Incidental Mutation 'R4864:Smg6'
ID 374768
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 042474-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4864 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 74816665-75055274 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 74820988 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 420 (S420P)
Ref Sequence ENSEMBL: ENSMUSP00000043555 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000045281] [ENSMUST00000065211] [ENSMUST00000108447] [ENSMUST00000108448] [ENSMUST00000121738] [ENSMUST00000123855] [ENSMUST00000128556] [ENSMUST00000138612]
AlphaFold P61406
Predicted Effect possibly damaging
Transcript: ENSMUST00000045281
AA Change: S420P

PolyPhen 2 Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290
AA Change: S420P

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: 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
Predicted Effect probably benign
Transcript: ENSMUST00000138612
SMART Domains Protein: ENSMUSP00000119256
Gene: ENSMUSG00000001323

DomainStartEndE-ValueType
Pfam:PALP 19 112 4.1e-28 PFAM
Meta Mutation Damage Score 0.0937 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 93.8%
Validation Efficiency 99% (93/94)
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: 85 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930578I06Rik C T 14: 64,210,658 (GRCm39) R190H probably benign Het
Acp6 T C 3: 97,066,683 (GRCm39) probably null Het
Adora3 T A 3: 105,815,131 (GRCm39) Y148N probably damaging Het
Ahnak2 G A 12: 112,740,040 (GRCm39) S538L probably damaging Het
Aox3 T G 1: 58,215,646 (GRCm39) V1026G probably damaging Het
Ap3d1 TTCTCTCTCTCTCTCTCT TTCTCTCTCTCTCTCT 10: 80,548,612 (GRCm39) probably null Het
Arhgef37 G A 18: 61,627,996 (GRCm39) A649V probably benign Het
Atp5f1a G A 18: 77,869,015 (GRCm39) R413H possibly damaging Het
Bace1 A T 9: 45,766,109 (GRCm39) I179F probably damaging Het
Brinp1 A G 4: 68,717,123 (GRCm39) F242L probably damaging Het
Brk1 T C 6: 113,592,805 (GRCm39) Y63H possibly damaging Het
Ccdc74a A G 16: 17,466,736 (GRCm39) T148A probably benign Het
Cenpc1 T A 5: 86,193,180 (GRCm39) L236F probably damaging Het
Col13a1 C T 10: 61,698,439 (GRCm39) E541K unknown Het
Copg1 T A 6: 87,866,678 (GRCm39) C44S probably damaging Het
D130043K22Rik A G 13: 25,047,595 (GRCm39) E380G probably damaging Het
Dchs1 T C 7: 105,404,460 (GRCm39) D2694G probably damaging Het
Dgkd A T 1: 87,844,560 (GRCm39) N242I possibly damaging Het
Dnah2 C T 11: 69,313,416 (GRCm39) V4248I probably damaging Het
Dpy19l3 T A 7: 35,411,607 (GRCm39) K376* probably null Het
Eef1d A G 15: 75,775,255 (GRCm39) S135P possibly damaging Het
Epc2 T A 2: 49,427,177 (GRCm39) S574T probably benign Het
Eps15 G A 4: 109,223,727 (GRCm39) probably benign Het
Eps8 T C 6: 137,455,967 (GRCm39) probably benign Het
Exoc5 A T 14: 49,289,839 (GRCm39) V13E probably benign Het
Fbn1 A T 2: 125,214,317 (GRCm39) C765S possibly damaging Het
Fbxo5 A T 10: 5,752,392 (GRCm39) C74S probably benign Het
Fbxw9 T C 8: 85,792,530 (GRCm39) S322P probably damaging Het
Fmo5 T A 3: 97,553,195 (GRCm39) I381N probably damaging Het
Fmo6 T C 1: 162,751,964 (GRCm39) D175G probably benign Het
Gm7361 A G 5: 26,467,008 (GRCm39) probably null Het
Gm9961 G A 16: 11,720,899 (GRCm39) probably benign Het
Golga7b T A 19: 42,255,405 (GRCm39) probably null Het
Gorab T C 1: 163,213,967 (GRCm39) E321G probably benign Het
Gpx1 T A 9: 108,216,594 (GRCm39) V28E probably benign Het
H2-T15 T A 17: 36,369,253 (GRCm39) probably benign Het
H3c14 T C 3: 96,154,575 (GRCm39) I125T probably damaging Het
Hk1 T C 10: 62,178,318 (GRCm39) S8G probably benign Het
Iqsec1 C T 6: 90,641,038 (GRCm39) R1026H probably damaging Het
Kdm4b A T 17: 56,660,091 (GRCm39) Y86F probably benign Het
Kprp C T 3: 92,731,829 (GRCm39) R407Q unknown Het
Lamb1 C T 12: 31,371,005 (GRCm39) T1400M probably benign Het
Lcor G T 19: 41,573,803 (GRCm39) A853S probably benign Het
Lrriq3 T A 3: 154,893,447 (GRCm39) Y383N possibly damaging Het
Map3k21 T C 8: 126,654,294 (GRCm39) I371T probably benign Het
Mllt1 A T 17: 57,212,819 (GRCm39) F105I probably damaging Het
Nfatc2 A G 2: 168,378,312 (GRCm39) M451T probably damaging Het
Nfkbiz A C 16: 55,638,787 (GRCm39) N224K probably damaging Het
Nlrp4d A G 7: 10,115,088 (GRCm39) V531A noncoding transcript Het
Noc3l A G 19: 38,778,081 (GRCm39) Y778H probably benign Het
Nup98 C A 7: 101,802,403 (GRCm39) A734S possibly damaging Het
Or2ag18 T C 7: 106,405,171 (GRCm39) Y166C probably damaging Het
Or4k2 T A 14: 50,424,039 (GRCm39) I212F probably damaging Het
Or9g20 A G 2: 85,630,033 (GRCm39) Y194H probably damaging Het
Or9r7 T A 10: 129,962,756 (GRCm39) R57* probably null Het
Pate4 A T 9: 35,519,535 (GRCm39) C52S probably damaging Het
Pecr C A 1: 72,316,490 (GRCm39) A72S probably benign Het
Pomt1 A G 2: 32,142,004 (GRCm39) N578S probably benign Het
Ppm1a T C 12: 72,830,738 (GRCm39) S88P probably benign Het
Ppm1l T A 3: 69,449,844 (GRCm39) probably benign Het
Prdm13 A G 4: 21,685,543 (GRCm39) S86P unknown Het
Prph2 T C 17: 47,221,848 (GRCm39) S76P probably benign Het
Sarnp G A 10: 128,669,212 (GRCm39) R23H probably damaging Het
Septin1 T C 7: 126,816,064 (GRCm39) probably benign Het
Serpini1 T C 3: 75,520,481 (GRCm39) I26T probably benign Het
Setdb2 A G 14: 59,646,715 (GRCm39) I616T probably benign Het
Slc2a10 T C 2: 165,356,541 (GRCm39) F67S probably benign Het
Slc38a6 T A 12: 73,390,424 (GRCm39) probably null Het
Srp72 T A 5: 77,132,009 (GRCm39) H229Q probably benign Het
Ston2 A G 12: 91,615,448 (GRCm39) V320A possibly damaging Het
Stx3 A T 19: 11,754,515 (GRCm39) I269N possibly damaging Het
Tdg-ps A G 15: 82,400,843 (GRCm39) noncoding transcript Het
Tecpr1 T A 5: 144,150,935 (GRCm39) N291I probably benign Het
Tmem177 A G 1: 119,838,553 (GRCm39) V42A probably benign Het
Trim26 T A 17: 37,168,886 (GRCm39) probably benign Het
Ttc17 A G 2: 94,196,980 (GRCm39) S456P probably benign Het
Tubgcp6 T C 15: 88,988,021 (GRCm39) Y984C probably benign Het
Unc5cl A G 17: 48,766,872 (GRCm39) E82G possibly damaging Het
Uncx T C 5: 139,529,875 (GRCm39) S43P probably damaging Het
Vmn1r1 A G 1: 181,985,332 (GRCm39) V111A probably benign Het
Vmn1r168 A G 7: 23,240,907 (GRCm39) I255V probably damaging Het
Vwce A G 19: 10,628,000 (GRCm39) T487A probably benign Het
Xaf1 A G 11: 72,197,682 (GRCm39) probably benign Het
Zfp27 G T 7: 29,594,261 (GRCm39) P568Q probably damaging Het
Zfp382 A T 7: 29,832,885 (GRCm39) I179F possibly damaging 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
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
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'- AGTAAAGACTCCCCTGTGGTG -3'
(R):5'- TGACGTGAATCACCCCAAGATG -3'

Sequencing Primer
(F):5'- CCCTGTGGTGAGGTCAGTCAAAG -3'
(R):5'- CCCCAAGATGTAGGGCTAATTTC -3'
Posted On 2016-03-17