Mutagenetix > Incidental Mutation

Incidental Mutation 'R0318:Smg9'

25507

Institutional Source

Beutler Lab

Gene Symbol

Smg9

Ensembl Gene

ENSMUSG00000002210

Gene Name

SMG9 nonsense mediated mRNA decay factor

Synonyms

smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans), 1500002O20Rik, N28092

MMRRC Submission

038528-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0318 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

24099106-24122197 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 24120313 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 429 (F429S)

Ref Sequence

ENSEMBL: ENSMUSP00000002280 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002280]

AlphaFold

Q9DB90

Predicted Effect

possibly damaging
Transcript: ENSMUST00000002280
AA Change: F429S

PolyPhen 2 Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000002280
Gene: ENSMUSG00000002210
AA Change: F429S

Domain	Start	End	E-Value	Type
low complexity region	79	93	N/A	INTRINSIC
low complexity region	112	135	N/A	INTRINSIC
Pfam:DUF2146	199	373	3.7e-8	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000123188
AA Change: F104S

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146686

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148288

Coding Region Coverage

1x: 98.8%
3x: 97.7%
10x: 94.4%
20x: 86.5%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a regulatory subunit of the SMG1 complex, which plays a critical role in nonsense-mediated mRNA decay (NMD). Binding of the encoded protein to the SMG1 complex kinase scaffold protein results in the inhibition of its kinase activity. Mutations in this gene cause a multiple congenital anomaly syndrome in human patients, characterized by brain malformation, congenital heart disease and other features. [provided by RefSeq, Jul 2016]
PHENOTYPE: Mice homozygous for a severe hypomorphic allele exhibit edema, hemorrhage, exencephaly, preaxial polydactyly, reduced size and growth, decreased mid- and hindrain size, microphthalmia, thin myocardium and atrioventricular septal defect. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9130401M01Rik	A	T	15: 57,892,370 (GRCm39)	L79Q	probably damaging	Het
Add1	T	C	5: 34,782,684 (GRCm39)	V130A	probably damaging	Het
Ankrd23	G	T	1: 36,573,153 (GRCm39)	T73K	probably benign	Het
Blk	A	G	14: 63,611,646 (GRCm39)	Y430H	probably damaging	Het
C3	C	T	17: 57,531,709 (GRCm39)	V272M	probably damaging	Het
Cerk	C	T	15: 86,035,766 (GRCm39)	A254T	possibly damaging	Het
Ces2a	G	A	8: 105,467,456 (GRCm39)	A494T	probably damaging	Het
Cfap46	T	C	7: 139,234,482 (GRCm39)	Y258C	probably damaging	Het
Chaf1a	C	T	17: 56,369,227 (GRCm39)	T486I	possibly damaging	Het
Colec12	A	G	18: 9,848,446 (GRCm39)	N208S	possibly damaging	Het
Coro7	T	A	16: 4,493,671 (GRCm39)	H63L	probably benign	Het
Cps1	T	A	1: 67,216,173 (GRCm39)	W833R	probably damaging	Het
Csmd3	A	T	15: 47,522,549 (GRCm39)	W2707R	probably damaging	Het
Dbn1	C	T	13: 55,622,729 (GRCm39)	E585K	probably damaging	Het
Ddx50	A	T	10: 62,478,616 (GRCm39)	I190K	probably damaging	Het
Dnmt3l	G	A	10: 77,890,889 (GRCm39)	V264M	probably damaging	Het
Dnpep	A	G	1: 75,293,270 (GRCm39)	V33A	probably damaging	Het
Fam163a	A	G	1: 155,955,715 (GRCm39)	C26R	probably damaging	Het
Fam83h	A	G	15: 75,875,478 (GRCm39)	S620P	probably benign	Het
Fcna	A	G	2: 25,515,071 (GRCm39)	S263P	probably benign	Het
Fnip2	A	T	3: 79,419,685 (GRCm39)	S165R	probably damaging	Het
Fpr-rs3	T	C	17: 20,844,410 (GRCm39)	T244A	probably benign	Het
Gpr152	T	C	19: 4,193,541 (GRCm39)	S361P	possibly damaging	Het
Grm5	A	T	7: 87,252,175 (GRCm39)	I142L	probably damaging	Het
Gucy2g	A	G	19: 55,226,230 (GRCm39)	S229P	probably benign	Het
Htr7	C	T	19: 35,946,886 (GRCm39)	G376D	probably damaging	Het
Irgc	T	C	7: 24,131,896 (GRCm39)	D307G	probably benign	Het
Irs1	A	T	1: 82,266,381 (GRCm39)	S612T	probably benign	Het
Maml2	C	T	9: 13,531,890 (GRCm39)	T368I	probably damaging	Het
Mapkapk2	A	G	1: 131,025,072 (GRCm39)	V64A	probably damaging	Het
Marf1	C	T	16: 13,960,398 (GRCm39)	A549T	probably damaging	Het
Nptx1	C	T	11: 119,433,367 (GRCm39)	E411K	probably damaging	Het
Or2z8	C	T	8: 72,812,244 (GRCm39)	T240M	probably damaging	Het
Or5ak25	C	A	2: 85,268,581 (GRCm39)	R307M	possibly damaging	Het
Pcgf5	A	T	19: 36,389,590 (GRCm39)	K22N	possibly damaging	Het
Psmd9	C	A	5: 123,372,712 (GRCm39)	A65E	possibly damaging	Het
Sh3bp1	A	G	15: 78,795,907 (GRCm39)	T679A	probably damaging	Het
Sipa1l2	G	A	8: 126,174,436 (GRCm39)	P1281S	possibly damaging	Het
Slc17a3	C	T	13: 24,039,841 (GRCm39)	S293F	probably damaging	Het
Slc25a24	A	G	3: 109,064,316 (GRCm39)	M222V	probably benign	Het
Snapc1	C	T	12: 74,021,806 (GRCm39)	R81C	probably damaging	Het
Sorl1	T	A	9: 41,993,250 (GRCm39)	Y258F	probably damaging	Het
Srp72	C	T	5: 77,132,047 (GRCm39)	T242I	probably benign	Het
Stc1	A	T	14: 69,275,867 (GRCm39)	Q220L	probably damaging	Het
Tas2r122	T	C	6: 132,688,795 (GRCm39)	T33A	possibly damaging	Het
Tbc1d10b	A	G	7: 126,798,206 (GRCm39)	L645P	probably damaging	Het
Thoc2l	T	C	5: 104,665,619 (GRCm39)	F47S	probably benign	Het
Timd4	T	A	11: 46,727,898 (GRCm39)	H272Q	probably benign	Het
Ttll5	T	G	12: 85,923,368 (GRCm39)		probably null	Het
Veph1	G	T	3: 65,964,680 (GRCm39)	S783Y	probably damaging	Het
Vmn1r230	T	C	17: 21,067,078 (GRCm39)	L89S	possibly damaging	Het
Xcr1	A	G	9: 123,685,219 (GRCm39)	V165A	possibly damaging	Het
Zfp286	T	C	11: 62,675,788 (GRCm39)	D58G	probably damaging	Het
Zfyve26	C	T	12: 79,323,055 (GRCm39)	R897H	probably damaging	Het

Other mutations in Smg9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01100:Smg9	APN	7	24,116,376 (GRCm39)	missense	probably damaging	1.00
IGL01432:Smg9	APN	7	24,120,691 (GRCm39)	critical splice donor site	probably null
IGL01869:Smg9	APN	7	24,115,949 (GRCm39)	missense	probably damaging	1.00
IGL02376:Smg9	APN	7	24,114,455 (GRCm39)	missense	probably benign	0.01
IGL03175:Smg9	APN	7	24,121,730 (GRCm39)	missense	probably damaging	1.00
IGL03204:Smg9	APN	7	24,120,337 (GRCm39)	missense	probably benign	0.02
R0578:Smg9	UTSW	7	24,114,468 (GRCm39)	missense	probably damaging	1.00
R0786:Smg9	UTSW	7	24,120,289 (GRCm39)	missense	probably benign	0.03
R2043:Smg9	UTSW	7	24,105,001 (GRCm39)	missense	possibly damaging	0.92
R2355:Smg9	UTSW	7	24,119,546 (GRCm39)	critical splice donor site	probably null
R3033:Smg9	UTSW	7	24,115,949 (GRCm39)	missense	probably damaging	1.00
R4091:Smg9	UTSW	7	24,120,292 (GRCm39)	missense	probably null	0.01
R4773:Smg9	UTSW	7	24,107,019 (GRCm39)	missense	possibly damaging	0.84
R5023:Smg9	UTSW	7	24,105,297 (GRCm39)	missense	possibly damaging	0.94
R5517:Smg9	UTSW	7	24,114,338 (GRCm39)	unclassified	probably benign
R6320:Smg9	UTSW	7	24,120,286 (GRCm39)	missense	probably benign
R6394:Smg9	UTSW	7	24,121,732 (GRCm39)	missense	probably damaging	1.00
R7156:Smg9	UTSW	7	24,120,286 (GRCm39)	missense	probably benign
R7269:Smg9	UTSW	7	24,105,495 (GRCm39)	missense	possibly damaging	0.88
R7311:Smg9	UTSW	7	24,120,058 (GRCm39)	missense	probably benign	0.14
R8972:Smg9	UTSW	7	24,120,055 (GRCm39)	missense	probably benign	0.04
R9323:Smg9	UTSW	7	24,114,465 (GRCm39)	missense	probably damaging	1.00
R9589:Smg9	UTSW	7	24,120,246 (GRCm39)	missense	probably damaging	1.00
R9707:Smg9	UTSW	7	24,102,869 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGATTGACCAGCTCATGGCACAC -3'
(R):5'- TGCTTCAGACCAGCTTTTCCCAAAC -3'

Sequencing Primer
(F):5'- ATAGATTGTATGCCACTCCCAGG -3'
(R):5'- AGCTTTTCCCAAACCTCTCCAG -3'

Posted On

2013-04-16