Incidental Mutation 'R6263:Smg5'
ID 506808
Institutional Source Beutler Lab
Gene Symbol Smg5
Ensembl Gene ENSMUSG00000001415
Gene Name SMG5 nonsense mediated mRNA decay factor
Synonyms Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)
MMRRC Submission 044437-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6263 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 88243567-88269645 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 88249208 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Tyrosine at position 40 (N40Y)
Ref Sequence ENSEMBL: ENSMUSP00000001451 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001451]
AlphaFold Q6ZPY2
Predicted Effect possibly damaging
Transcript: ENSMUST00000001451
AA Change: N40Y

PolyPhen 2 Score 0.904 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000001451
Gene: ENSMUSG00000001415
AA Change: N40Y

DomainStartEndE-ValueType
low complexity region 4 14 N/A INTRINSIC
Pfam:EST1 77 189 1.1e-26 PFAM
Pfam:EST1_DNA_bind 197 427 4.6e-53 PFAM
low complexity region 447 468 N/A INTRINSIC
low complexity region 481 501 N/A INTRINSIC
Pfam:EST1_DNA_bind 611 745 3.7e-9 PFAM
coiled coil region 801 842 N/A INTRINSIC
PINc 856 979 3.23e-15 SMART
low complexity region 990 999 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000192009
Predicted Effect noncoding transcript
Transcript: ENSMUST00000192057
Predicted Effect noncoding transcript
Transcript: ENSMUST00000193007
Predicted Effect noncoding transcript
Transcript: ENSMUST00000194942
Meta Mutation Damage Score 0.1133 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.4%
  • 20x: 95.7%
Validation Efficiency 97% (66/68)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] SMG5 is involved in nonsense-mediated mRNA decay (Ohnishi et al., 2003 [PubMed 14636577]).[supplied by OMIM, Mar 2008]
Allele List at MGI
Other mutations in this stock
Total: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ahnak A G 19: 8,995,641 (GRCm39) I5642V probably benign Het
Atp5f1a A G 18: 77,866,930 (GRCm39) probably null Het
Bltp1 T A 3: 36,985,260 (GRCm39) N863K probably benign Het
Bsn A T 9: 107,990,453 (GRCm39) F1766L probably damaging Het
Ccdc141 T C 2: 76,938,807 (GRCm39) Q266R probably damaging Het
Cdh10 T A 15: 18,964,154 (GRCm39) D105E possibly damaging Het
Clca3a1 T A 3: 144,455,539 (GRCm39) D418V probably damaging Het
Cnnm2 C A 19: 46,845,344 (GRCm39) T612K probably benign Het
Col3a1 T C 1: 45,360,735 (GRCm39) V55A unknown Het
Cpd A C 11: 76,737,097 (GRCm39) D232E probably benign Het
Csde1 A G 3: 102,947,333 (GRCm39) H95R probably benign Het
Ctcfl T A 2: 172,937,130 (GRCm39) H596L probably benign Het
Cwc22 T C 2: 77,726,515 (GRCm39) R855G possibly damaging Het
Cwc25 A G 11: 97,644,053 (GRCm39) Y227H probably damaging Het
Cyp2c38 G A 19: 39,380,659 (GRCm39) P409S probably damaging Het
Ddx5 A G 11: 106,679,139 (GRCm39) S2P possibly damaging Het
Dnah2 C A 11: 69,348,238 (GRCm39) G2570W probably damaging Het
Dnajc10 T A 2: 80,174,292 (GRCm39) V528E probably damaging Het
Efcab3 G A 11: 104,810,312 (GRCm39) D3150N unknown Het
Fmo1 A G 1: 162,677,629 (GRCm39) probably null Het
Gpatch1 C A 7: 35,002,848 (GRCm39) D221Y probably damaging Het
Ino80 T C 2: 119,213,895 (GRCm39) Y1225C probably damaging Het
Itga7 T A 10: 128,779,955 (GRCm39) D501E probably benign Het
Lgr4 T C 2: 109,842,243 (GRCm39) S743P possibly damaging Het
Lilra5 A T 7: 4,241,360 (GRCm39) Y99F probably damaging Het
Lmna A G 3: 88,410,265 (GRCm39) V49A probably damaging Het
Lrrc72 G A 12: 36,258,603 (GRCm39) R267* probably null Het
Mapkbp1 T C 2: 119,853,772 (GRCm39) S1199P probably damaging Het
Mmp25 G A 17: 23,849,768 (GRCm39) A541V possibly damaging Het
Myh10 A T 11: 68,701,058 (GRCm39) N1756Y probably damaging Het
Nfe2 A G 15: 103,159,378 (GRCm39) I31T probably damaging Het
Nfe2l1 A T 11: 96,708,570 (GRCm39) F732I probably benign Het
Or4a39 C G 2: 89,237,074 (GRCm39) M116I possibly damaging Het
Or4c12b T A 2: 89,647,104 (GRCm39) C145S probably damaging Het
Or52e19b C A 7: 103,032,403 (GRCm39) V269F possibly damaging Het
Pax6 T C 2: 105,523,199 (GRCm39) probably null Het
Phb1 A G 11: 95,568,941 (GRCm39) E192G probably damaging Het
Plekhn1 A T 4: 156,309,650 (GRCm39) probably null Het
Plxnb2 A T 15: 89,046,189 (GRCm39) V942E probably damaging Het
Potegl T A 2: 23,156,745 (GRCm39) probably benign Het
Rsrc2 G A 5: 123,877,751 (GRCm39) probably benign Het
Septin8 G A 11: 53,439,210 (GRCm39) C460Y probably benign Het
Slc13a2 CGTTATCTGT CGT 11: 78,294,306 (GRCm39) probably benign Het
Slc16a7 A G 10: 125,130,508 (GRCm39) I59T probably benign Het
Slc35d1 A T 4: 103,065,365 (GRCm39) I172N possibly damaging Het
Smurf1 A G 5: 144,818,541 (GRCm39) V633A probably damaging Het
Snx9 T C 17: 5,937,324 (GRCm39) V22A probably damaging Het
Sox6 A T 7: 115,076,295 (GRCm39) M741K probably damaging Het
Spata31d1d T C 13: 59,873,797 (GRCm39) Q1246R probably benign Het
Sval1 A G 6: 41,928,660 (GRCm39) E24G probably damaging Het
Tas2r124 A G 6: 132,731,867 (GRCm39) I59V probably benign Het
Tmem151b T A 17: 45,857,992 (GRCm39) T85S probably benign Het
Tpr T A 1: 150,317,996 (GRCm39) probably null Het
Trpm6 A C 19: 18,831,472 (GRCm39) T1446P possibly damaging Het
Tsc22d4 A T 5: 137,766,441 (GRCm39) K502N possibly damaging Het
Tssk3 C T 4: 129,383,051 (GRCm39) S207N probably benign Het
Ttbk1 G T 17: 46,778,188 (GRCm39) P618Q probably damaging Het
Ttll6 A T 11: 96,047,371 (GRCm39) M657L probably benign Het
Ubash3a T A 17: 31,434,069 (GRCm39) I138N probably benign Het
Ush2a A G 1: 188,090,839 (GRCm39) Y490C probably damaging Het
Vmn1r82 G T 7: 12,039,461 (GRCm39) V127F probably damaging Het
Vmn2r32 A T 7: 7,479,691 (GRCm39) S161T possibly damaging Het
Wdr49 T C 3: 75,388,824 (GRCm39) I58M possibly damaging Het
Wiz A T 17: 32,579,417 (GRCm39) probably null Het
Wrap53 A T 11: 69,453,619 (GRCm39) Y324* probably null Het
Zfp747 A C 7: 126,975,138 (GRCm39) probably benign Het
Zfp827 A G 8: 79,905,702 (GRCm39) Y33C probably damaging Het
Other mutations in Smg5
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00433:Smg5 APN 3 88,258,735 (GRCm39) nonsense probably null
IGL00902:Smg5 APN 3 88,260,392 (GRCm39) missense probably benign 0.00
IGL00990:Smg5 APN 3 88,250,345 (GRCm39) critical splice donor site probably null
IGL01371:Smg5 APN 3 88,266,951 (GRCm39) unclassified probably benign
IGL01536:Smg5 APN 3 88,256,552 (GRCm39) missense possibly damaging 0.58
IGL02215:Smg5 APN 3 88,260,305 (GRCm39) missense possibly damaging 0.47
IGL03366:Smg5 APN 3 88,253,759 (GRCm39) nonsense probably null
R0013:Smg5 UTSW 3 88,256,540 (GRCm39) missense probably benign 0.00
R0017:Smg5 UTSW 3 88,258,412 (GRCm39) missense probably damaging 1.00
R0017:Smg5 UTSW 3 88,258,412 (GRCm39) missense probably damaging 1.00
R0129:Smg5 UTSW 3 88,256,540 (GRCm39) missense probably benign 0.00
R0153:Smg5 UTSW 3 88,261,179 (GRCm39) unclassified probably benign
R1386:Smg5 UTSW 3 88,262,978 (GRCm39) missense probably damaging 1.00
R1941:Smg5 UTSW 3 88,252,687 (GRCm39) missense possibly damaging 0.71
R2185:Smg5 UTSW 3 88,258,868 (GRCm39) missense probably benign
R2282:Smg5 UTSW 3 88,252,705 (GRCm39) missense probably benign 0.02
R3615:Smg5 UTSW 3 88,243,758 (GRCm39) missense possibly damaging 0.94
R3616:Smg5 UTSW 3 88,243,758 (GRCm39) missense possibly damaging 0.94
R4008:Smg5 UTSW 3 88,256,465 (GRCm39) missense probably benign 0.01
R4687:Smg5 UTSW 3 88,249,776 (GRCm39) missense possibly damaging 0.83
R4726:Smg5 UTSW 3 88,243,758 (GRCm39) missense possibly damaging 0.94
R4801:Smg5 UTSW 3 88,262,999 (GRCm39) nonsense probably null
R4802:Smg5 UTSW 3 88,262,999 (GRCm39) nonsense probably null
R4977:Smg5 UTSW 3 88,263,032 (GRCm39) nonsense probably null
R5384:Smg5 UTSW 3 88,258,600 (GRCm39) missense probably damaging 1.00
R5443:Smg5 UTSW 3 88,261,896 (GRCm39) missense probably damaging 0.99
R5779:Smg5 UTSW 3 88,258,925 (GRCm39) unclassified probably benign
R5860:Smg5 UTSW 3 88,250,214 (GRCm39) missense probably damaging 0.97
R6080:Smg5 UTSW 3 88,258,816 (GRCm39) missense probably benign
R6431:Smg5 UTSW 3 88,258,527 (GRCm39) missense probably benign 0.00
R6722:Smg5 UTSW 3 88,260,332 (GRCm39) missense probably damaging 0.99
R6847:Smg5 UTSW 3 88,249,859 (GRCm39) missense probably damaging 1.00
R6950:Smg5 UTSW 3 88,256,576 (GRCm39) critical splice donor site probably null
R7091:Smg5 UTSW 3 88,258,654 (GRCm39) missense probably benign 0.00
R7395:Smg5 UTSW 3 88,268,378 (GRCm39) missense probably damaging 0.99
R7678:Smg5 UTSW 3 88,261,202 (GRCm39) missense possibly damaging 0.93
R7796:Smg5 UTSW 3 88,256,739 (GRCm39) missense probably damaging 0.96
R8209:Smg5 UTSW 3 88,258,838 (GRCm39) missense probably benign 0.00
R8327:Smg5 UTSW 3 88,252,714 (GRCm39) missense probably damaging 1.00
R8987:Smg5 UTSW 3 88,267,714 (GRCm39) critical splice donor site probably null
R9345:Smg5 UTSW 3 88,261,848 (GRCm39) missense probably damaging 1.00
R9534:Smg5 UTSW 3 88,252,759 (GRCm39) missense probably benign 0.13
R9602:Smg5 UTSW 3 88,250,214 (GRCm39) missense probably damaging 1.00
Z1177:Smg5 UTSW 3 88,260,297 (GRCm39) missense probably benign 0.33
Z1177:Smg5 UTSW 3 88,258,441 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CTGAGTGAAGTCTGCCTCTTC -3'
(R):5'- TGTTCTCTCAGGGAAGCCAGAG -3'

Sequencing Primer
(F):5'- GAAGTCTGCCTCTTCATTTTCCTAAC -3'
(R):5'- TCTCAGGGAAGCCAGAGACTTC -3'
Posted On 2018-03-15