Mutagenetix > Incidental Mutation

Incidental Mutation 'R5746:Smg6'

445793

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

043199-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5746 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

74816665-75055274 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 75030113 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Glutamic Acid at position 211 (G211E)

Ref Sequence

ENSEMBL: ENSMUSP00000120060 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000045281] [ENSMUST00000140197]

AlphaFold

P61406

Predicted Effect

probably damaging
Transcript: ENSMUST00000045281
AA Change: G1150E

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

SMART Domains

Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290
AA Change: G1150E

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: 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 damaging
Transcript: ENSMUST00000140197
AA Change: G211E

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

SMART Domains

Protein: ENSMUSP00000120060
Gene: ENSMUSG00000038290
AA Change: G211E

Domain	Start	End	E-Value	Type
Pfam:EST1_DNA_bind	2	167	4.9e-25	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142038

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.6%

Validation Efficiency

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: 28 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adora3	A	G	3: 105,815,126 (GRCm39)	E292G	possibly damaging	Het
Ank1	C	T	8: 23,606,612 (GRCm39)	T1187I	probably damaging	Het
Ankrd16	T	A	2: 11,789,178 (GRCm39)	I255K	probably damaging	Het
Atp6ap1l	T	C	13: 91,031,698 (GRCm39)	N328S	probably benign	Het
Cbln3	A	G	14: 56,120,601 (GRCm39)	S144P	probably damaging	Het
Cdh12	T	A	15: 21,358,810 (GRCm39)	L78Q	probably null	Het
Cpsf1	C	T	15: 76,484,037 (GRCm39)	R761H	probably benign	Het
Cyp2d10	T	G	15: 82,289,472 (GRCm39)	E213D	probably benign	Het
Gba2	T	C	4: 43,568,465 (GRCm39)		probably null	Het
Glb1l2	G	A	9: 26,708,086 (GRCm39)	A29V	probably benign	Het
Gm11149	C	T	9: 49,457,494 (GRCm39)	G393S	probably damaging	Het
Igkv6-29	C	A	6: 70,115,584 (GRCm39)	G70V	possibly damaging	Het
Kcnma1	T	C	14: 23,544,635 (GRCm39)	N574S	probably damaging	Het
Kdm2b	A	G	5: 123,017,427 (GRCm39)	V1099A	probably damaging	Het
Kel	C	T	6: 41,675,961 (GRCm39)	G243E	probably damaging	Het
Ly6g	A	T	15: 75,028,596 (GRCm39)	N19Y	possibly damaging	Het
Nexn	TCTTCCTTC	TCTTC	3: 151,948,513 (GRCm39)		probably benign	Het
Nod2	T	C	8: 89,390,970 (GRCm39)	S411P	probably damaging	Het
Plekha6	G	C	1: 133,200,045 (GRCm39)	R208P	possibly damaging	Het
Ptpn14	G	A	1: 189,578,610 (GRCm39)		probably null	Het
Stx16	G	A	2: 173,935,292 (GRCm39)	G156R	probably damaging	Het
Tbc1d15	T	C	10: 115,046,184 (GRCm39)	S440G	probably damaging	Het
Tpm2	A	G	4: 43,519,731 (GRCm39)	V85A	possibly damaging	Het
Ttf1	G	T	2: 28,955,754 (GRCm39)	A373S	probably damaging	Het
Vmn2r11	T	A	5: 109,201,560 (GRCm39)	T315S	probably benign	Het
Zcchc14	T	C	8: 122,331,378 (GRCm39)		probably benign	Het
Zfp146	T	C	7: 29,861,818 (GRCm39)	S75G	probably benign	Het
Zfp994	A	G	17: 22,420,254 (GRCm39)	Y232H	probably 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
R0511:Smg6	UTSW	11	74,819,884 (GRCm39)	missense	probably damaging	1.00
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
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'- CAGCTAGCAATGTCTCTCGTC -3'
(R):5'- AGTGCACTCTTGAGAGGTTG -3'

Sequencing Primer
(F):5'- GTCTTCATCCTCCCTCTCAGAAAATG -3'
(R):5'- TGAGAGGTTGCTGTCACCTCAAC -3'

Posted On

2016-11-21