Incidental Mutation 'R0786:Smg9'
ID 76856
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 038966-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0786 (G1)
Quality Score 187
Status Not validated
Chromosome 7
Chromosomal Location 24099106-24122197 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 24120289 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 421 (F421S)
Ref Sequence ENSEMBL: ENSMUSP00000002280 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002280]
AlphaFold Q9DB90
Predicted Effect probably benign
Transcript: ENSMUST00000002280
AA Change: F421S

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000002280
Gene: ENSMUSG00000002210
AA Change: F421S

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 unknown
Transcript: ENSMUST00000123188
AA Change: F96S
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146686
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148288
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 96.6%
  • 20x: 92.6%
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: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adrb3 T C 8: 27,716,880 (GRCm39) probably benign Het
Atg2b T C 12: 105,602,767 (GRCm39) H1592R probably benign Het
Bpifb1 C T 2: 154,044,581 (GRCm39) A16V probably benign Het
Cep57 T A 9: 13,721,166 (GRCm39) Y271F probably damaging Het
Cfap54 A T 10: 92,803,397 (GRCm39) N1548K possibly damaging Het
Chrna6 A T 8: 27,898,408 (GRCm39) D103E probably benign Het
Clec12b T C 6: 129,357,651 (GRCm39) N69S probably benign Het
Col27a1 T C 4: 63,209,815 (GRCm39) probably null Het
Cwh43 T A 5: 73,565,526 (GRCm39) Y30* probably null Het
Dnai7 A G 6: 145,127,483 (GRCm39) probably null Het
Dsg4 T C 18: 20,582,429 (GRCm39) probably null Het
Efna3 T C 3: 89,223,880 (GRCm39) N103S probably damaging Het
Efr3a A G 15: 65,725,400 (GRCm39) D532G possibly damaging Het
Fam227a A T 15: 79,510,469 (GRCm39) V395D probably benign Het
Fes T A 7: 80,036,668 (GRCm39) D93V probably damaging Het
Gbp3 T A 3: 142,276,732 (GRCm39) M510K possibly damaging Het
Gpr12 A T 5: 146,520,314 (GRCm39) S44T probably damaging Het
Gpr179 T C 11: 97,234,100 (GRCm39) N583S probably damaging Het
Hipk1 T C 3: 103,651,620 (GRCm39) T1093A probably benign Het
Hspb1 T C 5: 135,918,097 (GRCm39) L148P probably damaging Het
Kirrel3 A G 9: 34,946,161 (GRCm39) N640S probably damaging Het
Mak G T 13: 41,199,545 (GRCm39) Q365K probably benign Het
Melk A G 4: 44,303,649 (GRCm39) Y14C unknown Het
Myh7 T C 14: 55,230,330 (GRCm39) M1V probably null Het
Nsmf A G 2: 24,950,522 (GRCm39) Y330C probably damaging Het
Parp14 A G 16: 35,661,172 (GRCm39) F1592S possibly damaging Het
Pnpla6 A T 8: 3,573,317 (GRCm39) I394F probably benign Het
Ppl T C 16: 4,906,918 (GRCm39) R1126G probably damaging Het
Prss8 C T 7: 127,525,646 (GRCm39) R291Q probably benign Het
Ptpro T A 6: 137,420,592 (GRCm39) V1007D probably damaging Het
Rasgrp1 G T 2: 117,130,980 (GRCm39) D155E probably benign Het
Recql5 T C 11: 115,786,628 (GRCm39) I563V probably benign Het
Rhbg C T 3: 88,151,875 (GRCm39) M394I probably benign Het
Rnf130 A G 11: 49,978,264 (GRCm39) D275G probably damaging Het
Tgm2 T C 2: 157,966,301 (GRCm39) E451G probably damaging Het
Tle1 T A 4: 72,117,598 (GRCm39) T21S probably damaging Het
Tmc5 T C 7: 118,226,433 (GRCm39) I266T possibly damaging Het
Tmigd3 T A 3: 105,824,318 (GRCm39) C96S probably damaging Het
Trdn A T 10: 33,181,077 (GRCm39) T361S probably benign Het
Vgll3 A T 16: 65,657,568 (GRCm39) Q261L probably benign Het
Vmn2r104 A T 17: 20,262,987 (GRCm39) I158K probably benign Het
Zfp964 A G 8: 70,116,731 (GRCm39) K444E possibly 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
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
R7311:Smg9 UTSW 7 24,120,058 (GRCm39) missense probably benign 0.14
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'- TGATTGACCAGCTCATGGCACAC -3'
(R):5'- TGCTTCAGACCAGCTTTTCCCAAAC -3'

Sequencing Primer
(F):5'- CTACAAGGGTGAGCATCTCTG -3'
(R):5'- GTGCTGAAACACACAGCC -3'
Posted On 2013-10-16