Mutagenetix > Incidental Mutation

Incidental Mutation 'R5490:Smg1'

432043

Institutional Source

Beutler Lab

Gene Symbol

Smg1

Ensembl Gene

ENSMUSG00000030655

Gene Name

SMG1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)

Synonyms

2610207I05Rik, 5430435M13Rik, C130002K18Rik

MMRRC Submission

043051-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5490 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

118131308-118243670 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 118139436 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 3530 (T3530I)

Ref Sequence

ENSEMBL: ENSMUSP00000032891 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032891]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000032891
AA Change: T3530I

PolyPhen 2 Score 0.861 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000032891
Gene: ENSMUSG00000030655
AA Change: T3530I

Domain	Start	End	E-Value	Type
low complexity region	42	55	N/A	INTRINSIC
SCOP:d1gw5a_	147	621	7e-7	SMART
Pfam:SMG1	629	1240	9.8e-249	PFAM
low complexity region	1540	1551	N/A	INTRINSIC
SCOP:d1gw5a_	1680	1942	8e-3	SMART
low complexity region	2125	2141	N/A	INTRINSIC
PI3Kc	2149	2493	7.93e-50	SMART
low complexity region	2759	2770	N/A	INTRINSIC
low complexity region	3425	3442	N/A	INTRINSIC
FATC	3626	3658	8.66e-12	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000178025

Predicted Effect

probably benign
Transcript: ENSMUST00000179331

SMART Domains

Protein: ENSMUSP00000137592
Gene: ENSMUSG00000030655

Domain	Start	End	E-Value	Type
low complexity region	18	31	N/A	INTRINSIC
SCOP:d1gw5a_	71	545	1e-6	SMART
low complexity region	602	612	N/A	INTRINSIC
low complexity region	631	646	N/A	INTRINSIC
low complexity region	698	718	N/A	INTRINSIC
low complexity region	898	915	N/A	INTRINSIC
low complexity region	1135	1147	N/A	INTRINSIC
low complexity region	1464	1475	N/A	INTRINSIC
low complexity region	2049	2065	N/A	INTRINSIC
PI3Kc	2073	2417	7.93e-50	SMART
low complexity region	2683	2694	N/A	INTRINSIC
low complexity region	3349	3366	N/A	INTRINSIC
FATC	3550	3582	8.66e-12	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207162

Coding Region Coverage

1x: 98.3%
3x: 97.3%
10x: 95.2%
20x: 90.8%

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 involved in nonsense-mediated mRNA decay (NMD) as part of the mRNA surveillance complex. The protein has kinase activity and is thought to function in NMD by phosphorylating the regulator of nonsense transcripts 1 protein. Alternatively spliced transcript variants have been described, but their full-length nature has yet to be determined. [provided by RefSeq, Mar 2013]
PHENOTYPE: Mice homozygous for a gene trap allele exhibit early embryonic lethality. Mice heteroygous for a gene trap allele exhibit abnormal tooth development, chronic inflammation, increased body weight, increased incidence of tumor formation and premature death. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810013L24Rik	T	A	16: 8,855,857	V216E	probably damaging	Het
2310035C23Rik	T	A	1: 105,719,501	V672D	probably damaging	Het
4933406M09Rik	A	G	1: 134,389,928	D146G	probably damaging	Het
Aatf	C	T	11: 84,510,273	G174D	probably damaging	Het
Abcc1	G	T	16: 14,410,917	G343C	probably damaging	Het
Asic2	T	C	11: 80,889,820	N370S	probably benign	Het
Btnl9	T	C	11: 49,169,568	E451G	probably damaging	Het
Cblb	A	G	16: 52,174,370	H658R	possibly damaging	Het
Cdca2	T	C	14: 67,680,284	E555G	possibly damaging	Het
Chfr	A	G	5: 110,153,129	S299G	possibly damaging	Het
Eea1	A	G	10: 96,026,054	E741G	probably benign	Het
Gapvd1	T	C	2: 34,693,433	D1057G	probably benign	Het
Glyat	C	T	19: 12,650,281	T80M	probably benign	Het
Gpr87	T	C	3: 59,179,326	S253G	probably damaging	Het
Hmgxb3	A	G	18: 61,162,977	S320P	probably damaging	Het
Kcnq5	C	T	1: 21,479,468	G345D	probably damaging	Het
Kif5c	T	C	2: 49,758,858	V938A	probably benign	Het
Klk14	G	A	7: 43,692,077	C51Y	probably damaging	Het
Madd	G	T	2: 91,170,635	T467K	possibly damaging	Het
Mamdc4	T	C	2: 25,565,878	D706G	probably damaging	Het
Map2	A	G	1: 66,413,133	H476R	probably damaging	Het
Mpeg1	T	C	19: 12,461,693	S172P	probably damaging	Het
Nkx2-3	A	T	19: 43,612,654	T52S	probably benign	Het
Nup210	C	T	6: 91,085,988	V230I	probably damaging	Het
Olfr1009	G	T	2: 85,722,322	A306S	probably benign	Het
Olfr348	T	A	2: 36,787,181	Y219N	probably damaging	Het
Olfr568	T	C	7: 102,877,893	S258P	probably damaging	Het
Pepd	A	G	7: 34,942,690		probably null	Het
Ppp1r36	T	A	12: 76,437,986	W238R	probably damaging	Het
Ppp1r36	G	T	12: 76,437,987	W238L	possibly damaging	Het
Prpf6	T	G	2: 181,608,165	D39E	probably benign	Het
Rassf5	T	A	1: 131,181,195	Q163L	possibly damaging	Het
Rbm43	T	A	2: 51,925,595	T205S	probably benign	Het
Robo4	CGG	CG	9: 37,411,490		probably null	Het
Sds	C	A	5: 120,483,650	Q286K	possibly damaging	Het
Slc35a3	A	T	3: 116,681,190	C184*	probably null	Het
Sspo	T	C	6: 48,493,280	V591A	probably benign	Het
Stam2	T	C	2: 52,720,917	D31G	probably damaging	Het
Star	A	G	8: 25,809,917	K96E	probably damaging	Het
Syne3	A	G	12: 104,955,672	L495P	probably damaging	Het
Tceanc2	A	T	4: 107,165,649	M47K	probably benign	Het
Tecpr2	T	C	12: 110,914,684	L85P	probably damaging	Het
Tmem241	C	T	18: 12,043,263	R116K	probably benign	Het
Yipf2	G	A	9: 21,592,191	A20V	probably benign	Het
Zc3h4	T	A	7: 16,429,005	D443E	unknown	Het
Zfp184	T	A	13: 21,958,577	V151D	probably benign	Het
Zhx1	T	C	15: 58,053,299	Y517C	probably damaging	Het

Other mutations in Smg1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00272:Smg1	APN	7	118198271	utr 3 prime	probably benign
IGL00481:Smg1	APN	7	118210794	missense	possibly damaging	0.67
IGL00503:Smg1	APN	7	118185483	utr 3 prime	probably benign
IGL00927:Smg1	APN	7	118140632	missense	probably damaging	1.00
IGL01333:Smg1	APN	7	118163378	splice site	probably benign
IGL01344:Smg1	APN	7	118190836	utr 3 prime	probably benign
IGL01397:Smg1	APN	7	118163221	utr 3 prime	probably benign
IGL01403:Smg1	APN	7	118158132	utr 3 prime	probably benign
IGL01573:Smg1	APN	7	118167962	utr 3 prime	probably benign
IGL01872:Smg1	APN	7	118148944	utr 3 prime	probably benign
IGL02010:Smg1	APN	7	118186146	utr 3 prime	probably benign
IGL02158:Smg1	APN	7	118212946	missense	possibly damaging	0.77
IGL02268:Smg1	APN	7	118182541	missense	probably benign	0.19
IGL02314:Smg1	APN	7	118154709	utr 3 prime	probably benign
IGL02552:Smg1	APN	7	118195894	utr 3 prime	probably benign
IGL02577:Smg1	APN	7	118203122	missense	probably damaging	0.99
IGL02859:Smg1	APN	7	118148933	utr 3 prime	probably benign
IGL02890:Smg1	APN	7	118185501	utr 3 prime	probably benign
IGL02892:Smg1	APN	7	118167955	utr 3 prime	probably benign
IGL03119:Smg1	APN	7	118195113	utr 3 prime	probably benign
IGL03123:Smg1	APN	7	118157181	utr 3 prime	probably benign
IGL03128:Smg1	APN	7	118203059	missense	probably benign	0.03
IGL03184:Smg1	APN	7	118180380	missense	possibly damaging	0.86
PIT4508001:Smg1	UTSW	7	118185541	missense	unknown
R0010:Smg1	UTSW	7	118171859	utr 3 prime	probably benign
R0010:Smg1	UTSW	7	118171859	utr 3 prime	probably benign
R0025:Smg1	UTSW	7	118212443	missense	possibly damaging	0.92
R0025:Smg1	UTSW	7	118212443	missense	possibly damaging	0.92
R0098:Smg1	UTSW	7	118145467	missense	probably benign	0.02
R0139:Smg1	UTSW	7	118152675	critical splice donor site	probably null
R0371:Smg1	UTSW	7	118168300	utr 3 prime	probably benign
R0415:Smg1	UTSW	7	118182468	missense	probably benign	0.34
R0416:Smg1	UTSW	7	118184461	splice site	probably benign
R0423:Smg1	UTSW	7	118176880	missense	possibly damaging	0.53
R0600:Smg1	UTSW	7	118160383	utr 3 prime	probably benign
R0626:Smg1	UTSW	7	118182383	missense	possibly damaging	0.82
R0627:Smg1	UTSW	7	118167861	utr 3 prime	probably benign
R0727:Smg1	UTSW	7	118166422	utr 3 prime	probably benign
R0729:Smg1	UTSW	7	118146289	utr 3 prime	probably benign
R0841:Smg1	UTSW	7	118143301	missense	possibly damaging	0.96
R1114:Smg1	UTSW	7	118159790	utr 3 prime	probably benign
R1256:Smg1	UTSW	7	118203087	missense	probably damaging	1.00
R1298:Smg1	UTSW	7	118168211	utr 3 prime	probably benign
R1370:Smg1	UTSW	7	118159752	utr 3 prime	probably benign
R1591:Smg1	UTSW	7	118156919	utr 3 prime	probably benign
R1736:Smg1	UTSW	7	118165967	splice site	probably null
R1755:Smg1	UTSW	7	118203064	nonsense	probably null
R1765:Smg1	UTSW	7	118139715	missense	probably benign	0.03
R1789:Smg1	UTSW	7	118145798	missense	possibly damaging	0.73
R1845:Smg1	UTSW	7	118154622	utr 3 prime	probably benign
R1908:Smg1	UTSW	7	118154199	utr 3 prime	probably benign
R1909:Smg1	UTSW	7	118154199	utr 3 prime	probably benign
R1942:Smg1	UTSW	7	118158103	utr 3 prime	probably benign
R2064:Smg1	UTSW	7	118156867	utr 3 prime	probably benign
R2072:Smg1	UTSW	7	118163166	utr 3 prime	probably benign
R2154:Smg1	UTSW	7	118158076	utr 3 prime	probably benign
R2895:Smg1	UTSW	7	118189143	utr 3 prime	probably benign
R2915:Smg1	UTSW	7	118210879	splice site	probably benign
R3416:Smg1	UTSW	7	118148853	utr 3 prime	probably benign
R3417:Smg1	UTSW	7	118148853	utr 3 prime	probably benign
R3873:Smg1	UTSW	7	118154662	utr 3 prime	probably benign
R4082:Smg1	UTSW	7	118160246	utr 3 prime	probably benign
R4230:Smg1	UTSW	7	118148733	critical splice donor site	probably null
R4304:Smg1	UTSW	7	118139518	missense	probably benign	0.03
R4549:Smg1	UTSW	7	118159683	utr 3 prime	probably benign
R4571:Smg1	UTSW	7	118139465	missense	possibly damaging	0.72
R4638:Smg1	UTSW	7	118195926	utr 3 prime	probably benign
R4642:Smg1	UTSW	7	118154264	utr 3 prime	probably benign
R4656:Smg1	UTSW	7	118212951	missense	probably benign	0.00
R4754:Smg1	UTSW	7	118156731	utr 3 prime	probably benign
R4798:Smg1	UTSW	7	118180474	missense	probably benign	0.32
R4906:Smg1	UTSW	7	118152408	utr 3 prime	probably benign
R4978:Smg1	UTSW	7	118154247	utr 3 prime	probably benign
R4989:Smg1	UTSW	7	118158100	utr 3 prime	probably benign
R4989:Smg1	UTSW	7	118208051	missense	probably benign
R5026:Smg1	UTSW	7	118193545	utr 3 prime	probably benign
R5124:Smg1	UTSW	7	118213012	missense	probably benign	0.00
R5318:Smg1	UTSW	7	118160204	utr 3 prime	probably benign
R5356:Smg1	UTSW	7	118195133	utr 3 prime	probably benign
R5404:Smg1	UTSW	7	118206908	missense	probably damaging	1.00
R5423:Smg1	UTSW	7	118146071	missense	possibly damaging	0.70
R5441:Smg1	UTSW	7	118195081	utr 3 prime	probably benign
R5541:Smg1	UTSW	7	118157163	utr 3 prime	probably benign
R5564:Smg1	UTSW	7	118189819	utr 3 prime	probably benign
R5580:Smg1	UTSW	7	118148902	utr 3 prime	probably benign
R5600:Smg1	UTSW	7	118167884	utr 3 prime	probably benign
R5628:Smg1	UTSW	7	118154701	utr 3 prime	probably benign
R5646:Smg1	UTSW	7	118212559	missense	probably benign	0.42
R5656:Smg1	UTSW	7	118154664	utr 3 prime	probably benign
R5660:Smg1	UTSW	7	118143347	missense	probably benign	0.33
R5706:Smg1	UTSW	7	118145590	missense	possibly damaging	0.86
R5786:Smg1	UTSW	7	118212897	missense	probably benign	0.12
R5890:Smg1	UTSW	7	118190586	utr 3 prime	probably benign
R5912:Smg1	UTSW	7	118154586	utr 3 prime	probably benign
R5977:Smg1	UTSW	7	118141357	utr 3 prime	probably benign
R5993:Smg1	UTSW	7	118140509	missense	probably benign	0.33
R6161:Smg1	UTSW	7	118163330	utr 3 prime	probably benign
R6187:Smg1	UTSW	7	118189163	utr 3 prime	probably benign
R6264:Smg1	UTSW	7	118166087	utr 3 prime	probably benign
R6331:Smg1	UTSW	7	118154277	utr 3 prime	probably benign
R6561:Smg1	UTSW	7	118166077	utr 3 prime	probably benign
R6571:Smg1	UTSW	7	118184514	utr 3 prime	probably benign
R6736:Smg1	UTSW	7	118157166	utr 3 prime	probably benign
R6752:Smg1	UTSW	7	118163316	utr 3 prime	probably benign
R6777:Smg1	UTSW	7	118189117	utr 3 prime	probably benign
R6788:Smg1	UTSW	7	118184571	utr 3 prime	probably benign
R6883:Smg1	UTSW	7	118168180	utr 3 prime	probably benign
R6991:Smg1	UTSW	7	118167868	utr 3 prime	probably benign
R7056:Smg1	UTSW	7	118146400	splice site	probably benign
R7058:Smg1	UTSW	7	118198279	utr 3 prime	probably benign
R7100:Smg1	UTSW	7	118184520	missense	unknown
R7133:Smg1	UTSW	7	118152908	missense	unknown
R7221:Smg1	UTSW	7	118182797	missense	possibly damaging	0.86
R7229:Smg1	UTSW	7	118176955	missense	probably benign	0.03
R7293:Smg1	UTSW	7	118166099	missense	unknown
R7361:Smg1	UTSW	7	118184977	missense	unknown
R7438:Smg1	UTSW	7	118195893	missense	unknown
R7686:Smg1	UTSW	7	118167858	missense	unknown
R7798:Smg1	UTSW	7	118171939	missense	possibly damaging	0.73
R7908:Smg1	UTSW	7	118186134	missense	unknown
R7923:Smg1	UTSW	7	118143322	missense	possibly damaging	0.96
R7978:Smg1	UTSW	7	118193655	missense	unknown
R7997:Smg1	UTSW	7	118173141	missense	unknown
R7997:Smg1	UTSW	7	118173142	missense	unknown
R8025:Smg1	UTSW	7	118206989	nonsense	probably null
R8056:Smg1	UTSW	7	118160366	missense	unknown
R8061:Smg1	UTSW	7	118152387	missense	unknown
R8095:Smg1	UTSW	7	118173062	missense	unknown
R8198:Smg1	UTSW	7	118145606	missense	probably benign	0.03
R8399:Smg1	UTSW	7	118190571	missense	unknown
R8445:Smg1	UTSW	7	118136977	missense	possibly damaging	0.72
R8519:Smg1	UTSW	7	118171759	utr 3 prime	probably benign
R8817:Smg1	UTSW	7	118159664	missense	unknown
R8832:Smg1	UTSW	7	118139783	missense	probably benign	0.33
R8855:Smg1	UTSW	7	118206899	missense	unknown
R8866:Smg1	UTSW	7	118206899	missense	unknown
R8946:Smg1	UTSW	7	118152677	missense	probably null
R8954:Smg1	UTSW	7	118206992	missense	probably damaging	1.00
R8967:Smg1	UTSW	7	118166516	missense	unknown
R9072:Smg1	UTSW	7	118183809	missense	unknown
R9090:Smg1	UTSW	7	118212563	missense	unknown
R9156:Smg1	UTSW	7	118154661	missense	unknown
R9198:Smg1	UTSW	7	118195956	missense	unknown
R9240:Smg1	UTSW	7	118139808	missense	probably benign	0.18
R9271:Smg1	UTSW	7	118212563	missense	unknown
R9289:Smg1	UTSW	7	118145416	missense	possibly damaging	0.53
R9378:Smg1	UTSW	7	118178775	nonsense	probably null
R9396:Smg1	UTSW	7	118208080	missense	unknown
R9469:Smg1	UTSW	7	118140551	missense	possibly damaging	0.72
R9539:Smg1	UTSW	7	118145753	missense	probably benign	0.03
R9549:Smg1	UTSW	7	118196031	missense	unknown
R9563:Smg1	UTSW	7	118212985	missense	unknown
R9564:Smg1	UTSW	7	118212985	missense	unknown
R9597:Smg1	UTSW	7	118213047	missense	unknown
R9643:Smg1	UTSW	7	118156710	missense	unknown
R9703:Smg1	UTSW	7	118140521	missense	possibly damaging	0.73
R9730:Smg1	UTSW	7	118183781	missense	unknown
Z1088:Smg1	UTSW	7	118154635	utr 3 prime	probably benign
Z1088:Smg1	UTSW	7	118168661	nonsense	probably null
Z1088:Smg1	UTSW	7	118178399	missense	possibly damaging	0.96
Z1176:Smg1	UTSW	7	118206887	missense	unknown
Z1176:Smg1	UTSW	7	118206907	missense	unknown
Z1177:Smg1	UTSW	7	118168608	missense	probably null
Z1177:Smg1	UTSW	7	118213033	missense	unknown

Predicted Primers

PCR Primer
(F):5'- CAAAGTAGGCATCAGATCCTTAGG -3'
(R):5'- AGCCTGAGAAGTGTAGCTCC -3'

Sequencing Primer
(F):5'- ATCCTTAGGAGCTAAAGTTATGGG -3'
(R):5'- AGTGTAGCTCCTGTCATTTTTATTTC -3'

Posted On

2016-10-05