Mutagenetix > Incidental Mutation

Incidental Mutation 'R6619:Smg6'

524290

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

044742-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6619 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

74816665-75055274 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to C at 74823279 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000043555 (fasta)

Gene Model

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

AlphaFold

P61406

Predicted Effect

probably null
Transcript: ENSMUST00000045281

SMART Domains

Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290

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 null
Transcript: ENSMUST00000045281

SMART Domains

Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290

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

noncoding transcript
Transcript: ENSMUST00000158094

Meta Mutation Damage Score

0.9505

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.0%
20x: 93.9%

Validation Efficiency

100% (37/37)

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: 37 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Atp13a5	G	A	16: 29,167,833 (GRCm39)	P109S	probably benign	Het
Baiap2l1	T	C	5: 144,222,916 (GRCm39)	K106R	probably benign	Het
Coro6	A	G	11: 77,357,030 (GRCm39)	I111V	possibly damaging	Het
Crocc2	A	G	1: 93,118,223 (GRCm39)	E382G	probably benign	Het
Dhrs7l	A	T	12: 72,668,724 (GRCm39)	N44K	possibly damaging	Het
Dnah5	C	A	15: 28,409,266 (GRCm39)	N3561K	probably benign	Het
Dsc2	T	A	18: 20,165,335 (GRCm39)	E879D	probably benign	Het
Frk	A	G	10: 34,481,835 (GRCm39)	Y375C	probably benign	Het
Herc2	A	T	7: 55,717,840 (GRCm39)	R61*	probably null	Het
Jarid2	A	G	13: 45,027,872 (GRCm39)	D146G	probably damaging	Het
Lancl2	C	A	6: 57,699,566 (GRCm39)	T127K	probably damaging	Het
Large1	G	A	8: 73,609,892 (GRCm39)	Q359*	probably null	Het
Mast2	C	A	4: 116,173,694 (GRCm39)	E521*	probably null	Het
Mrc1	T	A	2: 14,299,597 (GRCm39)		probably null	Het
Obi1	T	C	14: 104,759,993 (GRCm39)	H19R	possibly damaging	Het
Or4z4	A	G	19: 12,076,727 (GRCm39)	I92T	probably damaging	Het
Or5ak23	T	C	2: 85,244,425 (GRCm39)	N266S	probably benign	Het
Or6c38	A	T	10: 128,929,323 (GRCm39)	D173E	possibly damaging	Het
Or8k38	T	C	2: 86,488,406 (GRCm39)	Y132C	probably damaging	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
P2ry14	T	C	3: 59,023,154 (GRCm39)	Y102C	probably damaging	Het
Pcdhga6	T	A	18: 37,842,702 (GRCm39)	D807E	probably benign	Het
Pcdhgb4	T	A	18: 37,854,737 (GRCm39)	N377K	probably damaging	Het
Phf13	T	A	4: 152,076,114 (GRCm39)	N263Y	probably damaging	Het
Rab19	T	A	6: 39,365,060 (GRCm39)	S107T	probably damaging	Het
Rasgrf2	A	T	13: 92,165,027 (GRCm39)	F380I	probably damaging	Het
Reep1	T	C	6: 71,784,826 (GRCm39)		probably benign	Het
Rpgrip1l	C	T	8: 91,959,499 (GRCm39)	E1134K	possibly damaging	Het
Serpina3m	A	T	12: 104,357,766 (GRCm39)	Y230F	probably benign	Het
Skint3	T	C	4: 112,111,061 (GRCm39)	I62T	probably damaging	Het
Sp4	G	A	12: 118,263,077 (GRCm39)	T323I	possibly damaging	Het
Strc	A	G	2: 121,198,913 (GRCm39)	I1378T	probably damaging	Het
Tepsin	C	T	11: 119,986,428 (GRCm39)	G128D	probably benign	Het
Togaram2	A	G	17: 71,996,266 (GRCm39)	N89D	probably damaging	Het
Trim36	T	C	18: 46,321,475 (GRCm39)	T191A	probably damaging	Het
Trp53bp1	A	T	2: 121,077,980 (GRCm39)		probably null	Het
Zfp418	G	A	7: 7,184,895 (GRCm39)	C286Y	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
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
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'- AAGGGTTGTTTGGCCAAGG -3'
(R):5'- TGTCCTGCTTATGACTATTAGTTGT -3'

Sequencing Primer
(F):5'- AAGGGTTGTTTGGCCAAGGATTTG -3'
(R):5'- AGAGGCCCTGAGTTCAATTC -3'

Posted On

2018-06-22