Mutagenetix > Incidental Mutation

Incidental Mutation 'R1109:Smg7'

98589

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

039182-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.923) question?

Stock #

R1109 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

152712746-152778397 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to C at 152721334 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Arginine at position 626 (P626R)

Ref Sequence

ENSEMBL: ENSMUSP00000041241 (fasta)

Gene Model

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

AlphaFold

Q5RJH6

Predicted Effect

probably damaging
Transcript: ENSMUST00000043560
AA Change: P626R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000041241
Gene: ENSMUSG00000042772
AA Change: P626R

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 damaging
Transcript: ENSMUST00000073441
AA Change: P664R

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000073144
Gene: ENSMUSG00000042772
AA Change: P664R

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 damaging
Transcript: ENSMUST00000111836
AA Change: P618R

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000107467
Gene: ENSMUSG00000042772
AA Change: P618R

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

noncoding transcript
Transcript: ENSMUST00000186692

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000186900

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000188937

Meta Mutation Damage Score

0.1869

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.3%
20x: 88.9%

Validation Efficiency

100% (80/80)

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: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcd3	T	G	3: 121,573,245 (GRCm39)	E262D	probably damaging	Het
Abcg1	G	A	17: 31,330,210 (GRCm39)	A504T	probably benign	Het
Acot11	T	C	4: 106,606,545 (GRCm39)	T515A	probably benign	Het
Alg8	A	T	7: 97,032,891 (GRCm39)		probably null	Het
Arhgap44	T	A	11: 64,917,642 (GRCm39)	H375L	probably benign	Het
Aspm	A	T	1: 139,384,496 (GRCm39)	I98F	probably damaging	Het
Atp8b5	T	C	4: 43,305,719 (GRCm39)		probably benign	Het
Coa3	T	C	11: 101,169,611 (GRCm39)	K48R	probably damaging	Het
Col12a1	A	G	9: 79,607,005 (GRCm39)	S473P	probably damaging	Het
Dnmt1	A	T	9: 20,833,684 (GRCm39)	Y451N	probably damaging	Het
Dock5	A	G	14: 68,043,927 (GRCm39)	Y819H	possibly damaging	Het
Dtx1	G	A	5: 120,848,484 (GRCm39)		probably benign	Het
Dus2	T	A	8: 106,780,114 (GRCm39)	F479I	probably benign	Het
Elp1	T	C	4: 56,786,723 (GRCm39)	T407A	probably benign	Het
Esrp1	T	C	4: 11,365,205 (GRCm39)	E262G	probably damaging	Het
Exoc4	A	G	6: 33,418,951 (GRCm39)	Y466C	probably damaging	Het
Fasn	A	G	11: 120,703,150 (GRCm39)	F1625S	possibly damaging	Het
Fbxw25	A	T	9: 109,479,128 (GRCm39)	H374Q	probably benign	Het
Focad	T	C	4: 88,114,984 (GRCm39)		probably benign	Het
Gad2	G	T	2: 22,571,406 (GRCm39)	R448L	probably damaging	Het
Gad2	G	A	2: 22,580,171 (GRCm39)		probably benign	Het
Galnt16	G	T	12: 80,637,405 (GRCm39)	E377D	probably benign	Het
Gcc1	A	C	6: 28,419,166 (GRCm39)	L389R	probably damaging	Het
Ggct	A	T	6: 54,966,554 (GRCm39)		probably benign	Het
Gm7052	G	A	17: 22,259,133 (GRCm39)		probably benign	Het
Gps2	T	A	11: 69,806,507 (GRCm39)	H177Q	possibly damaging	Het
Heg1	T	A	16: 33,583,961 (GRCm39)	L1256Q	probably damaging	Het
Il36a	G	A	2: 24,106,602 (GRCm39)	G62E	probably damaging	Het
Il3ra	C	T	14: 14,349,317 (GRCm38)	R138W	probably damaging	Het
Itprid1	G	T	6: 55,945,245 (GRCm39)	K655N	probably damaging	Het
Kdm4b	T	A	17: 56,706,430 (GRCm39)	I848N	probably damaging	Het
L3hypdh	A	G	12: 72,120,770 (GRCm39)	V327A	possibly damaging	Het
Lepr	G	T	4: 101,628,552 (GRCm39)	L552F	probably damaging	Het
Lpin3	T	C	2: 160,740,941 (GRCm39)	I449T	probably damaging	Het
Lrrn1	A	G	6: 107,544,225 (GRCm39)	K8E	probably benign	Het
Mex3a	G	T	3: 88,443,967 (GRCm39)	D348Y	possibly damaging	Het
Mindy2	G	A	9: 70,538,361 (GRCm39)	R325*	probably null	Het
Mkrn1	A	T	6: 39,376,268 (GRCm39)	M382K	probably damaging	Het
Mroh1	G	T	15: 76,330,709 (GRCm39)		probably benign	Het
Myo15a	T	A	11: 60,383,892 (GRCm39)	D1646E	probably damaging	Het
Neu2	A	G	1: 87,524,450 (GRCm39)	D145G	probably damaging	Het
Obi1	A	T	14: 104,717,200 (GRCm39)	L391*	probably null	Het
Or10ah1-ps1	A	T	5: 143,123,374 (GRCm39)	N216K	probably benign	Het
Or11g27	T	C	14: 50,771,159 (GRCm39)	S97P	possibly damaging	Het
Or2w3b	T	C	11: 58,623,742 (GRCm39)	Y83C	probably benign	Het
Plekhm2	T	A	4: 141,355,295 (GRCm39)	I938F	probably benign	Het
Pnma8a	A	T	7: 16,695,392 (GRCm39)	K416*	probably null	Het
Ppid	T	C	3: 79,506,168 (GRCm39)	S198P	probably benign	Het
Rabl6	G	T	2: 25,477,538 (GRCm39)	P304Q	probably damaging	Het
Rasal2	A	T	1: 157,005,208 (GRCm39)		probably benign	Het
Ripor1	G	T	8: 106,345,560 (GRCm39)		probably benign	Het
Rnf216	A	T	5: 143,054,124 (GRCm39)	L658Q	probably damaging	Het
Safb	T	A	17: 56,908,228 (GRCm39)		probably benign	Het
Sf3b5	T	C	10: 12,884,497 (GRCm39)	M44T	probably benign	Het
Slc26a9	A	T	1: 131,686,536 (GRCm39)	M419L	probably benign	Het
Slc38a8	T	C	8: 120,209,394 (GRCm39)	D393G	probably benign	Het
Slc6a3	A	G	13: 73,705,199 (GRCm39)	D230G	probably benign	Het
Smc1b	T	C	15: 84,997,016 (GRCm39)	T535A	probably damaging	Het
Smu1	C	T	4: 40,755,722 (GRCm39)	V48M	probably benign	Het
Spag17	T	C	3: 99,934,667 (GRCm39)	Y650H	possibly damaging	Het
Spata1	C	T	3: 146,181,053 (GRCm39)	V302I	possibly damaging	Het
Sptb	G	A	12: 76,650,377 (GRCm39)	A1780V	probably damaging	Het
Srrm2	G	A	17: 24,038,591 (GRCm39)		probably benign	Het
Sspo	A	C	6: 48,474,377 (GRCm39)	N4933H	probably damaging	Het
Sult2a2	T	C	7: 13,468,798 (GRCm39)	I88T	probably benign	Het
Tgfa	G	T	6: 86,247,072 (GRCm39)		probably benign	Het
Thsd1	T	A	8: 22,733,708 (GRCm39)	C252S	possibly damaging	Het
Tmem102	T	A	11: 69,695,630 (GRCm39)	H114L	probably damaging	Het
Tnni3k	T	A	3: 154,498,414 (GRCm39)	K808N	possibly damaging	Het
Trpm7	G	T	2: 126,639,713 (GRCm39)	L1628M	probably benign	Het
Ttn	A	G	2: 76,561,081 (GRCm39)	Y29107H	probably damaging	Het
Upb1	T	C	10: 75,273,999 (GRCm39)	L342P	probably damaging	Het
Vmn2r120	T	C	17: 57,832,829 (GRCm39)	T117A	probably benign	Het
Vmn2r16	A	G	5: 109,487,652 (GRCm39)	D175G	probably damaging	Het
Vps35l	A	T	7: 118,374,552 (GRCm39)	I351F	probably damaging	Het
Zfhx4	T	G	3: 5,464,930 (GRCm39)	M1696R	possibly damaging	Het
Zfp746	A	G	6: 48,041,856 (GRCm39)	V289A	possibly damaging	Het
Zfyve26	A	C	12: 79,318,901 (GRCm39)	F1146V	probably damaging	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
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
R2155:Smg7	UTSW	1	152,716,064 (GRCm39)	missense	possibly damaging	0.49
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'- CTGCAATTGGCTTGTAGACTGTGC -3'
(R):5'- CAGGGCTTTCTGTTCACTCACTGG -3'

Sequencing Primer
(F):5'- ATTGGCCCTGGTCCAGAG -3'
(R):5'- atctgcctgcctctgcc -3'

Posted On

2014-01-05