Mutagenetix > Incidental Mutation

Incidental Mutation 'R7124:Smg7'

552173

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

045212-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.924) question?

Stock #

R7124 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

152712746-152778397 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 152753831 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 5 (N5S)

Ref Sequence

ENSEMBL: ENSMUSP00000041241 (fasta)

Gene Model

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

AlphaFold

Q5RJH6

Predicted Effect

probably benign
Transcript: ENSMUST00000043560
AA Change: N5S

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000041241
Gene: ENSMUSG00000042772
AA Change: N5S

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

SMART Domains

Protein: ENSMUSP00000073144
Gene: ENSMUSG00000042772

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

SMART Domains

Protein: ENSMUSP00000107467
Gene: ENSMUSG00000042772

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.2%

Validation Efficiency

97% (72/74)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	A	C	3: 124,208,042 (GRCm39)	S212R	probably benign	Het
4930562C15Rik	T	C	16: 4,682,196 (GRCm39)	S170P	probably benign	Het
9330182O14Rik	G	A	15: 40,008,303 (GRCm39)	C59Y	unknown	Het
AA986860	A	G	1: 130,670,624 (GRCm39)	E282G	possibly damaging	Het
Adam1a	G	T	5: 121,657,397 (GRCm39)	T632K	probably benign	Het
Aspg	G	T	12: 112,089,417 (GRCm39)	A402S	probably damaging	Het
Capn7	C	T	14: 31,058,642 (GRCm39)		probably benign	Het
Card9	C	T	2: 26,246,896 (GRCm39)		probably null	Het
Cdh13	T	C	8: 119,694,912 (GRCm39)	V254A	probably damaging	Het
Colec10	T	C	15: 54,325,767 (GRCm39)	V199A	probably damaging	Het
Copb2	T	C	9: 98,459,106 (GRCm39)	S283P	probably damaging	Het
Csmd1	G	T	8: 15,953,202 (GRCm39)	S3426R	probably damaging	Het
Cyp4f14	A	G	17: 33,133,562 (GRCm39)	V98A	probably benign	Het
Disp1	C	A	1: 182,869,030 (GRCm39)	R1130L	probably damaging	Het
Dysf	A	G	6: 84,167,883 (GRCm39)		probably null	Het
Efcab3	T	C	11: 104,629,100 (GRCm39)	F926S	probably benign	Het
Eif4ebp1	T	C	8: 27,763,447 (GRCm39)	V80A	probably damaging	Het
Eloa	T	A	4: 135,736,452 (GRCm39)	I565F	probably damaging	Het
Espn	G	T	4: 152,215,721 (GRCm39)	H513N	probably benign	Het
Fam83c	C	T	2: 155,671,491 (GRCm39)	S648N	probably benign	Het
Fdxr	C	T	11: 115,160,403 (GRCm39)	V351M	probably benign	Het
Fras1	A	T	5: 96,862,260 (GRCm39)	D2213V	probably damaging	Het
Gbp4	T	A	5: 105,267,825 (GRCm39)	I474F	possibly damaging	Het
Golgb1	T	C	16: 36,734,035 (GRCm39)	V1135A	probably benign	Het
Gpt2	G	A	8: 86,244,681 (GRCm39)	E325K	probably benign	Het
Hipk2	A	T	6: 38,795,413 (GRCm39)	Y285*	probably null	Het
Ifi27l2b	T	C	12: 103,417,579 (GRCm39)	I203V	probably damaging	Het
Itga10	T	A	3: 96,559,081 (GRCm39)	M390K	probably damaging	Het
Itgb8	G	T	12: 119,166,159 (GRCm39)	S124*	probably null	Het
Klhdc10	T	A	6: 30,441,826 (GRCm39)	F173I	probably damaging	Het
Kng2	T	G	16: 22,830,805 (GRCm39)	N168T	probably damaging	Het
Krtap24-1	T	C	16: 88,408,434 (GRCm39)	T231A	probably damaging	Het
Lbx2	A	T	6: 83,065,045 (GRCm39)	D194V	probably damaging	Het
Lrrc39	C	A	3: 116,359,562 (GRCm39)	Q36K	probably benign	Het
Madd	T	C	2: 90,992,393 (GRCm39)	E1093G	possibly damaging	Het
Mfap3l	A	G	8: 61,124,303 (GRCm39)	T182A	probably damaging	Het
Myo9b	T	A	8: 71,786,345 (GRCm39)	Y670*	probably null	Het
Nbea	A	G	3: 55,899,865 (GRCm39)	L1428P	probably damaging	Het
Nkx2-3	T	C	19: 43,603,245 (GRCm39)	Y284H	possibly damaging	Het
Nphp4	A	G	4: 152,640,141 (GRCm39)	D1009G	probably benign	Het
Npy2r	G	A	3: 82,448,490 (GRCm39)	A95V	probably damaging	Het
Nuggc	A	G	14: 65,846,251 (GRCm39)	E70G	probably damaging	Het
Or5ap2	T	C	2: 85,680,254 (GRCm39)	S153P	probably benign	Het
Or5m11	T	A	2: 85,781,817 (GRCm39)	S137T	possibly damaging	Het
Palld	A	T	8: 61,969,679 (GRCm39)	V1215D	unknown	Het
Pard6g	T	C	18: 80,160,340 (GRCm39)	I151T	possibly damaging	Het
Parp12	T	C	6: 39,088,670 (GRCm39)	I189V	probably benign	Het
Parp4	A	G	14: 56,840,256 (GRCm39)	I554V	probably benign	Het
Pcnx2	G	A	8: 126,480,356 (GRCm39)	P1984S	probably damaging	Het
Piwil4	T	C	9: 14,648,196 (GRCm39)	M128V	probably benign	Het
Polr2a	C	A	11: 69,628,288 (GRCm39)	E1302*	probably null	Het
Psg17	C	A	7: 18,548,421 (GRCm39)	G450V	probably damaging	Het
Psg17	C	G	7: 18,548,422 (GRCm39)	G450R	probably damaging	Het
Rag1	T	C	2: 101,474,128 (GRCm39)	E338G	probably damaging	Het
Rev3l	A	T	10: 39,698,163 (GRCm39)	K887*	probably null	Het
Rragd	T	C	4: 32,996,027 (GRCm39)	F124S	possibly damaging	Het
Scube1	A	T	15: 83,513,712 (GRCm39)		probably null	Het
Sfpq	A	T	4: 126,919,725 (GRCm39)	D490V	possibly damaging	Het
Smc1b	G	T	15: 84,955,798 (GRCm39)	Q1034K	probably damaging	Het
Spata31d1a	A	C	13: 59,850,301 (GRCm39)	L609R	probably damaging	Het
Ssh2	A	G	11: 77,345,164 (GRCm39)	K1050E	probably benign	Het
Stab1	G	A	14: 30,882,824 (GRCm39)	T393I	possibly damaging	Het
Sult2a4	C	T	7: 13,722,320 (GRCm39)	W49*	probably null	Het
Thrap3	A	T	4: 126,074,231 (GRCm39)	S172T	unknown	Het
Tmem130	A	G	5: 144,687,721 (GRCm39)	V205A	probably damaging	Het
Ube2d2b	A	G	5: 107,978,717 (GRCm39)	I123V	probably benign	Het
Unc79	G	T	12: 103,027,652 (GRCm39)	L414F	probably damaging	Het
Vmn2r30	C	T	7: 7,337,183 (GRCm39)	S151N	probably benign	Het
Vmn2r54	T	A	7: 12,356,078 (GRCm39)	T443S	probably benign	Het
Zfp229	T	A	17: 21,961,597 (GRCm39)	S51T	probably damaging	Het
Zfp617	T	C	8: 72,686,384 (GRCm39)	L238P	probably damaging	Het
Zfp707	T	A	15: 75,845,398 (GRCm39)	C87*	probably null	Het
Zfp853	T	C	5: 143,275,362 (GRCm39)	K101R	unknown	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
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
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'- CCTAGATCATTTCTCATAAAGCCAC -3'
(R):5'- GTTTAAGCACATGAGGGCAACATAC -3'

Sequencing Primer
(F):5'- CCTTCAAGAAGTCGCAC -3'
(R):5'- CATGAGGGCAACATACAGGACC -3'

Posted On

2019-05-15