Mutagenetix > Incidental Mutations

Incidental Mutation 'R7051:Smg7'

547555

Institutional Source

Beutler Lab

Gene Symbol

Smg7

Ensembl Gene

ENSMUSG00000042772

Gene Name

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

Synonyms

9430023P16Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.922) question?

Stock #

R7051 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

152836995-152902646 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 152848850 bp

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 527 (S527P)

Ref Sequence

ENSEMBL: ENSMUSP00000107467 (fasta)

Gene Model

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

Predicted Effect

probably damaging
Transcript: ENSMUST00000043560
AA Change: S535P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000041241
Gene: ENSMUSG00000042772
AA Change: S535P

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: S527P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000073144
Gene: ENSMUSG00000042772
AA Change: S527P

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: S527P

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000107467
Gene: ENSMUSG00000042772
AA Change: S527P

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

0.3763

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

95% (80/84)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5930422O12Rik	C	T	8: 33,429,173	S7L	unknown	Het
Aggf1	T	C	13: 95,351,617	K674R	possibly damaging	Het
Ampd1	T	C	3: 103,090,073	F264L	probably damaging	Het
Ankle1	A	T	8: 71,407,743	S302C	probably damaging	Het
Ankrd17	G	A	5: 90,366,451		probably benign	Het
Arhgap18	T	A	10: 26,849,921	N47K	possibly damaging	Het
Atp5f1	T	C	3: 105,943,767	N205D	probably benign	Het
Atp8b3	C	T	10: 80,520,024	E1285K	probably benign	Het
Atp8b3	C	A	10: 80,529,718	V401L	probably damaging	Het
Cacna1a	G	A	8: 84,629,915	R1929Q	possibly damaging	Het
Cadm2	C	T	16: 66,882,879	S22N	possibly damaging	Het
Ccdc177	C	T	12: 80,759,153	V116M	probably damaging	Het
Cdkl2	A	T	5: 92,033,225	I185N	probably damaging	Het
Cfhr2	T	A	1: 139,810,978	I282L	probably benign	Het
Clns1a	T	A	7: 97,712,617		probably null	Het
Commd2	A	T	3: 57,646,686	I198N	probably damaging	Het
Creb3l2	C	T	6: 37,336,265	V365I	possibly damaging	Het
Dcaf6	A	T	1: 165,424,317	N79K	possibly damaging	Het
Dlg5	T	C	14: 24,146,195	N1622D	possibly damaging	Het
Dock7	C	T	4: 98,946,732	R1802H	probably damaging	Het
Dpy19l2	T	C	9: 24,584,493	K643R	probably benign	Het
Dscam	G	A	16: 96,819,786	T574M	probably benign	Het
Fam209	A	G	2: 172,474,049	T115A	probably damaging	Het
Fastkd5	C	T	2: 130,614,417	C751Y	probably damaging	Het
Fat3	C	A	9: 16,377,827	L133F	probably damaging	Het
Frmd6	T	C	12: 70,897,396	V516A	possibly damaging	Het
Fry	G	A	5: 150,395,169	D955N	possibly damaging	Het
Fuk	A	T	8: 110,890,339	I393N	probably damaging	Het
Gm281	A	G	14: 13,828,486	V758A		Het
Gm340	A	G	19: 41,585,752	D982G	probably benign	Het
Gm7298	T	C	6: 121,775,034		probably null	Het
Golga7b	T	A	19: 42,268,460	*168R	probably null	Het
Golim4	T	A	3: 75,893,002	Q395L	probably benign	Het
Gxylt2	T	A	6: 100,804,576	L404*	probably null	Het
Hist1h1e	A	G	13: 23,622,439	V20A	probably benign	Het
Ighmbp2	G	T	19: 3,261,462	S984R	probably damaging	Het
Irf8	C	T	8: 120,739,842	R9W	probably damaging	Het
Itga4	T	C	2: 79,318,126	V788A	possibly damaging	Het
Kifap3	G	A	1: 163,794,080	R99H	probably damaging	Het
Kiss1r	T	C	10: 79,918,854	S61P	probably damaging	Het
Krtap6-1	A	T	16: 89,031,718	M1L	unknown	Het
Large2	A	T	2: 92,367,022	M411K	probably damaging	Het
Lingo1	A	G	9: 56,620,183	V374A	probably benign	Het
Lrch1	A	G	14: 74,785,522	V637A	probably damaging	Het
Lyar	T	C	5: 38,224,680	V2A	probably damaging	Het
Nell1	C	T	7: 50,448,844	S298L	unknown	Het
Ogfod3	T	A	11: 121,195,205	I188F	probably damaging	Het
Olfr1487	T	A	19: 13,619,405	M81K	possibly damaging	Het
Olfr173	T	C	16: 58,797,175	T224A	probably benign	Het
Opa3	C	A	7: 19,245,036	A142E	possibly damaging	Het
Pald1	T	C	10: 61,323,346	R769G	probably benign	Het
Pappa2	T	A	1: 158,957,183	T86S	unknown	Het
Papss1	T	C	3: 131,602,050	Y266H	probably damaging	Het
Pcdhga7	C	A	18: 37,716,941	A667D	probably damaging	Het
Pcsk5	T	A	19: 17,433,731	T1766S	probably benign	Het
Pds5b	T	A	5: 150,794,282	N1129K	possibly damaging	Het
Pop7	T	C	5: 137,501,690	N127S	probably damaging	Het
Ppfibp2	A	G	7: 107,717,718	E300G	probably damaging	Het
Ppp4r3b	A	G	11: 29,182,507	K87E	probably damaging	Het
Psmd3	T	A	11: 98,682,833	M35K	possibly damaging	Het
Pus7	A	G	5: 23,775,679	V191A	probably damaging	Het
Rptor	C	T	11: 119,874,186		probably benign	Het
Sacs	A	G	14: 61,208,928	M2808V	probably benign	Het
Scube3	G	A	17: 28,167,599	V831I	probably benign	Het
Sin3a	A	T	9: 57,103,934	N492Y	probably damaging	Het
Slc12a3	A	G	8: 94,365,944	T998A	probably damaging	Het
Slc4a1	T	C	11: 102,356,258	N501S	probably benign	Het
Sltm	G	A	9: 70,559,066	G94R	probably damaging	Het
Smc4	T	A	3: 69,027,502	W650R	probably damaging	Het
Tcf20	T	C	15: 82,856,078	N391D	probably damaging	Het
Tiam2	G	A	17: 3,448,483	V845M	probably damaging	Het
Tln2	A	G	9: 67,346,417	F793L	probably benign	Het
Uckl1	T	C	2: 181,574,244	I193V	probably damaging	Het
Ugt1a5	A	G	1: 88,166,355	M102V	probably benign	Het
Usp38	G	A	8: 81,001,121	P328S	possibly damaging	Het
Vmn1r189	A	G	13: 22,102,115	V184A	possibly damaging	Het
Vps13d	C	A	4: 145,163,344	A597S	probably benign	Het
Wdr47	T	A	3: 108,618,524	L121Q	probably damaging	Het
Wiz	A	G	17: 32,361,533	S315P	probably damaging	Het
Zc3h13	T	C	14: 75,331,157	S1297P	probably damaging	Het
Zfp27	AATCCGCTTGTGCA	AA	7: 29,895,021		probably benign	Het

Other mutations in Smg7

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01751:Smg7	APN	1	152844061	missense	possibly damaging	0.68
IGL02320:Smg7	APN	1	152868337	missense	possibly damaging	0.49
IGL02336:Smg7	APN	1	152843279	missense	probably benign
IGL02680:Smg7	APN	1	152845394	missense	probably benign	0.15
IGL03232:Smg7	APN	1	152840156	missense	probably damaging	1.00
chill	UTSW	1	152840136	splice site	probably null
R0322:Smg7	UTSW	1	152849873	critical splice donor site	probably null
R0540:Smg7	UTSW	1	152855962	missense	probably benign	0.00
R0685:Smg7	UTSW	1	152866648	missense	probably damaging	1.00
R0707:Smg7	UTSW	1	152870757	splice site	probably null
R1109:Smg7	UTSW	1	152845583	missense	probably damaging	1.00
R1118:Smg7	UTSW	1	152866575	splice site	probably benign
R1119:Smg7	UTSW	1	152866575	splice site	probably benign
R1458:Smg7	UTSW	1	152855843	splice site	probably null
R1759:Smg7	UTSW	1	152848846	missense	probably benign	0.20
R1846:Smg7	UTSW	1	152848850	missense	probably damaging	1.00
R2015:Smg7	UTSW	1	152860508	missense	probably damaging	1.00
R2155:Smg7	UTSW	1	152840313	missense	possibly damaging	0.49
R2199:Smg7	UTSW	1	152854328	missense	probably damaging	1.00
R2234:Smg7	UTSW	1	152868313	missense	probably damaging	1.00
R2235:Smg7	UTSW	1	152868313	missense	probably damaging	1.00
R3861:Smg7	UTSW	1	152852598	missense	probably null	1.00
R4597:Smg7	UTSW	1	152840301	critical splice donor site	probably null
R4672:Smg7	UTSW	1	152845413	missense	probably damaging	1.00
R4851:Smg7	UTSW	1	152844269	missense	probably benign	0.00
R5486:Smg7	UTSW	1	152846176	missense	probably damaging	0.97
R5607:Smg7	UTSW	1	152843234	missense	probably damaging	0.98
R6131:Smg7	UTSW	1	152845211	critical splice donor site	probably null
R6396:Smg7	UTSW	1	152848600	missense	probably benign	0.33
R6401:Smg7	UTSW	1	152840136	splice site	probably null
R6905:Smg7	UTSW	1	152850006	splice site	probably null
R6961:Smg7	UTSW	1	152841583	nonsense	probably null
R7124:Smg7	UTSW	1	152878080	missense	probably benign	0.01
R7146:Smg7	UTSW	1	152861825	missense	probably benign	0.34
R7573:Smg7	UTSW	1	152859489	missense	probably damaging	1.00
R7578:Smg7	UTSW	1	152845430	missense	probably damaging	1.00
R7621:Smg7	UTSW	1	152841544	missense	possibly damaging	0.95
R7956:Smg7	UTSW	1	152844202	missense	probably benign	0.02
R8167:Smg7	UTSW	1	152844372	missense	possibly damaging	0.90

Predicted Primers

PCR Primer
(F):5'- AATACAGCTTACCTGCACTGCC -3'
(R):5'- AGGCTGATTCAGTGTGAAAATG -3'

Sequencing Primer
(F):5'- AAGGTGCATCTCTTGGTCTCAGC -3'
(R):5'- CTGATTCAGTGTGAAAATGAGGTAG -3'

Posted On

2019-05-13