Mutagenetix > Incidental Mutation

Incidental Mutation 'R2155:Smg7'

234676

Institutional Source

Beutler Lab

Gene Symbol

Smg7

Ensembl Gene

ENSMUSG00000042772

Gene Name

SMG7 nonsense mediated mRNA decay factor

Synonyms

9430023P16Rik, Smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)

MMRRC Submission

040158-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.924) question?

Stock #

R2155 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

152712746-152778397 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 152716064 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 1057 (T1057I)

Ref Sequence

ENSEMBL: ENSMUSP00000041241 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000027754] [ENSMUST00000043560] [ENSMUST00000073441] [ENSMUST00000111836] [ENSMUST00000186568]

AlphaFold

Q5RJH6

Predicted Effect

probably benign
Transcript: ENSMUST00000027754

SMART Domains

Protein: ENSMUSP00000027754
Gene: ENSMUSG00000026480

Domain	Start	End	E-Value	Type
TPR	37	70	1.42e0	SMART
TPR	71	104	3.58e-6	SMART
TPR	121	154	1.05e1	SMART
SH3	243	298	1.02e-13	SMART
low complexity region	312	326	N/A	INTRINSIC
PB1	350	428	2.6e-10	SMART
SH3	459	514	8.36e-19	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000043560
AA Change: T1057I

PolyPhen 2 Score 0.487 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000041241
Gene: ENSMUSG00000042772
AA Change: T1057I

Domain	Start	End	E-Value	Type
Pfam:EST1	63	177	3.4e-30	PFAM
Pfam:EST1_DNA_bind	179	438	3.3e-64	PFAM
low complexity region	457	465	N/A	INTRINSIC
low complexity region	615	633	N/A	INTRINSIC
low complexity region	682	710	N/A	INTRINSIC
low complexity region	711	729	N/A	INTRINSIC
low complexity region	874	898	N/A	INTRINSIC
low complexity region	906	922	N/A	INTRINSIC
low complexity region	931	947	N/A	INTRINSIC
low complexity region	1008	1034	N/A	INTRINSIC
low complexity region	1126	1140	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000073441
AA Change: T1045I

PolyPhen 2 Score 0.448 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000073144
Gene: ENSMUSG00000042772
AA Change: T1045I

Domain	Start	End	E-Value	Type
Pfam:EST1	52	172	2.3e-26	PFAM
Pfam:EST1_DNA_bind	171	430	3.6e-66	PFAM
low complexity region	449	457	N/A	INTRINSIC
low complexity region	653	671	N/A	INTRINSIC
low complexity region	720	748	N/A	INTRINSIC
low complexity region	749	767	N/A	INTRINSIC
low complexity region	919	935	N/A	INTRINSIC
low complexity region	996	1022	N/A	INTRINSIC
low complexity region	1114	1128	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000111836
AA Change: T1049I

PolyPhen 2 Score 0.355 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000107467
Gene: ENSMUSG00000042772
AA Change: T1049I

Domain	Start	End	E-Value	Type
Pfam:EST1	52	172	2.3e-26	PFAM
Pfam:EST1_DNA_bind	171	430	3.7e-66	PFAM
low complexity region	449	457	N/A	INTRINSIC
low complexity region	607	625	N/A	INTRINSIC
low complexity region	674	702	N/A	INTRINSIC
low complexity region	703	721	N/A	INTRINSIC
low complexity region	866	890	N/A	INTRINSIC
low complexity region	898	914	N/A	INTRINSIC
low complexity region	923	939	N/A	INTRINSIC
low complexity region	1000	1026	N/A	INTRINSIC
low complexity region	1118	1132	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000186568

SMART Domains

Protein: ENSMUSP00000140404
Gene: ENSMUSG00000026480

Domain	Start	End	E-Value	Type
TPR	37	70	1.42e0	SMART
TPR	71	104	3.58e-6	SMART
TPR	121	154	1.05e1	SMART
SH3	243	298	1.02e-13	SMART
low complexity region	312	326	N/A	INTRINSIC
PB1	350	428	2.6e-10	SMART
SH3	459	514	8.36e-19	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000186692

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000186900

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is essential for nonsense-mediated mRNA decay (NMD); a process whereby transcripts with premature termination codons are targeted for rapid degradation by a mRNA decay complex. The mRNA decay complex consists, in part, of this protein along with proteins SMG5 and UPF1. The N-terminal domain of this protein is thought to mediate its association with SMG5 or UPF1 while the C-terminal domain interacts with the mRNA decay complex. This protein may therefore couple changes in UPF1 phosphorylation state to the degradation of NMD-candidate transcripts. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Aug 2011]

Allele List at MGI

Other mutations in this stock

Total: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610318N02Rik	A	G	16: 16,939,260 (GRCm39)	L41P	probably damaging	Het
Aff4	C	T	11: 53,290,446 (GRCm39)	L469F	probably damaging	Het
AI182371	G	A	2: 34,975,366 (GRCm39)	H288Y	probably benign	Het
AK157302	A	T	13: 21,679,827 (GRCm39)	K118*	probably null	Het
Arhgef2	G	A	3: 88,543,351 (GRCm39)	R454Q	probably damaging	Het
Asb17	C	T	3: 153,550,322 (GRCm39)	T118M	probably damaging	Het
Atp7b	A	G	8: 22,503,600 (GRCm39)	V718A	possibly damaging	Het
Cdca2	A	G	14: 67,952,287 (GRCm39)	L28S	probably damaging	Het
Cdh20	G	T	1: 109,976,594 (GRCm39)	L86F	probably damaging	Het
Cela2a	A	T	4: 141,545,350 (GRCm39)		probably null	Het
Cers3	T	A	7: 66,433,162 (GRCm39)	Y160N	probably damaging	Het
Chmp2b	A	G	16: 65,343,877 (GRCm39)	V56A	probably benign	Het
Cryl1	A	G	14: 57,635,880 (GRCm39)	V9A	unknown	Het
Dmbt1	A	T	7: 130,699,305 (GRCm39)	H978L	possibly damaging	Het
Dnm1	C	T	2: 32,204,949 (GRCm39)	V673M	probably damaging	Het
Dtx4	T	A	19: 12,462,646 (GRCm39)	K378*	probably null	Het
Extl1	A	T	4: 134,090,491 (GRCm39)	M328K	possibly damaging	Het
Fcgbp	T	C	7: 27,806,628 (GRCm39)	S2199P	probably benign	Het
Glis3	G	T	19: 28,508,702 (GRCm39)	N427K	probably benign	Het
Hdac7	T	C	15: 97,691,944 (GRCm39)	K810E	probably benign	Het
Hesx1	A	G	14: 26,723,434 (GRCm39)	E88G	probably benign	Het
Hmcn2	A	T	2: 31,350,361 (GRCm39)	Q5086L	possibly damaging	Het
Ier3	A	G	17: 36,133,101 (GRCm39)	T128A	probably benign	Het
Igsf10	G	T	3: 59,239,101 (GRCm39)	T360K	probably damaging	Het
Ilkap	A	C	1: 91,312,345 (GRCm39)	C2G	possibly damaging	Het
Itih1	A	G	14: 30,660,028 (GRCm39)	F231S	probably damaging	Het
Jrkl	A	T	9: 13,244,913 (GRCm39)	Y249*	probably null	Het
Kat6a	AGAGGAGGAGGAGGAGGAGGAGGAG	AGAGGAGGAGGAGGAGGAGGAG	8: 23,425,663 (GRCm39)		probably benign	Het
Katnal2	A	T	18: 77,098,637 (GRCm39)	S184R	probably benign	Het
Kcnh5	T	A	12: 74,945,230 (GRCm39)		probably null	Het
Kcnj11	G	T	7: 45,748,781 (GRCm39)	L181I	probably damaging	Het
Klhl2	T	C	8: 65,202,804 (GRCm39)	T465A	probably benign	Het
Krt90	T	A	15: 101,471,046 (GRCm39)	Y72F	probably benign	Het
Lig4	G	A	8: 10,022,766 (GRCm39)	T338I	probably benign	Het
Lrrc37	T	C	11: 103,511,285 (GRCm39)	T228A	unknown	Het
Magel2	T	C	7: 62,030,540 (GRCm39)	V1148A	unknown	Het
Mak	C	A	13: 41,186,020 (GRCm39)	E549D	probably benign	Het
Marf1	G	T	16: 13,950,293 (GRCm39)	S1001Y	probably damaging	Het
Mcoln1	G	A	8: 3,561,787 (GRCm39)	V446I	probably damaging	Het
Meig1	T	C	2: 3,410,290 (GRCm39)	N70S	probably benign	Het
Mfsd14a	G	A	3: 116,441,479 (GRCm39)	T108I	probably damaging	Het
Mocs1	G	A	17: 49,761,386 (GRCm39)	M493I	probably damaging	Het
Mrpl11	C	A	19: 5,012,497 (GRCm39)	A26E	probably damaging	Het
Myh6	A	T	14: 55,191,251 (GRCm39)	D863E	probably benign	Het
Myom2	T	A	8: 15,134,555 (GRCm39)	Y453N	probably damaging	Het
Nhlh1	A	G	1: 171,881,524 (GRCm39)	I114T	probably damaging	Het
Odr4	A	G	1: 150,258,086 (GRCm39)	V183A	possibly damaging	Het
Or12j4	A	C	7: 140,046,504 (GRCm39)	H130P	probably benign	Het
Or2y3	G	T	17: 38,393,071 (GRCm39)	P266Q	probably damaging	Het
Or4k5	A	T	14: 50,386,154 (GRCm39)	M59K	probably damaging	Het
Or5k17	G	T	16: 58,746,486 (GRCm39)	F149L	probably benign	Het
Or5p80	C	G	7: 108,229,984 (GRCm39)	P262A	probably damaging	Het
Pclo	T	C	5: 14,764,309 (GRCm39)	S976P	probably benign	Het
Pde3a	G	A	6: 141,429,640 (GRCm39)	E734K	possibly damaging	Het
Pdzd2	A	T	15: 12,375,879 (GRCm39)	S1419T	probably benign	Het
Pdzd8	T	A	19: 59,288,853 (GRCm39)	Y849F	probably damaging	Het
Phldb3	A	G	7: 24,312,070 (GRCm39)	E128G	probably damaging	Het
Polg	A	G	7: 79,111,468 (GRCm39)	I261T	possibly damaging	Het
Ppp1r35	T	C	5: 137,778,267 (GRCm39)	M254T	probably benign	Het
Ppp3ca	G	T	3: 136,596,211 (GRCm39)	R292M	possibly damaging	Het
Ptk7	T	A	17: 46,890,543 (GRCm39)	T430S	probably benign	Het
Ptrh1	T	A	2: 32,667,040 (GRCm39)	N144K	possibly damaging	Het
Rbfox1	A	G	16: 7,111,946 (GRCm39)	T211A	possibly damaging	Het
Rbpjl	A	G	2: 164,256,343 (GRCm39)	D443G	possibly damaging	Het
Rcc1	A	G	4: 132,065,360 (GRCm39)		probably null	Het
Rimbp2	G	T	5: 128,865,229 (GRCm39)	S706R	probably damaging	Het
Rsph10b	G	C	5: 143,898,074 (GRCm39)	E96D	probably benign	Het
Scn10a	A	T	9: 119,438,514 (GRCm39)	I1784K	probably benign	Het
Sfxn2	A	G	19: 46,579,985 (GRCm39)		probably null	Het
Slamf6	T	A	1: 171,765,575 (GRCm39)	L233Q	probably damaging	Het
Slc17a5	A	T	9: 78,484,455 (GRCm39)	Y102N	probably damaging	Het
Slc25a53	T	C	X: 135,884,216 (GRCm39)	T42A	probably damaging	Het
Slco1a8	T	C	6: 141,926,670 (GRCm39)	D552G	probably damaging	Het
Speer2	T	A	16: 69,657,485 (GRCm39)	T53S	possibly damaging	Het
Srm	A	C	4: 148,676,948 (GRCm39)	I100L	probably benign	Het
Stoml3	A	C	3: 53,415,008 (GRCm39)	N267H	probably damaging	Het
Thsd7a	A	C	6: 12,379,632 (GRCm39)	C931G	probably damaging	Het
Tlr11	A	G	14: 50,598,139 (GRCm39)	I42V	probably benign	Het
Tmigd1	T	C	11: 76,800,999 (GRCm39)	V162A	probably benign	Het
Tmx3	A	G	18: 90,528,505 (GRCm39)		probably null	Het
Topors	T	A	4: 40,262,790 (GRCm39)	R165W	possibly damaging	Het
Ttc17	A	T	2: 94,196,987 (GRCm39)	S453R	possibly damaging	Het
Vmn1r49	G	T	6: 90,049,441 (GRCm39)	T187N	probably damaging	Het
Zbtb49	A	T	5: 38,371,464 (GRCm39)	V139E	possibly damaging	Het
Zfp11	T	C	5: 129,734,216 (GRCm39)	H415R	probably damaging	Het
Zfp677	A	T	17: 21,617,970 (GRCm39)	K342N	probably benign	Het
Zfp979	A	C	4: 147,697,915 (GRCm39)	C265G	possibly damaging	Het
Zfpl1	T	C	19: 6,134,459 (GRCm39)	R9G	probably damaging	Het
Zkscan8	A	T	13: 21,704,759 (GRCm39)	C321*	probably null	Het

Other mutations in Smg7

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01751:Smg7	APN	1	152,719,812 (GRCm39)	missense	possibly damaging	0.68
IGL02320:Smg7	APN	1	152,744,088 (GRCm39)	missense	possibly damaging	0.49
IGL02336:Smg7	APN	1	152,719,030 (GRCm39)	missense	probably benign
IGL02680:Smg7	APN	1	152,721,145 (GRCm39)	missense	probably benign	0.15
IGL03232:Smg7	APN	1	152,715,907 (GRCm39)	missense	probably damaging	1.00
chill	UTSW	1	152,715,887 (GRCm39)	splice site	probably null
R0322:Smg7	UTSW	1	152,725,624 (GRCm39)	critical splice donor site	probably null
R0540:Smg7	UTSW	1	152,731,713 (GRCm39)	missense	probably benign	0.00
R0685:Smg7	UTSW	1	152,742,399 (GRCm39)	missense	probably damaging	1.00
R0707:Smg7	UTSW	1	152,746,508 (GRCm39)	splice site	probably null
R1109:Smg7	UTSW	1	152,721,334 (GRCm39)	missense	probably damaging	1.00
R1118:Smg7	UTSW	1	152,742,326 (GRCm39)	splice site	probably benign
R1119:Smg7	UTSW	1	152,742,326 (GRCm39)	splice site	probably benign
R1458:Smg7	UTSW	1	152,731,594 (GRCm39)	splice site	probably null
R1759:Smg7	UTSW	1	152,724,597 (GRCm39)	missense	probably benign	0.20
R1846:Smg7	UTSW	1	152,724,601 (GRCm39)	missense	probably damaging	1.00
R2015:Smg7	UTSW	1	152,736,259 (GRCm39)	missense	probably damaging	1.00
R2199:Smg7	UTSW	1	152,730,079 (GRCm39)	missense	probably damaging	1.00
R2234:Smg7	UTSW	1	152,744,064 (GRCm39)	missense	probably damaging	1.00
R2235:Smg7	UTSW	1	152,744,064 (GRCm39)	missense	probably damaging	1.00
R3861:Smg7	UTSW	1	152,728,349 (GRCm39)	missense	probably null	1.00
R4597:Smg7	UTSW	1	152,716,052 (GRCm39)	critical splice donor site	probably null
R4672:Smg7	UTSW	1	152,721,164 (GRCm39)	missense	probably damaging	1.00
R4851:Smg7	UTSW	1	152,720,020 (GRCm39)	missense	probably benign	0.00
R5486:Smg7	UTSW	1	152,721,927 (GRCm39)	missense	probably damaging	0.97
R5607:Smg7	UTSW	1	152,718,985 (GRCm39)	missense	probably damaging	0.98
R6131:Smg7	UTSW	1	152,720,962 (GRCm39)	critical splice donor site	probably null
R6396:Smg7	UTSW	1	152,724,351 (GRCm39)	missense	probably benign	0.33
R6401:Smg7	UTSW	1	152,715,887 (GRCm39)	splice site	probably null
R6905:Smg7	UTSW	1	152,725,757 (GRCm39)	splice site	probably null
R6961:Smg7	UTSW	1	152,717,334 (GRCm39)	nonsense	probably null
R7051:Smg7	UTSW	1	152,724,601 (GRCm39)	missense	probably damaging	1.00
R7124:Smg7	UTSW	1	152,753,831 (GRCm39)	missense	probably benign	0.01
R7146:Smg7	UTSW	1	152,737,576 (GRCm39)	missense	probably benign	0.34
R7573:Smg7	UTSW	1	152,735,240 (GRCm39)	missense	probably damaging	1.00
R7578:Smg7	UTSW	1	152,721,181 (GRCm39)	missense	probably damaging	1.00
R7621:Smg7	UTSW	1	152,717,295 (GRCm39)	missense	possibly damaging	0.95
R7956:Smg7	UTSW	1	152,719,953 (GRCm39)	missense	probably benign	0.02
R8167:Smg7	UTSW	1	152,720,123 (GRCm39)	missense	possibly damaging	0.90
R8751:Smg7	UTSW	1	152,719,129 (GRCm39)	missense	probably damaging	0.99
R8905:Smg7	UTSW	1	152,715,817 (GRCm39)	missense	probably damaging	1.00
R9082:Smg7	UTSW	1	152,715,928 (GRCm39)	missense	probably damaging	0.96
R9229:Smg7	UTSW	1	152,720,971 (GRCm39)	missense	possibly damaging	0.72
R9260:Smg7	UTSW	1	152,737,549 (GRCm39)	missense	probably damaging	1.00
R9262:Smg7	UTSW	1	152,721,262 (GRCm39)	missense	probably damaging	1.00
R9323:Smg7	UTSW	1	152,731,753 (GRCm39)	missense	probably benign	0.01
R9519:Smg7	UTSW	1	152,735,196 (GRCm39)	missense	probably damaging	1.00
R9732:Smg7	UTSW	1	152,736,212 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GCTCTCAGATGATGACGTTGC -3'
(R):5'- CAGACAGACTGCTTCATGGTC -3'

Sequencing Primer
(F):5'- CGTTGCTGAGAGATAATCAACAC -3'
(R):5'- ACAGACTGCTTCATGGTCTTTATTTG -3'

Posted On

2014-10-01