
Catsper4 T A 4: 133,954,648 (GRCm39) M1L probably benign Het
Cc2d2b T C 19: 40,773,506 (GRCm39) V523A possibly damaging Het
Ccn4 C T 15: 66,791,047 (GRCm39) T283M probably benign Het
Cyp11a1 T C 9: 57,925,659 (GRCm39) F98S probably damaging Het
Cyp2d26 T C 15: 82,674,446 (GRCm39) S479G probably damaging Het
Dclre1a T G 19: 56,531,141 (GRCm39) Y735S probably damaging Het
Dio2 C T 12: 90,696,671 (GRCm39) G106R probably damaging Het
Efcab12 T C 6: 115,815,273 (GRCm39) probably benign Het
Ehhadh C A 16: 21,581,028 (GRCm39) V655L probably benign Het
Ercc2 G A 7: 19,127,615 (GRCm39) R379Q probably damaging Het
Fabp4 A G 3: 10,273,537 (GRCm39) V12A probably benign Het
Fbn1 T C 2: 125,223,980 (GRCm39) I590V probably benign Het
Grm8 C A 6: 27,981,281 (GRCm39) V210L probably damaging Het
Jakmip3 A G 7: 138,625,065 (GRCm39) D359G probably damaging Het
Lrit1 G C 14: 36,782,052 (GRCm39) V242L probably damaging Het
Ly75 A T 2: 60,136,749 (GRCm39) Y1493N probably benign Het
Lyst A G 13: 13,808,663 (GRCm39) N111S probably benign Het
Lyz2 G C 10: 117,114,607 (GRCm39) I107M possibly damaging Het
Mgat5 A T 1: 127,248,371 (GRCm39) D91V possibly damaging Het
Mical3 T A 6: 120,935,504 (GRCm39) D1674V probably damaging Het
Myom2 G A 8: 15,167,741 (GRCm39) A1109T probably null Het
Naa16 A G 14: 79,596,911 (GRCm39) Y358H possibly damaging Het
Nktr T A 9: 121,571,758 (GRCm39) H226Q probably damaging Het
Ocln T G 13: 100,635,380 (GRCm39) K503T possibly damaging Het
Olfm4 T C 14: 80,258,754 (GRCm39) L301S probably damaging Het
Or4f4b G A 2: 111,314,071 (GRCm39) V127I possibly damaging Het
Or6c74 T C 10: 129,869,972 (GRCm39) L159P probably benign Het
Paqr4 G A 17: 23,956,697 (GRCm39) A222V probably benign Het
Pcdhb13 A G 18: 37,576,509 (GRCm39) T296A probably benign Het
Phka2 G A X: 159,316,044 (GRCm39) V230I probably damaging Het
Pigg T C 5: 108,474,707 (GRCm39) V309A probably damaging Het
Ptger4 T C 15: 5,264,196 (GRCm39) R462G probably benign Het
Ptprc C T 1: 138,006,183 (GRCm39) probably null Het
Rabggta A C 14: 55,959,299 (GRCm39) probably null Het
Rnf25 A G 1: 74,634,403 (GRCm39) S207P possibly damaging Het
Rsf1 G GACGGCGGCC 7: 97,229,116 (GRCm39) probably benign Het
Rtf1 A G 2: 119,541,559 (GRCm39) Q264R probably damaging Het
Ryr2 A G 13: 11,816,129 (GRCm39) V619A probably benign Het
Serpinb6d A G 13: 33,855,181 (GRCm39) N285S probably benign Het
Slamf6 A G 1: 171,745,320 (GRCm39) M16V probably damaging Het
Slc22a23 A G 13: 34,528,140 (GRCm39) probably null Het
Slc23a2 T C 2: 131,933,173 (GRCm39) D95G probably damaging Het
Tarbp1 G A 8: 127,155,778 (GRCm39) T1320M possibly damaging Het
Tigd4 A T 3: 84,501,423 (GRCm39) K113N probably damaging Het
Tjp1 A T 7: 64,952,763 (GRCm39) F1444I possibly damaging Het
Tstd3 A T 4: 21,767,118 (GRCm39) M1K probably null Het
Zbtb46 T C 2: 181,065,217 (GRCm39) D311G probably damaging 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
R2073:Smc3 UTSW 19 53,619,964 (GRCm39) missense probably benign 0.08
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
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'- TACAGCCTGGCAGTAAAGATGTG -3'
(R):5'- AGCCCACTGTCACTCTGAAG -3'

Sequencing Primer
(F):5'- CCTGGCAGTAAAGATGTGTCTTATTC -3'
(R):5'- CCACTGTCACTCTGAAGATGAAC -3'
Posted On 2018-11-28