Incidental Mutation 'R3943:Smg6'
ID 307552
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 040924-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3943 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 74816665-75055274 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 74820367 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Arginine at position 213 (G213R)
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: G213R

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290
AA Change: G213R

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: ENSMUST00000135587
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147817
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
Meta Mutation Damage Score 0.8307 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.7%
Validation Efficiency 98% (49/50)
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adnp A G 2: 168,026,980 (GRCm39) I105T possibly damaging Het
Atf3 A G 1: 190,903,713 (GRCm39) I171T possibly damaging Het
Atp6v0a1 A G 11: 100,946,343 (GRCm39) I773V probably benign Het
Bltp2 T A 11: 78,160,350 (GRCm39) L603* probably null Het
Cad T A 5: 31,229,729 (GRCm39) probably null Het
Camkv T A 9: 107,825,182 (GRCm39) D366E possibly damaging Het
Dnah8 T A 17: 30,913,039 (GRCm39) probably benign Het
Dock7 A G 4: 98,880,668 (GRCm39) S932P probably damaging Het
Fam227a C T 15: 79,505,060 (GRCm39) probably benign Het
Fbp2 A G 13: 62,989,607 (GRCm39) F233S possibly damaging Het
Gnptab G T 10: 88,269,756 (GRCm39) V820L probably benign Het
Gpat4 G A 8: 23,670,171 (GRCm39) P286L probably damaging Het
Gpr158 C A 2: 21,373,370 (GRCm39) R102S possibly damaging Het
Gramd1b A T 9: 40,442,340 (GRCm39) M1K probably null Het
H2-T23 A G 17: 36,341,535 (GRCm39) V312A probably benign Het
Hltf A T 3: 20,146,908 (GRCm39) I494F probably damaging Het
Il16 G A 7: 83,301,223 (GRCm39) L300F probably damaging Het
Insyn1 AGAGGAGGAGGAGGAGG AGAGGAGGAGGAGG 9: 58,406,715 (GRCm39) probably benign Het
Kcnq1 T C 7: 142,979,825 (GRCm39) L657P probably damaging Het
Krt4 G A 15: 101,829,685 (GRCm39) T281M probably benign Het
Mia3 A G 1: 183,140,127 (GRCm39) F196S possibly damaging Het
Naip6 T C 13: 100,431,247 (GRCm39) T1197A probably benign Het
Nrxn2 T A 19: 6,523,365 (GRCm39) N204K probably damaging Het
Or7g27 T A 9: 19,250,371 (GRCm39) M205K probably benign Het
Rassf6 G T 5: 90,752,185 (GRCm39) Q258K possibly damaging Het
Rhpn1 T C 15: 75,583,655 (GRCm39) L380P probably damaging Het
Ribc2 A G 15: 85,019,451 (GRCm39) M78V probably benign Het
Shroom3 G T 5: 93,090,945 (GRCm39) V1151F probably damaging Het
Skint5 T A 4: 113,799,950 (GRCm39) H73L probably damaging Het
Sspn T A 6: 145,880,083 (GRCm39) W62R probably damaging Het
Stard9 A G 2: 120,528,710 (GRCm39) S1656G probably benign Het
Svep1 T A 4: 58,084,807 (GRCm39) probably null Het
Tab1 T C 15: 80,037,941 (GRCm39) L258P probably damaging Het
Tmem59l A G 8: 70,939,951 (GRCm39) L6S unknown Het
Tnrc6c C T 11: 117,614,355 (GRCm39) R838W probably damaging Het
Trf T A 9: 103,100,151 (GRCm39) I271F probably benign Het
Trpm7 A T 2: 126,673,138 (GRCm39) N538K possibly damaging Het
Usp28 T A 9: 48,911,666 (GRCm39) L25I probably benign Het
Vmn2r14 A T 5: 109,363,930 (GRCm39) I662N probably damaging Het
Vmn2r42 A T 7: 8,197,779 (GRCm39) F280Y possibly damaging Het
Vps8 A T 16: 21,288,873 (GRCm39) N411Y probably damaging Het
Vwa2 T G 19: 56,897,747 (GRCm39) L684R probably damaging Het
Zfp712 T C 13: 67,189,396 (GRCm39) Q377R probably benign Het
Zfp947 C A 17: 22,364,801 (GRCm39) G291V probably damaging Het
Zpld2 T C 4: 133,927,656 (GRCm39) T366A probably benign 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
R2513:Smg6 UTSW 11 74,820,502 (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'- CAGATCTACCAGCCTGGAAG -3'
(R):5'- CATCCATTATCGGTCAGGCCAG -3'

Sequencing Primer
(F):5'- GTTGCAGACCATTACCAAAGAGTCAG -3'
(R):5'- TCAGGCCAGCTCCCTCAG -3'
Posted On 2015-04-17