Incidental Mutation 'R4091:Smg9'
ID317607
Institutional Source Beutler Lab
Gene Symbol Smg9
Ensembl Gene ENSMUSG00000002210
Gene Namesmg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)
Synonyms1500002O20Rik, N28092
MMRRC Submission 041626-MU
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #R4091 (G1)
Quality Score225
Status Validated
Chromosome7
Chromosomal Location24399619-24422778 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to A at 24420867 bp
ZygosityHeterozygous
Amino Acid Change Leucine to Glutamine at position 422 (L422Q)
Ref Sequence ENSEMBL: ENSMUSP00000002280 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000002280]
Predicted Effect probably null
Transcript: ENSMUST00000002280
AA Change: L422Q

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)
SMART Domains Protein: ENSMUSP00000002280
Gene: ENSMUSG00000002210
AA Change: L422Q

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 probably null
Transcript: ENSMUST00000123188
AA Change: L97Q
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146686
Predicted Effect noncoding transcript
Transcript: ENSMUST00000148288
Meta Mutation Damage Score 0.1047 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.6%
  • 20x: 96.1%
Validation Efficiency 98% (61/62)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4932414N04Rik T C 2: 68,745,378 S674P possibly damaging Het
4932438A13Rik G A 3: 37,030,589 A3897T probably benign Het
A530099J19Rik T A 13: 19,729,465 noncoding transcript Het
Abca3 C T 17: 24,397,482 T966M probably damaging Het
Adam2 A T 14: 66,029,723 Y696N probably damaging Het
Aes G A 10: 81,565,584 G162D probably damaging Het
Alas1 G T 9: 106,241,801 probably null Het
Arhgap25 G T 6: 87,463,035 S543R probably benign Het
Bckdk C A 7: 127,905,418 R105S probably damaging Het
Carns1 C T 19: 4,171,683 R191Q probably damaging Het
Casp8ap2 C A 4: 32,643,611 P895T probably damaging Het
Col12a1 T A 9: 79,702,364 I287F probably damaging Het
Cystm1 A G 18: 36,366,547 N5S unknown Het
Dnah8 T C 17: 30,769,839 V3261A probably damaging Het
Dnajc11 A G 4: 151,978,093 probably benign Het
Dock4 T C 12: 40,844,267 S1847P probably damaging Het
Dync2h1 A G 9: 7,131,881 V1642A probably benign Het
Eftud2 T C 11: 102,839,416 probably null Het
Fam221b A G 4: 43,665,987 I208T probably benign Het
Gpr37l1 T C 1: 135,161,563 I255V probably benign Het
Grm7 G A 6: 110,914,340 S178N probably damaging Het
Hspa12b T A 2: 131,133,488 probably null Het
Kctd3 A T 1: 188,995,720 probably benign Het
Kynu G A 2: 43,679,872 V389M possibly damaging Het
Lcat A G 8: 105,939,906 L328P probably benign Het
Lrrn2 C T 1: 132,937,652 Q152* probably null Het
Maml1 G A 11: 50,291,829 P78L probably benign Het
Mef2b G A 8: 70,165,102 V37M probably damaging Het
Mindy2 A T 9: 70,634,060 M281K probably damaging Het
Mon2 C T 10: 123,038,510 R311H probably damaging Het
Mtr A T 13: 12,231,057 V394E probably damaging Het
Myh14 T A 7: 44,632,991 T745S possibly damaging Het
Nme9 T A 9: 99,464,527 D131E possibly damaging Het
Nphp4 C A 4: 152,547,018 Q792K probably damaging Het
Nrxn2 T A 19: 6,473,414 C479S probably damaging Het
Nsmf T C 2: 25,060,859 I406T probably damaging Het
Olfr1431 A T 19: 12,209,779 D71V probably damaging Het
Olfr517 G A 7: 108,868,443 A237V probably damaging Het
Olfr945 T A 9: 39,258,034 I213F possibly damaging Het
Pbrm1 A G 14: 31,036,003 T197A probably benign Het
Pla2r1 T A 2: 60,432,593 N1034I probably damaging Het
Rps6-ps2 A G 8: 88,806,691 noncoding transcript Het
Rufy4 T C 1: 74,147,663 C537R probably damaging Het
Rxfp1 A T 3: 79,644,761 D744E probably benign Het
Samd9l T C 6: 3,376,887 N125D probably benign Het
Serpina3a G A 12: 104,116,366 V133I probably benign Het
Slc22a30 C T 19: 8,404,545 V121M probably damaging Het
Smarcc1 T A 9: 110,164,829 D247E possibly damaging Het
Speer3 C G 5: 13,796,380 A238G possibly damaging Het
Ttc23l CT CTTGGATT 15: 10,537,562 probably benign Het
Ttc23l G A 15: 10,537,566 S206L probably benign Het
Utrn T A 10: 12,710,171 D954V probably benign Het
Vmn1r227 T A 17: 20,735,516 noncoding transcript Het
Vmn2r11 A C 5: 109,054,750 probably null Het
Vmn2r84 A T 10: 130,391,369 M200K probably damaging Het
Vmn2r88 T A 14: 51,415,426 Y469N probably damaging Het
Wdcp A G 12: 4,855,279 N600S probably null Het
Wdfy4 T G 14: 33,125,880 R838S possibly damaging Het
Other mutations in Smg9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01100:Smg9 APN 7 24416951 missense probably damaging 1.00
IGL01432:Smg9 APN 7 24421266 critical splice donor site probably null
IGL01869:Smg9 APN 7 24416524 missense probably damaging 1.00
IGL02376:Smg9 APN 7 24415030 missense probably benign 0.01
IGL03175:Smg9 APN 7 24422305 missense probably damaging 1.00
IGL03204:Smg9 APN 7 24420912 missense probably benign 0.02
R0318:Smg9 UTSW 7 24420888 missense possibly damaging 0.80
R0578:Smg9 UTSW 7 24415043 missense probably damaging 1.00
R0786:Smg9 UTSW 7 24420864 missense probably benign 0.03
R2043:Smg9 UTSW 7 24405576 missense possibly damaging 0.92
R2355:Smg9 UTSW 7 24420121 critical splice donor site probably null
R3033:Smg9 UTSW 7 24416524 missense probably damaging 1.00
R4773:Smg9 UTSW 7 24407594 missense possibly damaging 0.84
R5023:Smg9 UTSW 7 24405872 missense possibly damaging 0.94
R5517:Smg9 UTSW 7 24414913 unclassified probably benign
R6320:Smg9 UTSW 7 24420861 missense probably benign
R6394:Smg9 UTSW 7 24422307 missense probably damaging 1.00
R7156:Smg9 UTSW 7 24420861 missense probably benign
R7269:Smg9 UTSW 7 24406070 missense possibly damaging 0.88
R7311:Smg9 UTSW 7 24420633 missense probably benign 0.14
Predicted Primers PCR Primer
(F):5'- GGTGAGCATCTCTGAGCTTC -3'
(R):5'- TTCAGACCAGCTTTTCCCAAAC -3'

Sequencing Primer
(F):5'- GAGCTTCTCATAGATTGTATGCCAC -3'
(R):5'- CCAAACCTCTCCAGTGCTG -3'
Posted On2015-05-15