Mutagenetix > Incidental Mutation

Incidental Mutation 'R5860:Smg5'

453829

Institutional Source

Beutler Lab

Gene Symbol

Smg5

Ensembl Gene

ENSMUSG00000001415

Gene Name

SMG5 nonsense mediated mRNA decay factor

Synonyms

Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)

MMRRC Submission

044072-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5860 (G1)

Quality Score

204

Status

Validated

Chromosome

Chromosomal Location

88243567-88269645 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 88250214 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 109 (C109S)

Ref Sequence

ENSEMBL: ENSMUSP00000001451 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001451]

AlphaFold

Q6ZPY2

Predicted Effect

probably damaging
Transcript: ENSMUST00000001451
AA Change: C109S

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000001451
Gene: ENSMUSG00000001415
AA Change: C109S

Domain	Start	End	E-Value	Type
low complexity region	4	14	N/A	INTRINSIC
Pfam:EST1	77	189	1.1e-26	PFAM
Pfam:EST1_DNA_bind	197	427	4.6e-53	PFAM
low complexity region	447	468	N/A	INTRINSIC
low complexity region	481	501	N/A	INTRINSIC
Pfam:EST1_DNA_bind	611	745	3.7e-9	PFAM
coiled coil region	801	842	N/A	INTRINSIC
PINc	856	979	3.23e-15	SMART
low complexity region	990	999	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000192009
AA Change: C51S

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192057

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193007

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194942

Meta Mutation Damage Score

0.1208

Coding Region Coverage

1x: 99.9%
3x: 99.4%
10x: 97.1%
20x: 90.8%

Validation Efficiency

97% (75/77)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] SMG5 is involved in nonsense-mediated mRNA decay (Ohnishi et al., 2003 [PubMed 14636577]).[supplied by OMIM, Mar 2008]

Allele List at MGI

Other mutations in this stock

Total: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930568A12Rik	A	G	1: 34,524,661 (GRCm39)		noncoding transcript	Het
A2ml1	T	C	6: 128,518,024 (GRCm39)	T1421A	probably benign	Het
Actr8	T	A	14: 29,708,242 (GRCm39)	Y150*	probably null	Het
Adamts1	A	G	16: 85,595,432 (GRCm39)	C249R	probably damaging	Het
Adgre1	T	A	17: 57,752,034 (GRCm39)	I594N	probably damaging	Het
Atf6	A	T	1: 170,669,344 (GRCm39)	L119H	probably damaging	Het
Atf6	G	A	1: 170,669,345 (GRCm39)	L119F	possibly damaging	Het
B3gat2	G	A	1: 23,854,400 (GRCm39)	W33*	probably null	Het
Bach2	A	G	4: 32,580,268 (GRCm39)	D831G	probably damaging	Het
Ccnk	A	T	12: 108,153,466 (GRCm39)	I76F	probably damaging	Het
Cdyl	A	C	13: 36,042,066 (GRCm39)	K368T	possibly damaging	Het
Chi3l1	A	G	1: 134,112,909 (GRCm39)	T114A	probably benign	Het
Cnppd1	A	G	1: 75,113,131 (GRCm39)	V379A	probably benign	Het
Col11a2	C	A	17: 34,283,159 (GRCm39)		probably benign	Het
Creb3l1	T	C	2: 91,854,399 (GRCm39)	S18G	probably benign	Het
Crybg3	A	C	16: 59,385,632 (GRCm39)	D197E	probably damaging	Het
Cryga	T	C	1: 65,142,527 (GRCm39)		probably benign	Het
Cthrc1	T	C	15: 38,950,080 (GRCm39)	C146R	probably damaging	Het
Cyp2c39	A	T	19: 39,525,270 (GRCm39)	D191V	probably damaging	Het
Dchs1	C	T	7: 105,421,242 (GRCm39)	A393T	probably damaging	Het
Dhx30	G	A	9: 109,913,645 (GRCm39)	T1126I	probably damaging	Het
Dock2	C	T	11: 34,206,562 (GRCm39)	G1345R	probably damaging	Het
Dsc1	T	C	18: 20,228,081 (GRCm39)	E425G	probably damaging	Het
Dynlt2b	A	G	16: 32,247,614 (GRCm39)	Y143C	probably damaging	Het
Exosc8	C	T	3: 54,642,463 (GRCm39)		probably benign	Het
Fat1	C	T	8: 45,504,166 (GRCm39)	A4553V	probably benign	Het
Flnb	T	A	14: 7,931,135 (GRCm38)	L2119Q	probably damaging	Het
Fnbp4	T	A	2: 90,587,826 (GRCm39)	D401E	probably benign	Het
Glyctk	T	C	9: 106,032,906 (GRCm39)	E369G	possibly damaging	Het
Gm14149	C	A	2: 151,066,225 (GRCm39)		noncoding transcript	Het
Golga4	T	C	9: 118,387,174 (GRCm39)	L1432P	probably damaging	Het
Gtpbp4	A	T	13: 9,023,196 (GRCm39)	S623T	probably benign	Het
Insc	A	C	7: 114,390,383 (GRCm39)	S85R	probably damaging	Het
Lgr4	G	A	2: 109,821,496 (GRCm39)	R126H	probably damaging	Het
M1ap	T	A	6: 82,980,795 (GRCm39)	L227Q	probably damaging	Het
Marchf7	T	C	2: 60,067,187 (GRCm39)	I569T	probably damaging	Het
Mbd1	C	A	18: 74,409,768 (GRCm39)	C339*	probably null	Het
Moxd2	T	A	6: 40,857,341 (GRCm39)	Y473F	probably damaging	Het
Mrgpra6	T	C	7: 46,839,099 (GRCm39)	H2R	probably benign	Het
Mtus1	T	G	8: 41,529,303 (GRCm39)	L742F	probably damaging	Het
Nek11	A	G	9: 105,270,160 (GRCm39)	Y21H	probably benign	Het
Notch4	G	T	17: 34,801,392 (GRCm39)	C1080F	probably damaging	Het
Nsd3	C	A	8: 26,156,107 (GRCm39)	P558Q	probably damaging	Het
Oas1e	A	T	5: 120,930,015 (GRCm39)	S168T	probably benign	Het
Ogfr	T	C	2: 180,234,285 (GRCm39)	S119P	probably damaging	Het
Or2y15	A	G	11: 49,350,563 (GRCm39)	D19G	probably damaging	Het
Or8g20	T	A	9: 39,395,767 (GRCm39)	M261L	probably benign	Het
Pde4dip	A	G	3: 97,631,504 (GRCm39)	I1135T	possibly damaging	Het
Prex1	G	A	2: 166,486,604 (GRCm39)		probably benign	Het
Ptprf	T	C	4: 118,068,486 (GRCm39)		probably benign	Het
Rapsn	T	C	2: 90,875,859 (GRCm39)	V359A	probably damaging	Het
Ric1	A	G	19: 29,577,245 (GRCm39)	S1050G	possibly damaging	Het
Rnft2	A	G	5: 118,366,868 (GRCm39)	I290T	possibly damaging	Het
Senp7	C	A	16: 55,975,722 (GRCm39)	A476E	possibly damaging	Het
Serpinh1	G	A	7: 98,995,571 (GRCm39)	S337L	probably damaging	Het
Slc5a12	C	A	2: 110,427,969 (GRCm39)	A8D	probably benign	Het
Speer4b	T	C	5: 27,705,226 (GRCm39)	H49R	possibly damaging	Het
Tas2r109	T	C	6: 132,957,664 (GRCm39)	I89V	probably benign	Het
Tet1	A	G	10: 62,648,399 (GRCm39)		probably null	Het
Tmed6	G	T	8: 107,790,786 (GRCm39)	T87K	probably damaging	Het
Tpgs1	G	A	10: 79,505,545 (GRCm39)	G101D	probably damaging	Het
Trim13	T	G	14: 61,842,188 (GRCm39)	S68R	probably damaging	Het
Vwf	A	G	6: 125,620,053 (GRCm39)	N1577S		Het
Vwf	G	T	6: 125,656,228 (GRCm39)		probably benign	Het
Xpr1	T	C	1: 155,207,868 (GRCm39)		probably benign	Het
Ylpm1	C	T	12: 85,087,660 (GRCm39)	P1148L	probably damaging	Het
Zftraf1	A	T	15: 76,532,391 (GRCm39)	I239N	probably damaging	Het
Zftraf1	T	C	15: 76,540,615 (GRCm39)	Y101C	probably damaging	Het
Zscan29	G	T	2: 120,994,518 (GRCm39)	T489N	probably damaging	Het

Other mutations in Smg5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00433:Smg5	APN	3	88,258,735 (GRCm39)	nonsense	probably null
IGL00902:Smg5	APN	3	88,260,392 (GRCm39)	missense	probably benign	0.00
IGL00990:Smg5	APN	3	88,250,345 (GRCm39)	critical splice donor site	probably null
IGL01371:Smg5	APN	3	88,266,951 (GRCm39)	unclassified	probably benign
IGL01536:Smg5	APN	3	88,256,552 (GRCm39)	missense	possibly damaging	0.58
IGL02215:Smg5	APN	3	88,260,305 (GRCm39)	missense	possibly damaging	0.47
IGL03366:Smg5	APN	3	88,253,759 (GRCm39)	nonsense	probably null
R0013:Smg5	UTSW	3	88,256,540 (GRCm39)	missense	probably benign	0.00
R0017:Smg5	UTSW	3	88,258,412 (GRCm39)	missense	probably damaging	1.00
R0017:Smg5	UTSW	3	88,258,412 (GRCm39)	missense	probably damaging	1.00
R0129:Smg5	UTSW	3	88,256,540 (GRCm39)	missense	probably benign	0.00
R0153:Smg5	UTSW	3	88,261,179 (GRCm39)	unclassified	probably benign
R1386:Smg5	UTSW	3	88,262,978 (GRCm39)	missense	probably damaging	1.00
R1941:Smg5	UTSW	3	88,252,687 (GRCm39)	missense	possibly damaging	0.71
R2185:Smg5	UTSW	3	88,258,868 (GRCm39)	missense	probably benign
R2282:Smg5	UTSW	3	88,252,705 (GRCm39)	missense	probably benign	0.02
R3615:Smg5	UTSW	3	88,243,758 (GRCm39)	missense	possibly damaging	0.94
R3616:Smg5	UTSW	3	88,243,758 (GRCm39)	missense	possibly damaging	0.94
R4008:Smg5	UTSW	3	88,256,465 (GRCm39)	missense	probably benign	0.01
R4687:Smg5	UTSW	3	88,249,776 (GRCm39)	missense	possibly damaging	0.83
R4726:Smg5	UTSW	3	88,243,758 (GRCm39)	missense	possibly damaging	0.94
R4801:Smg5	UTSW	3	88,262,999 (GRCm39)	nonsense	probably null
R4802:Smg5	UTSW	3	88,262,999 (GRCm39)	nonsense	probably null
R4977:Smg5	UTSW	3	88,263,032 (GRCm39)	nonsense	probably null
R5384:Smg5	UTSW	3	88,258,600 (GRCm39)	missense	probably damaging	1.00
R5443:Smg5	UTSW	3	88,261,896 (GRCm39)	missense	probably damaging	0.99
R5779:Smg5	UTSW	3	88,258,925 (GRCm39)	unclassified	probably benign
R6080:Smg5	UTSW	3	88,258,816 (GRCm39)	missense	probably benign
R6263:Smg5	UTSW	3	88,249,208 (GRCm39)	missense	possibly damaging	0.90
R6431:Smg5	UTSW	3	88,258,527 (GRCm39)	missense	probably benign	0.00
R6722:Smg5	UTSW	3	88,260,332 (GRCm39)	missense	probably damaging	0.99
R6847:Smg5	UTSW	3	88,249,859 (GRCm39)	missense	probably damaging	1.00
R6950:Smg5	UTSW	3	88,256,576 (GRCm39)	critical splice donor site	probably null
R7091:Smg5	UTSW	3	88,258,654 (GRCm39)	missense	probably benign	0.00
R7395:Smg5	UTSW	3	88,268,378 (GRCm39)	missense	probably damaging	0.99
R7678:Smg5	UTSW	3	88,261,202 (GRCm39)	missense	possibly damaging	0.93
R7796:Smg5	UTSW	3	88,256,739 (GRCm39)	missense	probably damaging	0.96
R8209:Smg5	UTSW	3	88,258,838 (GRCm39)	missense	probably benign	0.00
R8327:Smg5	UTSW	3	88,252,714 (GRCm39)	missense	probably damaging	1.00
R8987:Smg5	UTSW	3	88,267,714 (GRCm39)	critical splice donor site	probably null
R9345:Smg5	UTSW	3	88,261,848 (GRCm39)	missense	probably damaging	1.00
R9534:Smg5	UTSW	3	88,252,759 (GRCm39)	missense	probably benign	0.13
R9602:Smg5	UTSW	3	88,250,214 (GRCm39)	missense	probably damaging	1.00
Z1177:Smg5	UTSW	3	88,260,297 (GRCm39)	missense	probably benign	0.33
Z1177:Smg5	UTSW	3	88,258,441 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CTCTAAGGCTGTGGGGTAAC -3'
(R):5'- CCATTTGGAGAGCATCGGAAGG -3'

Sequencing Primer
(F):5'- AAGGCTGTGGGGTAACGTGTG -3'
(R):5'- GGCTGGTTACTAGCTATTCAAACAC -3'

Posted On

2017-02-10