Incidental Mutation 'R7311:Smg9'
ID 567582
Institutional Source Beutler Lab
Gene Symbol Smg9
Ensembl Gene ENSMUSG00000002210
Gene Name SMG9 nonsense mediated mRNA decay factor
Synonyms smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans), 1500002O20Rik, N28092
MMRRC Submission 045367-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7311 (G1)
Quality Score 225.009
Status Not validated
Chromosome 7
Chromosomal Location 24099106-24122197 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 24120058 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 387 (M387K)
Ref Sequence ENSEMBL: ENSMUSP00000002280 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002280]
AlphaFold Q9DB90
Predicted Effect probably benign
Transcript: ENSMUST00000002280
AA Change: M387K

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000002280
Gene: ENSMUSG00000002210
AA Change: M387K

DomainStartEndE-ValueType
low complexity region 79 93 N/A INTRINSIC
low complexity region 112 135 N/A INTRINSIC
Pfam:DUF2146 199 373 3.7e-8 PFAM
Predicted Effect
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a regulatory subunit of the SMG1 complex, which plays a critical role in nonsense-mediated mRNA decay (NMD). Binding of the encoded protein to the SMG1 complex kinase scaffold protein results in the inhibition of its kinase activity. Mutations in this gene cause a multiple congenital anomaly syndrome in human patients, characterized by brain malformation, congenital heart disease and other features. [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a severe hypomorphic allele exhibit edema, hemorrhage, exencephaly, preaxial polydactyly, reduced size and growth, decreased mid- and hindrain size, microphthalmia, thin myocardium and atrioventricular septal defect. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001K19Rik A G 12: 110,635,184 (GRCm39) V118A probably benign Het
Accsl C T 2: 93,696,160 (GRCm39) G146D possibly damaging Het
Acsm1 A T 7: 119,237,305 (GRCm39) H206L probably damaging Het
Acta2 A G 19: 34,219,186 (GRCm39) Y339H probably damaging Het
Adcy2 T C 13: 68,779,073 (GRCm39) D989G probably damaging Het
Ahnak G A 19: 8,979,507 (GRCm39) A264T probably benign Het
Ahnak A G 19: 8,987,191 (GRCm39) D2825G possibly damaging Het
Akt1 G T 12: 112,623,587 (GRCm39) T291K probably damaging Het
Arhgap24 A G 5: 103,040,551 (GRCm39) D589G probably damaging Het
B4galnt3 G A 6: 120,192,396 (GRCm39) Q447* probably null Het
BC024063 C T 10: 81,945,993 (GRCm39) R538C possibly damaging Het
Bod1l A G 5: 41,951,676 (GRCm39) S2912P possibly damaging Het
Bysl A G 17: 47,912,710 (GRCm39) V360A possibly damaging Het
C1qb A G 4: 136,607,877 (GRCm39) V162A possibly damaging Het
Ccdc57 G A 11: 120,764,567 (GRCm39) P736L probably benign Het
Cep290 T A 10: 100,373,580 (GRCm39) F1287I probably damaging Het
Cntn1 T C 15: 92,130,156 (GRCm39) probably null Het
Col6a3 C T 1: 90,750,013 (GRCm39) G274R probably damaging Het
Cplane1 G T 15: 8,210,399 (GRCm39) V291F probably damaging Het
Cyb5r4 T C 9: 86,937,835 (GRCm39) C285R probably damaging Het
Cyp4f39 G A 17: 32,708,629 (GRCm39) C392Y probably damaging Het
Dcun1d3 A T 7: 119,458,734 (GRCm39) D100E probably damaging Het
Dhx58 A T 11: 100,588,997 (GRCm39) D516E probably benign Het
Dock5 T A 14: 68,065,951 (GRCm39) I351F probably benign Het
Elmod2 A C 8: 84,046,041 (GRCm39) probably null Het
Endov G A 11: 119,398,077 (GRCm39) A281T probably benign Het
Epyc A G 10: 97,485,562 (GRCm39) M1V probably null Het
Espnl T A 1: 91,251,290 (GRCm39) H128Q probably damaging Het
Fam20a A T 11: 109,565,454 (GRCm39) C452* probably null Het
Fam241b A G 10: 61,944,733 (GRCm39) V88A probably damaging Het
Fbxl9 A G 8: 106,042,299 (GRCm39) probably benign Het
Fgd3 A T 13: 49,450,166 (GRCm39) S28T possibly damaging Het
Fmn1 C A 2: 113,356,025 (GRCm39) P920Q unknown Het
Gpr139 G C 7: 118,744,089 (GRCm39) D165E probably benign Het
Hoxb1 A G 11: 96,257,927 (GRCm39) T286A possibly damaging Het
Ifi204 T A 1: 173,587,134 (GRCm39) E174D probably benign Het
Igf2bp2 A G 16: 21,880,632 (GRCm39) I555T possibly damaging Het
Ighv1-85 A G 12: 115,963,799 (GRCm39) I67T probably damaging Het
Ihh G C 1: 74,990,306 (GRCm39) P23R unknown Het
Irx2 T C 13: 72,779,396 (GRCm39) S227P probably damaging Het
Itga4 A G 2: 79,086,526 (GRCm39) I68V probably benign Het
Jsrp1 T A 10: 80,647,906 (GRCm39) T51S probably benign Het
Khdc4 T C 3: 88,619,002 (GRCm39) S569P probably damaging Het
Kifc2 G T 15: 76,547,010 (GRCm39) G306V probably damaging Het
L3mbtl2 T A 15: 81,551,588 (GRCm39) S85T possibly damaging Het
Lama1 T C 17: 68,074,380 (GRCm39) S944P Het
Lama4 T A 10: 38,902,631 (GRCm39) C202S probably damaging Het
Morc3 G A 16: 93,646,061 (GRCm39) D218N probably damaging Het
Mrtfb T A 16: 13,223,718 (GRCm39) Y866* probably null Het
Myorg A G 4: 41,498,577 (GRCm39) I351T probably damaging Het
N4bp2l1 G A 5: 150,496,389 (GRCm39) T179I probably damaging Het
Narf A G 11: 121,139,976 (GRCm39) E270G probably benign Het
Nsd2 A G 5: 34,049,380 (GRCm39) D1205G probably damaging Het
Or10x1 T C 1: 174,196,759 (GRCm39) V92A probably benign Het
Or5an11 T C 19: 12,246,068 (GRCm39) V158A probably benign Het
Parl T C 16: 20,106,625 (GRCm39) T195A probably benign Het
Phrf1 A G 7: 140,820,846 (GRCm39) I158V unknown Het
Phtf1 T C 3: 103,904,980 (GRCm39) F543L possibly damaging Het
Plod2 T A 9: 92,466,611 (GRCm39) D190E probably damaging Het
Polr1a G T 6: 71,927,863 (GRCm39) K871N possibly damaging Het
Ppp2r5a A T 1: 191,089,998 (GRCm39) I252K probably damaging Het
Ptgir T A 7: 16,640,973 (GRCm39) D88E probably damaging Het
Raly T C 2: 154,699,340 (GRCm39) V48A probably damaging Het
Ripor1 T A 8: 106,344,447 (GRCm39) L527* probably null Het
Rnf213 T C 11: 119,307,373 (GRCm39) S678P Het
Rpf1 T A 3: 146,212,918 (GRCm39) Q306L probably benign Het
Rpl14 T C 9: 120,403,171 (GRCm39) I122T probably damaging Het
Scn9a C A 2: 66,314,748 (GRCm39) A1657S possibly damaging Het
Serpinb10 A G 1: 107,474,477 (GRCm39) Y213C probably damaging Het
Slc25a23 A G 17: 57,359,827 (GRCm39) L308P probably damaging Het
Socs3 G A 11: 117,858,614 (GRCm39) P148L probably benign Het
Susd3 A G 13: 49,401,906 (GRCm39) L14P probably benign Het
Syt14 T A 1: 192,662,858 (GRCm39) M80L probably benign Het
Tmprss2 T A 16: 97,369,616 (GRCm39) Y386F possibly damaging Het
Tmx3 T A 18: 90,558,195 (GRCm39) S416T probably benign Het
Treh A G 9: 44,597,245 (GRCm39) T555A probably benign Het
Ttc5 T G 14: 51,003,400 (GRCm39) Q428P probably damaging Het
Vmn2r73 A G 7: 85,521,192 (GRCm39) S259P possibly damaging Het
Vps4b A T 1: 106,719,434 (GRCm39) V38E probably damaging Het
Wdr83 C A 8: 85,802,890 (GRCm39) R177L probably benign Het
Zfp780b A G 7: 27,662,588 (GRCm39) F656L possibly damaging Het
Zfp995 A T 17: 22,099,641 (GRCm39) F198I probably benign Het
Zswim8 A T 14: 20,771,552 (GRCm39) Y1495F probably damaging Het
Other mutations in Smg9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01100:Smg9 APN 7 24,116,376 (GRCm39) missense probably damaging 1.00
IGL01432:Smg9 APN 7 24,120,691 (GRCm39) critical splice donor site probably null
IGL01869:Smg9 APN 7 24,115,949 (GRCm39) missense probably damaging 1.00
IGL02376:Smg9 APN 7 24,114,455 (GRCm39) missense probably benign 0.01
IGL03175:Smg9 APN 7 24,121,730 (GRCm39) missense probably damaging 1.00
IGL03204:Smg9 APN 7 24,120,337 (GRCm39) missense probably benign 0.02
R0318:Smg9 UTSW 7 24,120,313 (GRCm39) missense possibly damaging 0.80
R0578:Smg9 UTSW 7 24,114,468 (GRCm39) missense probably damaging 1.00
R0786:Smg9 UTSW 7 24,120,289 (GRCm39) missense probably benign 0.03
R2043:Smg9 UTSW 7 24,105,001 (GRCm39) missense possibly damaging 0.92
R2355:Smg9 UTSW 7 24,119,546 (GRCm39) critical splice donor site probably null
R3033:Smg9 UTSW 7 24,115,949 (GRCm39) missense probably damaging 1.00
R4091:Smg9 UTSW 7 24,120,292 (GRCm39) missense probably null 0.01
R4773:Smg9 UTSW 7 24,107,019 (GRCm39) missense possibly damaging 0.84
R5023:Smg9 UTSW 7 24,105,297 (GRCm39) missense possibly damaging 0.94
R5517:Smg9 UTSW 7 24,114,338 (GRCm39) unclassified probably benign
R6320:Smg9 UTSW 7 24,120,286 (GRCm39) missense probably benign
R6394:Smg9 UTSW 7 24,121,732 (GRCm39) missense probably damaging 1.00
R7156:Smg9 UTSW 7 24,120,286 (GRCm39) missense probably benign
R7269:Smg9 UTSW 7 24,105,495 (GRCm39) missense possibly damaging 0.88
R8972:Smg9 UTSW 7 24,120,055 (GRCm39) missense probably benign 0.04
R9323:Smg9 UTSW 7 24,114,465 (GRCm39) missense probably damaging 1.00
R9589:Smg9 UTSW 7 24,120,246 (GRCm39) missense probably damaging 1.00
R9707:Smg9 UTSW 7 24,102,869 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TCTTGATCACACAGCTGTCC -3'
(R):5'- ACTGTAGCATGGACAGCGTC -3'

Sequencing Primer
(F):5'- GATCACACAGCTGTCCTCATC -3'
(R):5'- GTCCCTGGAAAGCAGACACTTC -3'
Posted On 2019-06-26