Incidental Mutation 'R2513:Smg6'
ID 253661
Institutional Source Beutler Lab
Gene Symbol Smg6
Ensembl Gene ENSMUSG00000038290
Gene Name SMG6 nonsense mediated mRNA decay factor
Synonyms Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)
MMRRC Submission 040419-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2513 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 74816665-75055274 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 74820502 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 258 (T258A)
Ref Sequence ENSEMBL: ENSMUSP00000043555 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000045281] [ENSMUST00000065211] [ENSMUST00000108447] [ENSMUST00000108448] [ENSMUST00000121738] [ENSMUST00000123855] [ENSMUST00000138612] [ENSMUST00000128556]
AlphaFold P61406
Predicted Effect probably damaging
Transcript: ENSMUST00000045281
AA Change: T258A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290
AA Change: T258A

DomainStartEndE-ValueType
internal_repeat_1 42 99 7.68e-6 PROSPERO
internal_repeat_1 135 188 7.68e-6 PROSPERO
low complexity region 212 227 N/A INTRINSIC
low complexity region 257 271 N/A INTRINSIC
low complexity region 376 390 N/A INTRINSIC
low complexity region 417 426 N/A INTRINSIC
low complexity region 436 453 N/A INTRINSIC
low complexity region 538 549 N/A INTRINSIC
coiled coil region 574 600 N/A INTRINSIC
Pfam:EST1 637 742 1.8e-18 PFAM
Pfam:EST1_DNA_bind 750 1106 1.6e-78 PFAM
coiled coil region 1197 1234 N/A INTRINSIC
PINc 1245 1396 2.85e-25 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000065211
SMART Domains Protein: ENSMUSP00000067552
Gene: ENSMUSG00000001323

DomainStartEndE-ValueType
Pfam:PALP 19 314 3.3e-75 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000108447
SMART Domains Protein: ENSMUSP00000104086
Gene: ENSMUSG00000001323

DomainStartEndE-ValueType
Pfam:PALP 19 179 1.8e-41 PFAM
Pfam:PALP 173 289 4.2e-19 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000108448
SMART Domains Protein: ENSMUSP00000104087
Gene: ENSMUSG00000001323

DomainStartEndE-ValueType
Pfam:PALP 19 314 2.1e-75 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000121738
SMART Domains Protein: ENSMUSP00000113372
Gene: ENSMUSG00000001323

DomainStartEndE-ValueType
Pfam:PALP 19 314 3.3e-75 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000123855
SMART Domains Protein: ENSMUSP00000118485
Gene: ENSMUSG00000001323

DomainStartEndE-ValueType
Pfam:PALP 19 166 1.5e-39 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135587
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147817
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127499
Predicted Effect probably benign
Transcript: ENSMUST00000138612
SMART Domains Protein: ENSMUSP00000119256
Gene: ENSMUSG00000001323

DomainStartEndE-ValueType
Pfam:PALP 19 112 4.1e-28 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000128556
SMART Domains Protein: ENSMUSP00000120012
Gene: ENSMUSG00000001323

DomainStartEndE-ValueType
Pfam:PALP 19 182 2.6e-44 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000130145
SMART Domains Protein: ENSMUSP00000120229
Gene: ENSMUSG00000038290

DomainStartEndE-ValueType
coiled coil region 35 61 N/A INTRINSIC
Pfam:EST1 99 204 1.3e-19 PFAM
Pfam:EST1_DNA_bind 212 339 7.3e-37 PFAM
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.4%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a component of the telomerase ribonucleoprotein complex responsible for the replication and maintenance of chromosome ends. The encoded protein also plays a role in the nonsense-mediated mRNA decay (NMD) pathway, providing the endonuclease activity near the premature translation termination codon that is needed to initiate NMD. Alternatively spliced transcript variants encoding distinct protein isoforms have been described. [provided by RefSeq, Feb 2014]
PHENOTYPE: Homozygosity for insertion of a transgene into intron 6 of the gene results in embryonic lethality. Mice homozygous for a knock-out allele exhibit prenatal lethality. Mice homozygous for a conditional allele activated in embryonic stem cells exhibit defective telomere maintenance and NMD. [provided by MGI curators]
Allele List at MGI

All alleles(52) : Gene trapped(52)

Other mutations in this stock
Total: 90 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3425401B19Rik T C 14: 32,383,809 (GRCm39) T719A possibly damaging Het
Abcc1 A G 16: 14,290,873 (GRCm39) probably null Het
Aftph C T 11: 20,658,676 (GRCm39) probably null Het
Als2 C A 1: 59,254,276 (GRCm39) K360N probably benign Het
Atg2a T A 19: 6,308,076 (GRCm39) probably null Het
Axl T C 7: 25,486,941 (GRCm39) D22G probably benign Het
Baiap2 G A 11: 119,890,052 (GRCm39) A438T probably benign Het
Bean1 G C 8: 104,908,643 (GRCm39) A7P probably benign Het
Birc6 C G 17: 74,954,724 (GRCm39) P3431R probably damaging Het
Camk1d A G 2: 5,719,047 (GRCm39) M1T probably null Het
Carmil3 T C 14: 55,741,295 (GRCm39) Y1027H probably damaging Het
Ccdc6 G A 10: 70,023,658 (GRCm39) probably benign Het
Cemip C A 7: 83,591,233 (GRCm39) V1280L probably benign Het
Cfap58 C A 19: 47,950,981 (GRCm39) N447K probably benign Het
Chd3 A G 11: 69,251,471 (GRCm39) L520P probably damaging Het
Col1a2 T A 6: 4,531,223 (GRCm39) probably null Het
Cpne7 A C 8: 123,844,406 (GRCm39) probably null Het
Ctla4 T C 1: 60,951,723 (GRCm39) V84A probably damaging Het
Dap3 A G 3: 88,835,565 (GRCm39) V263A probably benign Het
Dhx57 T A 17: 80,549,378 (GRCm39) probably null Het
Dlg5 C A 14: 24,214,593 (GRCm39) K663N probably damaging Het
Dsg3 C A 18: 20,656,719 (GRCm39) F196L possibly damaging Het
Eif2ak4 C A 2: 118,257,064 (GRCm39) D402E probably damaging Het
Fance T C 17: 28,537,068 (GRCm39) V24A probably benign Het
Fasn A T 11: 120,705,574 (GRCm39) L1149Q probably damaging Het
Fcgbpl1 C G 7: 27,831,060 (GRCm39) S91C probably damaging Het
Flg T A 3: 93,187,093 (GRCm39) S182T possibly damaging Het
Gm128 T A 3: 95,147,293 (GRCm39) S334C possibly damaging Het
Gm3727 A C 14: 7,264,561 (GRCm38) H31Q probably damaging Het
Gm4841 T G 18: 60,403,977 (GRCm39) T39P probably damaging Het
Golgb1 G T 16: 36,735,513 (GRCm39) V1587L possibly damaging Het
Golm1 G A 13: 59,790,072 (GRCm39) P243S probably benign Het
Gstcd C A 3: 132,788,081 (GRCm39) A206S possibly damaging Het
Gstcd C A 3: 132,788,082 (GRCm39) K205N possibly damaging Het
Gtf3c1 A G 7: 125,280,345 (GRCm39) V355A probably benign Het
Hhatl T C 9: 121,618,236 (GRCm39) D173G probably benign Het
Kcnu1 T A 8: 26,395,994 (GRCm39) C660S probably benign Het
Kctd8 T C 5: 69,267,988 (GRCm39) D374G probably benign Het
Kif21a T C 15: 90,878,594 (GRCm39) I229V possibly damaging Het
L3mbtl1 A T 2: 162,809,505 (GRCm39) I702F probably benign Het
Lce1d T C 3: 92,593,066 (GRCm39) probably benign Het
Lrig1 C T 6: 94,594,347 (GRCm39) probably null Het
Lrp12 A T 15: 39,739,507 (GRCm39) D563E probably damaging Het
Lrp2 C T 2: 69,336,718 (GRCm39) probably null Het
Map3k5 G A 10: 19,970,201 (GRCm39) V703I possibly damaging Het
Mecr A G 4: 131,581,076 (GRCm39) R110G probably benign Het
Mtrr T A 13: 68,715,092 (GRCm39) K445* probably null Het
Nanos1 T A 19: 60,744,990 (GRCm39) L96Q probably benign Het
Or13a24 T G 7: 140,154,069 (GRCm39) M1R probably null Het
Or51t4 T A 7: 102,598,700 (GRCm39) F333I probably benign Het
Or6c214 T A 10: 129,591,021 (GRCm39) L99F probably damaging Het
Otog T C 7: 45,955,014 (GRCm39) probably null Het
Pcdhb3 G T 18: 37,434,294 (GRCm39) V87F probably benign Het
Pcdhb3 T A 18: 37,434,292 (GRCm39) L86* probably null Het
Pcdhb3 A T 18: 37,434,293 (GRCm39) L86F probably damaging Het
Pdgfd A G 9: 6,359,894 (GRCm39) K322E probably damaging Het
Picalm T C 7: 89,846,217 (GRCm39) S648P probably damaging Het
Pigr T C 1: 130,774,357 (GRCm39) S446P possibly damaging Het
Pik3cb A C 9: 98,943,895 (GRCm39) L636W probably damaging Het
Pla2g2f A T 4: 138,481,473 (GRCm39) L92Q probably damaging Het
Plod3 G C 5: 137,017,000 (GRCm39) A50P probably benign Het
Prkar2b C T 12: 32,025,928 (GRCm39) V191I possibly damaging Het
Prune1 C A 3: 95,165,430 (GRCm39) A281S probably benign Het
Ptges3l A T 11: 101,314,868 (GRCm39) C42S possibly damaging Het
Reg3b A T 6: 78,348,802 (GRCm39) I33L probably benign Het
Rel A G 11: 23,695,823 (GRCm39) I188T probably damaging Het
Rif1 GCCACCA GCCA 2: 52,000,336 (GRCm39) probably benign Het
Ripor1 G T 8: 106,344,254 (GRCm39) V463L probably benign Het
Rrm1 T A 7: 102,109,896 (GRCm39) D510E probably damaging Het
Setd7 A G 3: 51,440,436 (GRCm39) S202P probably damaging Het
Shank3 T A 15: 89,432,889 (GRCm39) D1211E probably benign Het
Slc30a1 A T 1: 191,639,674 (GRCm39) T186S possibly damaging Het
Slc4a4 G A 5: 89,304,257 (GRCm39) V523I probably benign Het
Slc9a2 T A 1: 40,781,768 (GRCm39) probably null Het
Sptlc1 C T 13: 53,491,676 (GRCm39) D408N possibly damaging Het
Tasor2 G T 13: 3,632,150 (GRCm39) L784I possibly damaging Het
Tbl3 T C 17: 24,923,524 (GRCm39) probably null Het
Tdo2 T C 3: 81,876,812 (GRCm39) D139G possibly damaging Het
Ticam1 T A 17: 56,578,612 (GRCm39) H161L possibly damaging Het
Tnfaip3 T A 10: 18,881,407 (GRCm39) D293V probably benign Het
Trim72 G A 7: 127,603,878 (GRCm39) V75M possibly damaging Het
Trip11 T A 12: 101,803,986 (GRCm39) N1632I possibly damaging Het
Tspan18 A T 2: 93,050,440 (GRCm39) M61K possibly damaging Het
Tuba8 A T 6: 121,202,932 (GRCm39) E415V probably damaging Het
Ung A G 5: 114,275,253 (GRCm39) H214R probably benign Het
Uqcrc1 T C 9: 108,765,836 (GRCm39) L17P probably damaging Het
Usp24 A G 4: 106,236,602 (GRCm39) probably null Het
Vps39 A C 2: 120,169,268 (GRCm39) Y245D probably damaging Het
Whrn T A 4: 63,353,649 (GRCm39) T373S probably benign Het
Zc2hc1a C T 3: 7,581,596 (GRCm39) probably null Het
Other mutations in Smg6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00952:Smg6 APN 11 74,819,974 (GRCm39) missense probably benign
IGL01146:Smg6 APN 11 74,821,254 (GRCm39) nonsense probably null
IGL01505:Smg6 APN 11 75,047,117 (GRCm39) missense probably damaging 1.00
IGL01541:Smg6 APN 11 74,816,770 (GRCm39) missense probably benign 0.43
IGL01636:Smg6 APN 11 74,825,929 (GRCm39) critical splice donor site probably null
IGL02379:Smg6 APN 11 74,944,751 (GRCm39) missense probably damaging 1.00
IGL02794:Smg6 APN 11 74,944,760 (GRCm39) missense probably damaging 0.99
IGL02964:Smg6 APN 11 74,821,576 (GRCm39) critical splice donor site probably null
IGL03057:Smg6 APN 11 74,826,260 (GRCm39) nonsense probably null
1mM(1):Smg6 UTSW 11 74,825,815 (GRCm39) splice site probably benign
IGL03097:Smg6 UTSW 11 74,823,252 (GRCm39) missense probably damaging 1.00
PIT4802001:Smg6 UTSW 11 75,046,991 (GRCm39) missense probably damaging 0.96
R0269:Smg6 UTSW 11 75,053,757 (GRCm39) missense probably benign
R0344:Smg6 UTSW 11 74,820,647 (GRCm39) missense probably damaging 1.00
R0437:Smg6 UTSW 11 74,820,527 (GRCm39) missense probably damaging 1.00
R0452:Smg6 UTSW 11 74,821,039 (GRCm39) missense probably benign
R0511:Smg6 UTSW 11 74,819,884 (GRCm39) missense probably damaging 1.00
R0617:Smg6 UTSW 11 75,053,757 (GRCm39) missense probably benign
R0737:Smg6 UTSW 11 75,050,662 (GRCm39) missense probably damaging 1.00
R1715:Smg6 UTSW 11 74,820,256 (GRCm39) missense probably benign
R1780:Smg6 UTSW 11 74,836,942 (GRCm39) missense probably damaging 1.00
R1927:Smg6 UTSW 11 75,033,674 (GRCm39) missense probably damaging 1.00
R2073:Smg6 UTSW 11 74,821,120 (GRCm39) missense probably damaging 1.00
R2171:Smg6 UTSW 11 74,929,472 (GRCm39) missense probably damaging 1.00
R3943:Smg6 UTSW 11 74,820,367 (GRCm39) missense probably damaging 1.00
R3944:Smg6 UTSW 11 74,820,367 (GRCm39) missense probably damaging 1.00
R4275:Smg6 UTSW 11 74,884,700 (GRCm39) intron probably benign
R4369:Smg6 UTSW 11 74,823,269 (GRCm39) nonsense probably null
R4452:Smg6 UTSW 11 74,880,967 (GRCm39) missense probably benign 0.14
R4864:Smg6 UTSW 11 74,820,988 (GRCm39) missense possibly damaging 0.89
R4885:Smg6 UTSW 11 74,932,744 (GRCm39) missense probably damaging 1.00
R5043:Smg6 UTSW 11 74,820,721 (GRCm39) missense possibly damaging 0.86
R5189:Smg6 UTSW 11 74,932,822 (GRCm39) missense probably damaging 1.00
R5378:Smg6 UTSW 11 74,932,820 (GRCm39) missense possibly damaging 0.61
R5518:Smg6 UTSW 11 74,944,724 (GRCm39) missense probably damaging 0.99
R5725:Smg6 UTSW 11 74,821,439 (GRCm39) missense probably benign 0.45
R5746:Smg6 UTSW 11 75,030,113 (GRCm39) missense probably damaging 1.00
R6151:Smg6 UTSW 11 75,047,033 (GRCm39) missense probably damaging 0.96
R6319:Smg6 UTSW 11 75,047,048 (GRCm39) missense probably damaging 1.00
R6349:Smg6 UTSW 11 74,944,600 (GRCm39) missense possibly damaging 0.94
R6500:Smg6 UTSW 11 74,821,331 (GRCm39) missense possibly damaging 0.74
R6619:Smg6 UTSW 11 74,823,279 (GRCm39) critical splice donor site probably null
R6820:Smg6 UTSW 11 74,932,790 (GRCm39) missense probably damaging 0.99
R6923:Smg6 UTSW 11 74,820,169 (GRCm39) missense possibly damaging 0.50
R7361:Smg6 UTSW 11 74,820,979 (GRCm39) missense probably benign 0.00
R7494:Smg6 UTSW 11 74,820,449 (GRCm39) missense probably benign
R7498:Smg6 UTSW 11 74,819,932 (GRCm39) missense probably benign 0.01
R7681:Smg6 UTSW 11 74,822,531 (GRCm39) missense probably damaging 1.00
R7710:Smg6 UTSW 11 74,821,445 (GRCm39) missense probably benign 0.26
R7770:Smg6 UTSW 11 74,884,687 (GRCm39) missense unknown
R8159:Smg6 UTSW 11 74,929,465 (GRCm39) missense probably damaging 1.00
R8381:Smg6 UTSW 11 74,822,566 (GRCm39) missense probably damaging 1.00
R8463:Smg6 UTSW 11 74,820,886 (GRCm39) missense probably benign 0.14
R8509:Smg6 UTSW 11 74,932,702 (GRCm39) missense probably benign 0.04
R8557:Smg6 UTSW 11 75,047,064 (GRCm39) missense probably damaging 0.98
R8743:Smg6 UTSW 11 74,820,859 (GRCm39) missense probably benign
R9240:Smg6 UTSW 11 74,825,884 (GRCm39) missense probably damaging 1.00
R9312:Smg6 UTSW 11 74,820,877 (GRCm39) missense probably benign 0.27
X0018:Smg6 UTSW 11 74,820,812 (GRCm39) missense possibly damaging 0.76
Z1186:Smg6 UTSW 11 75,047,092 (GRCm39) missense probably benign 0.06
Z1187:Smg6 UTSW 11 75,047,092 (GRCm39) missense probably benign 0.06
Z1188:Smg6 UTSW 11 75,047,092 (GRCm39) missense probably benign 0.06
Z1189:Smg6 UTSW 11 75,047,092 (GRCm39) missense probably benign 0.06
Z1190:Smg6 UTSW 11 75,047,092 (GRCm39) missense probably benign 0.06
Z1191:Smg6 UTSW 11 75,047,092 (GRCm39) missense probably benign 0.06
Z1192:Smg6 UTSW 11 75,047,092 (GRCm39) missense probably benign 0.06
Predicted Primers PCR Primer
(F):5'- TCAACCAAGTGGAGCAGTTGAG -3'
(R):5'- GGACATCAGGCTCATCAACTC -3'

Sequencing Primer
(F):5'- CCAAGTGGAGCAGTTGAGGATAG -3'
(R):5'- ACTCTGTCCTCATCTAAGGAATCAG -3'
Posted On 2014-12-04