Incidental Mutation 'R2073:Smg6'
ID 227351
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 040078-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2073 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 74816665-75055274 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to G at 74821120 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Alanine at position 464 (P464A)
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: P464A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290
AA Change: P464A

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: ENSMUST00000127499
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147817
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135587
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
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
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 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: 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
Smc3 A G 19: 53,619,964 (GRCm39) D620G probably benign 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 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
R2171:Smg6 UTSW 11 74,929,472 (GRCm39) missense probably damaging 1.00
R2513:Smg6 UTSW 11 74,820,502 (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'- AGATCGTGGTCGTGGTATCC -3'
(R):5'- CATTTGTAGGGCCTACTGGG -3'

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