Mutagenetix > Incidental Mutation

Incidental Mutation 'R0511:Smg6'

46939

Institutional Source

Beutler Lab

Gene Symbol

Smg6

Ensembl Gene

ENSMUSG00000038290

Gene Name

SMG6 nonsense mediated mRNA decay factor

Synonyms

Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)

MMRRC Submission

038705-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0511 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

74816665-75055274 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 74819884 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Asparagine at position 52 (Y52N)

Ref Sequence

ENSEMBL: ENSMUSP00000043555 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000045281] [ENSMUST00000065211] [ENSMUST00000108447] [ENSMUST00000108448] [ENSMUST00000121738] [ENSMUST00000123855] [ENSMUST00000128556] [ENSMUST00000138612]

AlphaFold

P61406

Predicted Effect

probably damaging
Transcript: ENSMUST00000045281
AA Change: Y52N

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

SMART Domains

Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290
AA Change: Y52N

Domain	Start	End	E-Value	Type
internal_repeat_1	42	99	7.68e-6	PROSPERO
internal_repeat_1	135	188	7.68e-6	PROSPERO
low complexity region	212	227	N/A	INTRINSIC
low complexity region	257	271	N/A	INTRINSIC
low complexity region	376	390	N/A	INTRINSIC
low complexity region	417	426	N/A	INTRINSIC
low complexity region	436	453	N/A	INTRINSIC
low complexity region	538	549	N/A	INTRINSIC
coiled coil region	574	600	N/A	INTRINSIC
Pfam:EST1	637	742	1.8e-18	PFAM
Pfam:EST1_DNA_bind	750	1106	1.6e-78	PFAM
coiled coil region	1197	1234	N/A	INTRINSIC
PINc	1245	1396	2.85e-25	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000065211

SMART Domains

Protein: ENSMUSP00000067552
Gene: ENSMUSG00000001323

Domain	Start	End	E-Value	Type
Pfam:PALP	19	314	3.3e-75	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108447

SMART Domains

Protein: ENSMUSP00000104086
Gene: ENSMUSG00000001323

Domain	Start	End	E-Value	Type
Pfam:PALP	19	179	1.8e-41	PFAM
Pfam:PALP	173	289	4.2e-19	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108448

SMART Domains

Protein: ENSMUSP00000104087
Gene: ENSMUSG00000001323

Domain	Start	End	E-Value	Type
Pfam:PALP	19	314	2.1e-75	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000121738

SMART Domains

Protein: ENSMUSP00000113372
Gene: ENSMUSG00000001323

Domain	Start	End	E-Value	Type
Pfam:PALP	19	314	3.3e-75	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000123855

SMART Domains

Protein: ENSMUSP00000118485
Gene: ENSMUSG00000001323

Domain	Start	End	E-Value	Type
Pfam:PALP	19	166	1.5e-39	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127499

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000135587

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147817

Predicted Effect

probably benign
Transcript: ENSMUST00000130145

SMART Domains

Protein: ENSMUSP00000120229
Gene: ENSMUSG00000038290

Domain	Start	End	E-Value	Type
coiled coil region	35	61	N/A	INTRINSIC
Pfam:EST1	99	204	1.3e-19	PFAM
Pfam:EST1_DNA_bind	212	339	7.3e-37	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000128556

SMART Domains

Protein: ENSMUSP00000120012
Gene: ENSMUSG00000001323

Domain	Start	End	E-Value	Type
Pfam:PALP	19	182	2.6e-44	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000138612

SMART Domains

Protein: ENSMUSP00000119256
Gene: ENSMUSG00000001323

Domain	Start	End	E-Value	Type
Pfam:PALP	19	112	4.1e-28	PFAM

Meta Mutation Damage Score

0.4128

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.8%

Validation Efficiency

100% (116/116)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a component of the telomerase ribonucleoprotein complex responsible for the replication and maintenance of chromosome ends. The encoded protein also plays a role in the nonsense-mediated mRNA decay (NMD) pathway, providing the endonuclease activity near the premature translation termination codon that is needed to initiate NMD. Alternatively spliced transcript variants encoding distinct protein isoforms have been described. [provided by RefSeq, Feb 2014]
PHENOTYPE: Homozygosity for insertion of a transgene into intron 6 of the gene results in embryonic lethality. Mice homozygous for a knock-out allele exhibit prenatal lethality. Mice homozygous for a conditional allele activated in embryonic stem cells exhibit defective telomere maintenance and NMD. [provided by MGI curators]

Allele List at MGI

All alleles(52) : Gene trapped(52)

Other mutations in this stock

Total: 118 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl2fm1	A	G	3: 59,843,771 (GRCm39)	H155R	possibly damaging	Het
Abca13	G	T	11: 9,244,559 (GRCm39)	V2141L	probably benign	Het
Adam17	T	C	12: 21,390,459 (GRCm39)		probably benign	Het
Adam3	A	T	8: 25,185,331 (GRCm39)	C456S	probably damaging	Het
Aldh4a1	G	T	4: 139,369,882 (GRCm39)		probably benign	Het
Anapc4	A	G	5: 52,999,359 (GRCm39)		probably benign	Het
Ank3	A	T	10: 69,718,198 (GRCm39)	Q483L	probably damaging	Het
Ankle2	A	G	5: 110,389,925 (GRCm39)		probably benign	Het
Ankrd13b	T	A	11: 77,364,114 (GRCm39)	T150S	possibly damaging	Het
Apeh	A	G	9: 107,964,254 (GRCm39)	M524T	probably benign	Het
Arl14epl	T	A	18: 47,059,484 (GRCm39)		probably null	Het
Atg2a	T	C	19: 6,302,569 (GRCm39)	F964S	possibly damaging	Het
Atg2b	C	T	12: 105,583,412 (GRCm39)	V2050M	probably damaging	Het
Atp2b4	A	T	1: 133,659,956 (GRCm39)		probably benign	Het
Bbof1	T	A	12: 84,477,045 (GRCm39)	S512T	probably benign	Het
Camta1	C	A	4: 151,159,597 (GRCm39)	R1614L	probably damaging	Het
Car10	T	C	11: 93,381,408 (GRCm39)	Y100H	probably damaging	Het
Ccdc81	T	A	7: 89,542,504 (GRCm39)	E124V	probably damaging	Het
Cd84	A	G	1: 171,700,494 (GRCm39)	T204A	probably benign	Het
Celf2	A	G	2: 6,608,987 (GRCm39)	S178P	probably damaging	Het
Chat	G	A	14: 32,130,976 (GRCm39)	T555M	probably damaging	Het
Chd6	A	G	2: 160,834,111 (GRCm39)	F917S	probably damaging	Het
Chrna2	C	A	14: 66,386,553 (GRCm39)	T233N	probably damaging	Het
Cnpy2	T	C	10: 128,162,054 (GRCm39)	V109A	probably benign	Het
Col4a1	T	C	8: 11,258,333 (GRCm39)		probably null	Het
Csmd1	C	T	8: 15,982,529 (GRCm39)	V2713M	possibly damaging	Het
Cuedc1	G	A	11: 88,074,231 (GRCm39)	R255Q	probably damaging	Het
Cxcl15	A	T	5: 90,945,897 (GRCm39)		probably benign	Het
Dach1	A	T	14: 98,138,765 (GRCm39)	H559Q	possibly damaging	Het
Dele1	T	C	18: 38,387,124 (GRCm39)		probably null	Het
Dennd4c	C	T	4: 86,744,259 (GRCm39)	T1367M	probably damaging	Het
Depdc5	T	A	5: 33,102,372 (GRCm39)	Y365*	probably null	Het
Dicer1	T	C	12: 104,669,100 (GRCm39)	Y1194C	possibly damaging	Het
Dmxl1	C	G	18: 50,024,534 (GRCm39)	S1736*	probably null	Het
Dnah7a	C	T	1: 53,536,285 (GRCm39)	R2586K	probably benign	Het
Dnajb8	T	C	6: 88,199,467 (GRCm39)	M1T	probably null	Het
Dync2h1	G	A	9: 7,122,692 (GRCm39)	P2088L	probably benign	Het
Eftud2	T	G	11: 102,735,048 (GRCm39)	H617P	probably damaging	Het
Ephb1	A	G	9: 101,873,179 (GRCm39)		probably benign	Het
Fam184a	G	T	10: 53,574,975 (GRCm39)	H155Q	probably benign	Het
Firrm	T	C	1: 163,799,412 (GRCm39)		probably null	Het
Ganc	G	T	2: 120,278,882 (GRCm39)	E700*	probably null	Het
Gm10912	A	G	2: 103,897,290 (GRCm39)		probably benign	Het
Haus5	A	T	7: 30,358,492 (GRCm39)	I294N	probably damaging	Het
Hmgcr	G	T	13: 96,796,651 (GRCm39)		probably null	Het
Hr	T	A	14: 70,799,352 (GRCm39)	C641*	probably null	Het
Itga10	A	G	3: 96,565,490 (GRCm39)	N1038S	probably damaging	Het
Itgb1bp1	T	G	12: 21,321,436 (GRCm39)	Y172S	probably damaging	Het
Kprp	T	C	3: 92,732,030 (GRCm39)	N340S	probably damaging	Het
Kremen1	A	G	11: 5,165,447 (GRCm39)	I41T	probably damaging	Het
Krt6b	A	G	15: 101,586,042 (GRCm39)		probably benign	Het
Krt81	C	A	15: 101,361,508 (GRCm39)	R24L	possibly damaging	Het
Ldhd	A	G	8: 112,356,309 (GRCm39)	Y86H	probably benign	Het
Lilra6	A	T	7: 3,915,784 (GRCm39)	I76N	possibly damaging	Het
Mak	T	C	13: 41,199,743 (GRCm39)	T299A	probably benign	Het
Med25	A	G	7: 44,534,502 (GRCm39)		probably null	Het
Mpg	A	T	11: 32,180,039 (GRCm39)	N189I	probably damaging	Het
Mroh8	A	G	2: 157,071,838 (GRCm39)	Y556H	probably damaging	Het
Myh8	T	A	11: 67,175,333 (GRCm39)	S294T	probably benign	Het
Myom1	T	A	17: 71,391,312 (GRCm39)	D842E	probably benign	Het
Myorg	A	G	4: 41,498,538 (GRCm39)	F364S	probably damaging	Het
Nat2	C	T	8: 67,953,982 (GRCm39)	Q31*	probably null	Het
Nf1	T	A	11: 79,329,595 (GRCm39)	M653K	probably benign	Het
Nhs	C	A	X: 160,620,355 (GRCm39)	R1467I	probably damaging	Het
Npr2	A	G	4: 43,632,801 (GRCm39)	E206G	probably benign	Het
Nsd3	G	A	8: 26,168,732 (GRCm39)	G629D	possibly damaging	Het
Nwd1	G	A	8: 73,408,633 (GRCm39)	C831Y	probably damaging	Het
Or52r1c	T	C	7: 102,735,058 (GRCm39)	I111T	probably damaging	Het
Or5t9	A	G	2: 86,659,950 (GRCm39)	I285V	probably benign	Het
P2ry14	A	G	3: 59,023,449 (GRCm39)	S4P	possibly damaging	Het
Parp4	A	G	14: 56,873,172 (GRCm39)		probably benign	Het
Pate14	A	T	9: 36,549,873 (GRCm39)		probably null	Het
Pclo	A	G	5: 14,728,299 (GRCm39)		probably benign	Het
Pclo	T	C	5: 14,729,412 (GRCm39)		probably benign	Het
Pcnt	A	T	10: 76,240,429 (GRCm39)	S1202T	possibly damaging	Het
Pfkfb4	A	G	9: 108,856,825 (GRCm39)	Y412C	probably damaging	Het
Pgm2	T	A	5: 64,267,898 (GRCm39)	V449D	probably damaging	Het
Poldip3	T	A	15: 83,022,436 (GRCm39)	D116V	probably damaging	Het
Pom121	G	T	5: 135,410,686 (GRCm39)	Q824K	unknown	Het
Prkdc	G	T	16: 15,649,146 (GRCm39)	G3707*	probably null	Het
Prr14l	T	C	5: 33,001,560 (GRCm39)		probably benign	Het
Ptbp2	T	G	3: 119,514,613 (GRCm39)	I405L	probably benign	Het
Rad21l	A	T	2: 151,490,989 (GRCm39)		probably benign	Het
Rbm6	G	A	9: 107,724,488 (GRCm39)	Q488*	probably null	Het
Rdh1	T	A	10: 127,600,652 (GRCm39)	M225K	probably benign	Het
Recql5	T	C	11: 115,819,209 (GRCm39)	D119G	probably benign	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Robo1	T	C	16: 72,810,013 (GRCm39)		probably null	Het
Samd12	G	A	15: 53,723,567 (GRCm39)	T42I	probably benign	Het
Scn10a	A	T	9: 119,442,766 (GRCm39)	M1494K	probably damaging	Het
Sec31a	G	A	5: 100,523,099 (GRCm39)	P864L	probably benign	Het
Senp2	T	C	16: 21,855,320 (GRCm39)	V344A	probably benign	Het
Serpina5	G	A	12: 104,069,621 (GRCm39)	D278N	probably benign	Het
Sh3tc1	A	T	5: 35,860,806 (GRCm39)	V1017D	probably damaging	Het
Sin3a	T	A	9: 57,004,179 (GRCm39)	Y310*	probably null	Het
Slc25a32	T	C	15: 38,960,940 (GRCm39)	T248A	probably benign	Het
Slc35e1	T	C	8: 73,246,415 (GRCm39)		probably benign	Het
Slc4a10	G	A	2: 62,117,206 (GRCm39)	V722M	probably damaging	Het
Slco1a4	A	G	6: 141,776,586 (GRCm39)		probably benign	Het
Sncb	T	G	13: 54,913,400 (GRCm39)	T33P	probably damaging	Het
Spef2	A	G	15: 9,584,070 (GRCm39)		probably null	Het
Spmip1	G	T	6: 29,478,169 (GRCm39)		probably benign	Het
Sugp1	A	G	8: 70,512,013 (GRCm39)	E203G	probably damaging	Het
Suv39h2	A	T	2: 3,473,616 (GRCm39)	C105S	probably damaging	Het
Tlr1	A	T	5: 65,083,963 (GRCm39)	F205I	probably damaging	Het
Tnip1	A	T	11: 54,808,699 (GRCm39)	M496K	probably damaging	Het
Tnxb	G	A	17: 34,937,219 (GRCm39)	E2889K	probably damaging	Het
Trim30b	T	A	7: 104,015,010 (GRCm39)	H126L	possibly damaging	Het
Trpm7	A	T	2: 126,668,638 (GRCm39)	Y759*	probably null	Het
Ttc17	A	G	2: 94,153,465 (GRCm39)	I1000T	possibly damaging	Het
Ttc27	A	T	17: 75,025,710 (GRCm39)	N61I	probably benign	Het
Uba6	T	C	5: 86,260,609 (GRCm39)	Y990C	probably damaging	Het
Vav3	A	G	3: 109,571,756 (GRCm39)		probably benign	Het
Vmn2r55	C	T	7: 12,404,945 (GRCm39)	A153T	possibly damaging	Het
Wars2	A	G	3: 99,123,865 (GRCm39)	D242G	probably damaging	Het
Xylt2	G	A	11: 94,560,762 (GRCm39)	Q259*	probably null	Het
Zfp27	G	A	7: 29,593,947 (GRCm39)	P673S	probably damaging	Het
Zgrf1	T	C	3: 127,378,309 (GRCm39)	I1023T	possibly damaging	Het

Other mutations in Smg6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00952:Smg6	APN	11	74,819,974 (GRCm39)	missense	probably benign
IGL01146:Smg6	APN	11	74,821,254 (GRCm39)	nonsense	probably null
IGL01505:Smg6	APN	11	75,047,117 (GRCm39)	missense	probably damaging	1.00
IGL01541:Smg6	APN	11	74,816,770 (GRCm39)	missense	probably benign	0.43
IGL01636:Smg6	APN	11	74,825,929 (GRCm39)	critical splice donor site	probably null
IGL02379:Smg6	APN	11	74,944,751 (GRCm39)	missense	probably damaging	1.00
IGL02794:Smg6	APN	11	74,944,760 (GRCm39)	missense	probably damaging	0.99
IGL02964:Smg6	APN	11	74,821,576 (GRCm39)	critical splice donor site	probably null
IGL03057:Smg6	APN	11	74,826,260 (GRCm39)	nonsense	probably null
1mM(1):Smg6	UTSW	11	74,825,815 (GRCm39)	splice site	probably benign
IGL03097:Smg6	UTSW	11	74,823,252 (GRCm39)	missense	probably damaging	1.00
PIT4802001:Smg6	UTSW	11	75,046,991 (GRCm39)	missense	probably damaging	0.96
R0269:Smg6	UTSW	11	75,053,757 (GRCm39)	missense	probably benign
R0344:Smg6	UTSW	11	74,820,647 (GRCm39)	missense	probably damaging	1.00
R0437:Smg6	UTSW	11	74,820,527 (GRCm39)	missense	probably damaging	1.00
R0452:Smg6	UTSW	11	74,821,039 (GRCm39)	missense	probably benign
R0617:Smg6	UTSW	11	75,053,757 (GRCm39)	missense	probably benign
R0737:Smg6	UTSW	11	75,050,662 (GRCm39)	missense	probably damaging	1.00
R1715:Smg6	UTSW	11	74,820,256 (GRCm39)	missense	probably benign
R1780:Smg6	UTSW	11	74,836,942 (GRCm39)	missense	probably damaging	1.00
R1927:Smg6	UTSW	11	75,033,674 (GRCm39)	missense	probably damaging	1.00
R2073:Smg6	UTSW	11	74,821,120 (GRCm39)	missense	probably damaging	1.00
R2171:Smg6	UTSW	11	74,929,472 (GRCm39)	missense	probably damaging	1.00
R2513:Smg6	UTSW	11	74,820,502 (GRCm39)	missense	probably damaging	1.00
R3943:Smg6	UTSW	11	74,820,367 (GRCm39)	missense	probably damaging	1.00
R3944:Smg6	UTSW	11	74,820,367 (GRCm39)	missense	probably damaging	1.00
R4275:Smg6	UTSW	11	74,884,700 (GRCm39)	intron	probably benign
R4369:Smg6	UTSW	11	74,823,269 (GRCm39)	nonsense	probably null
R4452:Smg6	UTSW	11	74,880,967 (GRCm39)	missense	probably benign	0.14
R4864:Smg6	UTSW	11	74,820,988 (GRCm39)	missense	possibly damaging	0.89
R4885:Smg6	UTSW	11	74,932,744 (GRCm39)	missense	probably damaging	1.00
R5043:Smg6	UTSW	11	74,820,721 (GRCm39)	missense	possibly damaging	0.86
R5189:Smg6	UTSW	11	74,932,822 (GRCm39)	missense	probably damaging	1.00
R5378:Smg6	UTSW	11	74,932,820 (GRCm39)	missense	possibly damaging	0.61
R5518:Smg6	UTSW	11	74,944,724 (GRCm39)	missense	probably damaging	0.99
R5725:Smg6	UTSW	11	74,821,439 (GRCm39)	missense	probably benign	0.45
R5746:Smg6	UTSW	11	75,030,113 (GRCm39)	missense	probably damaging	1.00
R6151:Smg6	UTSW	11	75,047,033 (GRCm39)	missense	probably damaging	0.96
R6319:Smg6	UTSW	11	75,047,048 (GRCm39)	missense	probably damaging	1.00
R6349:Smg6	UTSW	11	74,944,600 (GRCm39)	missense	possibly damaging	0.94
R6500:Smg6	UTSW	11	74,821,331 (GRCm39)	missense	possibly damaging	0.74
R6619:Smg6	UTSW	11	74,823,279 (GRCm39)	critical splice donor site	probably null
R6820:Smg6	UTSW	11	74,932,790 (GRCm39)	missense	probably damaging	0.99
R6923:Smg6	UTSW	11	74,820,169 (GRCm39)	missense	possibly damaging	0.50
R7361:Smg6	UTSW	11	74,820,979 (GRCm39)	missense	probably benign	0.00
R7494:Smg6	UTSW	11	74,820,449 (GRCm39)	missense	probably benign
R7498:Smg6	UTSW	11	74,819,932 (GRCm39)	missense	probably benign	0.01
R7681:Smg6	UTSW	11	74,822,531 (GRCm39)	missense	probably damaging	1.00
R7710:Smg6	UTSW	11	74,821,445 (GRCm39)	missense	probably benign	0.26
R7770:Smg6	UTSW	11	74,884,687 (GRCm39)	missense	unknown
R8159:Smg6	UTSW	11	74,929,465 (GRCm39)	missense	probably damaging	1.00
R8381:Smg6	UTSW	11	74,822,566 (GRCm39)	missense	probably damaging	1.00
R8463:Smg6	UTSW	11	74,820,886 (GRCm39)	missense	probably benign	0.14
R8509:Smg6	UTSW	11	74,932,702 (GRCm39)	missense	probably benign	0.04
R8557:Smg6	UTSW	11	75,047,064 (GRCm39)	missense	probably damaging	0.98
R8743:Smg6	UTSW	11	74,820,859 (GRCm39)	missense	probably benign
R9240:Smg6	UTSW	11	74,825,884 (GRCm39)	missense	probably damaging	1.00
R9312:Smg6	UTSW	11	74,820,877 (GRCm39)	missense	probably benign	0.27
X0018:Smg6	UTSW	11	74,820,812 (GRCm39)	missense	possibly damaging	0.76
Z1186:Smg6	UTSW	11	75,047,092 (GRCm39)	missense	probably benign	0.06
Z1187:Smg6	UTSW	11	75,047,092 (GRCm39)	missense	probably benign	0.06
Z1188:Smg6	UTSW	11	75,047,092 (GRCm39)	missense	probably benign	0.06
Z1189:Smg6	UTSW	11	75,047,092 (GRCm39)	missense	probably benign	0.06
Z1190:Smg6	UTSW	11	75,047,092 (GRCm39)	missense	probably benign	0.06
Z1191:Smg6	UTSW	11	75,047,092 (GRCm39)	missense	probably benign	0.06
Z1192:Smg6	UTSW	11	75,047,092 (GRCm39)	missense	probably benign	0.06

Predicted Primers

PCR Primer
(F):5'- TGCCTTTGTAGAAACGTTCTTTCCTGA -3'
(R):5'- CCTGCCTGCTGACTCTTTGGTAATG -3'

Sequencing Primer
(F):5'- GTAGAAACGTTCTTTCCTGATCACC -3'
(R):5'- GAAAAGTTTCCTGTGCCTGAC -3'

Posted On

2013-06-11