Mutagenetix > Incidental Mutation

Incidental Mutation 'R1780:Smg6'

197465

Institutional Source

Beutler Lab

Gene Symbol

Smg6

Ensembl Gene

ENSMUSG00000038290

Gene Name

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

Synonyms

MMRRC Submission

039811-MU

Accession Numbers

Genbank: NM_001002764.1; Ensembl: ENSMUST00000045281

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1780 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

74925823-75164448 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 74946116 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 852 (L852Q)

Ref Sequence

ENSEMBL: ENSMUSP00000043555 (fasta)

Gene Model

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

AlphaFold

P61406

Predicted Effect

probably damaging
Transcript: ENSMUST00000045281
AA Change: L852Q

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

SMART Domains

Protein: ENSMUSP00000043555
Gene: ENSMUSG00000038290
AA Change: L852Q

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

unknown
Transcript: ENSMUST00000130145
AA Change: L313Q

SMART Domains

Protein: ENSMUSP00000120229
Gene: ENSMUSG00000038290
AA Change: L313Q

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

Meta Mutation Damage Score

0.2268

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.2%
20x: 92.3%

Validation Efficiency

98% (80/82)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrl2	T	C	3: 148,852,593	E493G	probably damaging	Het
Aff3	A	T	1: 38,535,702	S66T	probably damaging	Het
Ankrd17	T	A	5: 90,232,415	K2470N	probably damaging	Het
Ap3m1	T	C	14: 21,041,070	T156A	probably benign	Het
Arhgef4	T	A	1: 34,724,160	S832R	possibly damaging	Het
Asb10	T	C	5: 24,533,676	D423G	possibly damaging	Het
Ash1l	A	G	3: 88,965,984	T25A	probably benign	Het
Atp13a2	T	A	4: 141,002,460	L663I	possibly damaging	Het
Atp9b	A	T	18: 80,776,897	Y174*	probably null	Het
Bche	A	G	3: 73,700,620	I491T	probably benign	Het
Bckdhb	T	C	9: 83,953,783		probably null	Het
Cadps2	C	T	6: 23,320,932		probably null	Het
Cdc42bpb	A	T	12: 111,322,907	V468E	probably damaging	Het
Chrnd	T	C	1: 87,192,548	V33A	possibly damaging	Het
Col6a5	A	T	9: 105,936,878	V645D	unknown	Het
Cpa1	C	T	6: 30,643,008	L312F	probably damaging	Het
Cyp2a5	A	G	7: 26,841,876		probably benign	Het
Cyp2c39	C	A	19: 39,538,851		probably benign	Het
Cyp2d26	T	C	15: 82,794,007	N56S	probably damaging	Het
Ddx21	A	G	10: 62,594,147		probably benign	Het
Dnah11	A	T	12: 118,027,558	C2358S	probably damaging	Het
Entpd8	T	C	2: 25,084,306	S368P	probably benign	Het
Epg5	A	T	18: 78,023,990	Q2222L	probably damaging	Het
Ercc5	T	A	1: 44,167,796	V623E	probably benign	Het
Flg2	A	G	3: 93,202,999	E778G	unknown	Het
Gbe1	C	T	16: 70,495,324	R515*	probably null	Het
Hsd17b6	A	G	10: 127,994,327		probably null	Het
Hyal6	C	T	6: 24,734,032		probably benign	Het
Ifi27l2b	A	G	12: 103,451,319	I203T	probably damaging	Het
Kcnk9	A	C	15: 72,512,401	D309E	unknown	Het
Lrp6	C	T	6: 134,464,451	R1184Q	probably damaging	Het
Mdn1	T	C	4: 32,700,103	F1399L	probably damaging	Het
Mroh2a	C	T	1: 88,230,680	R150*	probably null	Het
Mx1	T	C	16: 97,451,512	*289W	probably null	Het
Myo7b	T	C	18: 31,961,185	E1970G	probably damaging	Het
Mypn	T	C	10: 63,121,964	Y24C	probably damaging	Het
Naxe	G	C	3: 88,057,133	P167A	probably benign	Het
Nmnat2	A	T	1: 153,112,440	K272*	probably null	Het
Nmnat3	C	T	9: 98,354,111	T19M	probably damaging	Het
Olfr1275	T	C	2: 111,231,698	I32V	probably benign	Het
Olfr1412	G	A	1: 92,588,389	V20M	probably benign	Het
Olfr1474	A	G	19: 13,471,362	T131A	probably benign	Het
Olfr64	A	T	7: 103,893,555	F60Y	probably damaging	Het
Olfr66	A	G	7: 103,881,592	V217A	probably benign	Het
Pgm3	T	G	9: 86,556,204	E509D	probably damaging	Het
Phf3	A	T	1: 30,811,942	D1110E	probably damaging	Het
Pkd1	T	G	17: 24,581,569	S3062A	probably benign	Het
Pogz	A	T	3: 94,870,126	K372N	possibly damaging	Het
Pou1f1	A	G	16: 65,523,470	Y15C	probably benign	Het
Ppfia2	A	G	10: 106,896,507	T972A	possibly damaging	Het
Rasip1	A	G	7: 45,635,318	Y703C	possibly damaging	Het
Recql	T	A	6: 142,364,598	Q502L	probably benign	Het
Rgs9	A	T	11: 109,239,499	Y383*	probably null	Het
Rimbp3	T	C	16: 17,212,632	S1307P	probably benign	Het
Rspo1	A	G	4: 125,007,745	T200A	probably damaging	Het
Ryr3	C	T	2: 112,867,292	M922I	probably damaging	Het
Samm50	C	T	15: 84,211,127	A438V	probably damaging	Het
Sec1	A	C	7: 45,678,832	S264A	probably benign	Het
Sec31a	A	T	5: 100,381,336		probably null	Het
Slc13a3	T	C	2: 165,406,699	N553S	unknown	Het
Spata13	A	G	14: 60,691,725	N244S	probably damaging	Het
Srbd1	T	C	17: 86,057,685	R648G	probably damaging	Het
Sugct	T	G	13: 17,452,454		probably null	Het
Tmed10	A	G	12: 85,354,879	Y85H	probably damaging	Het
Trim68	A	G	7: 102,684,073	I134T	possibly damaging	Het
Trio	A	G	15: 27,744,038	C2603R	possibly damaging	Het
Tspyl3	G	A	2: 153,225,256	R21W	probably damaging	Het
Ttn	T	C	2: 76,810,699	I11863V	probably null	Het
Ubp1	G	A	9: 113,964,579	A283T	possibly damaging	Het
Ubtf	A	T	11: 102,314,918	F60L	probably damaging	Het
Vmn1r235	T	C	17: 21,261,737	I108T	probably benign	Het
Vmn2r125	T	C	4: 156,351,373	S349P	probably damaging	Het
Vmn2r25	A	G	6: 123,828,465	S478P	probably damaging	Het
Vmn2r88	T	A	14: 51,418,572	V746D	probably damaging	Het
Zcwpw1	A	G	5: 137,796,652	K37E	probably damaging	Het
Zdhhc24	T	C	19: 4,883,766	S284P	probably damaging	Het
Zswim8	C	A	14: 20,716,327	H841N	probably damaging	Het

Other mutations in Smg6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00952:Smg6	APN	11	74929148	missense	probably benign
IGL01146:Smg6	APN	11	74930428	nonsense	probably null
IGL01505:Smg6	APN	11	75156291	missense	probably damaging	1.00
IGL01541:Smg6	APN	11	74925944	missense	probably benign	0.43
IGL01636:Smg6	APN	11	74935103	critical splice donor site	probably null
IGL02379:Smg6	APN	11	75053925	missense	probably damaging	1.00
IGL02794:Smg6	APN	11	75053934	missense	probably damaging	0.99
IGL02964:Smg6	APN	11	74930750	critical splice donor site	probably null
IGL03057:Smg6	APN	11	74935434	nonsense	probably null
1mM(1):Smg6	UTSW	11	74934989	splice site	probably benign
IGL03097:Smg6	UTSW	11	74932426	missense	probably damaging	1.00
PIT4802001:Smg6	UTSW	11	75156165	missense	probably damaging	0.96
R0269:Smg6	UTSW	11	75162931	missense	probably benign
R0344:Smg6	UTSW	11	74929821	missense	probably damaging	1.00
R0437:Smg6	UTSW	11	74929701	missense	probably damaging	1.00
R0452:Smg6	UTSW	11	74930213	missense	probably benign
R0511:Smg6	UTSW	11	74929058	missense	probably damaging	1.00
R0617:Smg6	UTSW	11	75162931	missense	probably benign
R0737:Smg6	UTSW	11	75159836	missense	probably damaging	1.00
R1715:Smg6	UTSW	11	74929430	missense	probably benign
R1927:Smg6	UTSW	11	75142848	missense	probably damaging	1.00
R2073:Smg6	UTSW	11	74930294	missense	probably damaging	1.00
R2171:Smg6	UTSW	11	75038646	missense	probably damaging	1.00
R2513:Smg6	UTSW	11	74929676	missense	probably damaging	1.00
R3943:Smg6	UTSW	11	74929541	missense	probably damaging	1.00
R3944:Smg6	UTSW	11	74929541	missense	probably damaging	1.00
R4275:Smg6	UTSW	11	74993874	intron	probably benign
R4369:Smg6	UTSW	11	74932443	nonsense	probably null
R4452:Smg6	UTSW	11	74990141	missense	probably benign	0.14
R4864:Smg6	UTSW	11	74930162	missense	possibly damaging	0.89
R4885:Smg6	UTSW	11	75041918	missense	probably damaging	1.00
R5043:Smg6	UTSW	11	74929895	missense	possibly damaging	0.86
R5189:Smg6	UTSW	11	75041996	missense	probably damaging	1.00
R5378:Smg6	UTSW	11	75041994	missense	possibly damaging	0.61
R5518:Smg6	UTSW	11	75053898	missense	probably damaging	0.99
R5725:Smg6	UTSW	11	74930613	missense	probably benign	0.45
R5746:Smg6	UTSW	11	75139287	missense	probably damaging	1.00
R6151:Smg6	UTSW	11	75156207	missense	probably damaging	0.96
R6319:Smg6	UTSW	11	75156222	missense	probably damaging	1.00
R6349:Smg6	UTSW	11	75053774	missense	possibly damaging	0.94
R6500:Smg6	UTSW	11	74930505	missense	possibly damaging	0.74
R6619:Smg6	UTSW	11	74932453	critical splice donor site	probably null
R6820:Smg6	UTSW	11	75041964	missense	probably damaging	0.99
R6923:Smg6	UTSW	11	74929343	missense	possibly damaging	0.50
R7361:Smg6	UTSW	11	74930153	missense	probably benign	0.00
R7494:Smg6	UTSW	11	74929623	missense	probably benign
R7498:Smg6	UTSW	11	74929106	missense	probably benign	0.01
R7681:Smg6	UTSW	11	74931705	missense	probably damaging	1.00
R7710:Smg6	UTSW	11	74930619	missense	probably benign	0.26
R7770:Smg6	UTSW	11	74993861	missense	unknown
R8159:Smg6	UTSW	11	75038639	missense	probably damaging	1.00
R8381:Smg6	UTSW	11	74931740	missense	probably damaging	1.00
R8463:Smg6	UTSW	11	74930060	missense	probably benign	0.14
R8509:Smg6	UTSW	11	75041876	missense	probably benign	0.04
R8557:Smg6	UTSW	11	75156238	missense	probably damaging	0.98
R8743:Smg6	UTSW	11	74930033	missense	probably benign
R9240:Smg6	UTSW	11	74935058	missense	probably damaging	1.00
R9312:Smg6	UTSW	11	74930051	missense	probably benign	0.27
X0018:Smg6	UTSW	11	74929986	missense	possibly damaging	0.76
Z1186:Smg6	UTSW	11	75156266	missense	probably benign	0.06
Z1187:Smg6	UTSW	11	75156266	missense	probably benign	0.06
Z1188:Smg6	UTSW	11	75156266	missense	probably benign	0.06
Z1189:Smg6	UTSW	11	75156266	missense	probably benign	0.06
Z1190:Smg6	UTSW	11	75156266	missense	probably benign	0.06
Z1191:Smg6	UTSW	11	75156266	missense	probably benign	0.06
Z1192:Smg6	UTSW	11	75156266	missense	probably benign	0.06

Predicted Primers

PCR Primer
(F):5'- TAGAGCGTACCTGTTCCACAGCAC -3'
(R):5'- CTTAAAGCTGGGACCTGTCTATGCC -3'

Sequencing Primer
(F):5'- GCTACTTTGGTACTGTAGCAGAATC -3'
(R):5'- GGACCTGTCTATGCCTCAGC -3'

Posted On

2014-05-23