Mutagenetix > Incidental Mutation

Incidental Mutation 'R4091:Smg9'

317607

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

041626-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4091 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

24099106-24122197 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 24120292 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 422 (L422Q)

Ref Sequence

ENSEMBL: ENSMUSP00000002280 (fasta)

Gene Model

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

AlphaFold

Q9DB90

Predicted Effect

probably null
Transcript: ENSMUST00000002280
AA Change: L422Q

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000002280
Gene: ENSMUSG00000002210
AA Change: L422Q

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

probably null
Transcript: ENSMUST00000123188
AA Change: L97Q

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000146686

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000148288

Meta Mutation Damage Score

0.1047

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.6%
20x: 96.1%

Validation Efficiency

98% (61/62)

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932414N04Rik	T	C	2: 68,575,722 (GRCm39)	S674P	possibly damaging	Het
Abca3	C	T	17: 24,616,456 (GRCm39)	T966M	probably damaging	Het
Adam2	A	T	14: 66,267,172 (GRCm39)	Y696N	probably damaging	Het
Alas1	G	T	9: 106,119,000 (GRCm39)		probably null	Het
Arhgap25	G	T	6: 87,440,017 (GRCm39)	S543R	probably benign	Het
Bckdk	C	A	7: 127,504,590 (GRCm39)	R105S	probably damaging	Het
Bltp1	G	A	3: 37,084,738 (GRCm39)	A3897T	probably benign	Het
Carns1	C	T	19: 4,221,682 (GRCm39)	R191Q	probably damaging	Het
Casp8ap2	C	A	4: 32,643,611 (GRCm39)	P895T	probably damaging	Het
Col12a1	T	A	9: 79,609,646 (GRCm39)	I287F	probably damaging	Het
Cystm1	A	G	18: 36,499,600 (GRCm39)	N5S	unknown	Het
Dnah8	T	C	17: 30,988,813 (GRCm39)	V3261A	probably damaging	Het
Dnajc11	A	G	4: 152,062,550 (GRCm39)		probably benign	Het
Dock4	T	C	12: 40,894,266 (GRCm39)	S1847P	probably damaging	Het
Dync2h1	A	G	9: 7,131,881 (GRCm39)	V1642A	probably benign	Het
Eftud2	T	C	11: 102,730,242 (GRCm39)		probably null	Het
Fam221b	A	G	4: 43,665,987 (GRCm39)	I208T	probably benign	Het
Gpr141b	T	A	13: 19,913,635 (GRCm39)		noncoding transcript	Het
Gpr37l1	T	C	1: 135,089,301 (GRCm39)	I255V	probably benign	Het
Grm7	G	A	6: 110,891,301 (GRCm39)	S178N	probably damaging	Het
Hspa12b	T	A	2: 130,975,408 (GRCm39)		probably null	Het
Kctd3	A	T	1: 188,727,917 (GRCm39)		probably benign	Het
Kynu	G	A	2: 43,569,884 (GRCm39)	V389M	possibly damaging	Het
Lcat	A	G	8: 106,666,538 (GRCm39)	L328P	probably benign	Het
Lrrn2	C	T	1: 132,865,390 (GRCm39)	Q152*	probably null	Het
Maml1	G	A	11: 50,182,656 (GRCm39)	P78L	probably benign	Het
Mef2b	G	A	8: 70,617,752 (GRCm39)	V37M	probably damaging	Het
Mindy2	A	T	9: 70,541,342 (GRCm39)	M281K	probably damaging	Het
Mon2	C	T	10: 122,874,415 (GRCm39)	R311H	probably damaging	Het
Mtr	A	T	13: 12,245,943 (GRCm39)	V394E	probably damaging	Het
Myh14	T	A	7: 44,282,415 (GRCm39)	T745S	possibly damaging	Het
Nme9	T	A	9: 99,346,580 (GRCm39)	D131E	possibly damaging	Het
Nphp4	C	A	4: 152,631,475 (GRCm39)	Q792K	probably damaging	Het
Nrxn2	T	A	19: 6,523,444 (GRCm39)	C479S	probably damaging	Het
Nsmf	T	C	2: 24,950,871 (GRCm39)	I406T	probably damaging	Het
Or10a49	G	A	7: 108,467,650 (GRCm39)	A237V	probably damaging	Het
Or5an9	A	T	19: 12,187,143 (GRCm39)	D71V	probably damaging	Het
Or8g28	T	A	9: 39,169,330 (GRCm39)	I213F	possibly damaging	Het
Pbrm1	A	G	14: 30,757,960 (GRCm39)	T197A	probably benign	Het
Pla2r1	T	A	2: 60,262,937 (GRCm39)	N1034I	probably damaging	Het
Rps6-ps2	A	G	8: 89,533,319 (GRCm39)		noncoding transcript	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Rxfp1	A	T	3: 79,552,068 (GRCm39)	D744E	probably benign	Het
Samd9l	T	C	6: 3,376,887 (GRCm39)	N125D	probably benign	Het
Serpina3a	G	A	12: 104,082,625 (GRCm39)	V133I	probably benign	Het
Slc22a30	C	T	19: 8,381,909 (GRCm39)	V121M	probably damaging	Het
Smarcc1	T	A	9: 109,993,897 (GRCm39)	D247E	possibly damaging	Het
Speer3	C	G	5: 13,846,394 (GRCm39)	A238G	possibly damaging	Het
Tle5	G	A	10: 81,401,418 (GRCm39)	G162D	probably damaging	Het
Ttc23l	CT	CTTGGATT	15: 10,537,648 (GRCm39)		probably benign	Het
Ttc23l	G	A	15: 10,537,652 (GRCm39)	S206L	probably benign	Het
Utrn	T	A	10: 12,585,915 (GRCm39)	D954V	probably benign	Het
Vmn1r227	T	A	17: 20,955,778 (GRCm39)		noncoding transcript	Het
Vmn2r11	A	C	5: 109,202,616 (GRCm39)		probably null	Het
Vmn2r84	A	T	10: 130,227,238 (GRCm39)	M200K	probably damaging	Het
Vmn2r88	T	A	14: 51,652,883 (GRCm39)	Y469N	probably damaging	Het
Wdcp	A	G	12: 4,905,279 (GRCm39)	N600S	probably null	Het
Wdfy4	T	G	14: 32,847,837 (GRCm39)	R838S	possibly 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
R0318:Smg9	UTSW	7	24,120,313 (GRCm39)	missense	possibly damaging	0.80
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
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'- GGTGAGCATCTCTGAGCTTC -3'
(R):5'- TTCAGACCAGCTTTTCCCAAAC -3'

Sequencing Primer
(F):5'- GAGCTTCTCATAGATTGTATGCCAC -3'
(R):5'- CCAAACCTCTCCAGTGCTG -3'

Posted On

2015-05-15