Mutagenetix > Incidental Mutation

Incidental Mutation 'R1463:Edem3'

159192

Institutional Source

Beutler Lab

Gene Symbol

Edem3

Ensembl Gene

ENSMUSG00000043019

Gene Name

ER degradation enhancer, mannosidase alpha-like 3

Synonyms

2310050N11Rik

MMRRC Submission

039517-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.296) question?

Stock #

R1463 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

151631122-151697802 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 151683261 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 646 (T646A)

Ref Sequence

ENSEMBL: ENSMUSP00000140234 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000059498] [ENSMUST00000187951] [ENSMUST00000188145] [ENSMUST00000191070]

AlphaFold

Q2HXL6

Predicted Effect

possibly damaging
Transcript: ENSMUST00000059498
AA Change: T665A

PolyPhen 2 Score 0.814 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000058941
Gene: ENSMUSG00000043019
AA Change: T665A

Domain	Start	End	E-Value	Type
signal peptide	1	34	N/A	INTRINSIC
Pfam:Glyco_hydro_47	60	499	3.5e-118	PFAM
low complexity region	635	648	N/A	INTRINSIC
Pfam:PA	672	778	9.4e-16	PFAM
low complexity region	838	855	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000187951
AA Change: T647A

PolyPhen 2 Score 0.068 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000140775
Gene: ENSMUSG00000043019
AA Change: T647A

Domain	Start	End	E-Value	Type
signal peptide	1	34	N/A	INTRINSIC
Pfam:Glyco_hydro_47	60	499	1.8e-147	PFAM
low complexity region	617	630	N/A	INTRINSIC
Pfam:PA	658	762	1.6e-17	PFAM
low complexity region	820	837	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000188145
AA Change: T665A

PolyPhen 2 Score 0.711 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000140443
Gene: ENSMUSG00000043019
AA Change: T665A

Domain	Start	End	E-Value	Type
signal peptide	1	42	N/A	INTRINSIC
Pfam:Glyco_hydro_47	60	499	3.3e-144	PFAM
low complexity region	635	648	N/A	INTRINSIC
Pfam:PA	676	780	4.3e-15	PFAM
low complexity region	854	871	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000191070
AA Change: T646A

PolyPhen 2 Score 0.814 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000140234
Gene: ENSMUSG00000043019
AA Change: T646A

Domain	Start	End	E-Value	Type
signal peptide	1	42	N/A	INTRINSIC
Pfam:Glyco_hydro_47	60	499	3e-144	PFAM
low complexity region	616	629	N/A	INTRINSIC
Pfam:PA	657	761	4.1e-15	PFAM
low complexity region	824	841	N/A	INTRINSIC

Meta Mutation Damage Score

0.0763

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 96.0%
20x: 91.6%

Validation Efficiency

97% (97/100)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Quality control in the endoplasmic reticulum (ER) ensures that only properly folded proteins are retained in the cell through recognition and degradation of misfolded or unassembled proteins. EDEM3 belongs to a group of proteins that accelerate degradation of misfolded glycoproteins in the ER (Hirao et al., 2006 [PubMed 16431915]).[supplied by OMIM, Mar 2008]

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca5	A	T	11: 110,205,384 (GRCm39)	I299N	probably damaging	Het
Abcc8	T	C	7: 45,803,936 (GRCm39)	T413A	probably benign	Het
Actc1	G	A	2: 113,880,010 (GRCm39)	S201F	probably damaging	Het
Adam30	G	A	3: 98,069,841 (GRCm39)	C558Y	probably damaging	Het
Adcy4	T	A	14: 56,016,396 (GRCm39)	I352F	probably damaging	Het
Adgrl4	A	T	3: 151,216,233 (GRCm39)	D472V	probably damaging	Het
Afap1l2	T	A	19: 56,918,583 (GRCm39)	M117L	probably benign	Het
AI597479	T	C	1: 43,152,389 (GRCm39)	V229A	probably damaging	Het
Ascc1	T	C	10: 59,898,338 (GRCm39)	V267A	probably benign	Het
Asxl3	A	G	18: 22,649,810 (GRCm39)	S600G	possibly damaging	Het
Atg14	T	C	14: 47,786,451 (GRCm39)	I268V	probably benign	Het
Bcas1	C	T	2: 170,260,584 (GRCm39)	V32I	probably benign	Het
Cacna1c	G	T	6: 118,570,955 (GRCm39)	D2106E	probably benign	Het
Cacna1i	A	G	15: 80,263,255 (GRCm39)	H1440R	possibly damaging	Het
Catsper2	G	A	2: 121,236,927 (GRCm39)	T240M	probably damaging	Het
Ccn4	T	A	15: 66,791,120 (GRCm39)	N307K	possibly damaging	Het
Cd163	A	G	6: 124,288,406 (GRCm39)	E279G	probably damaging	Het
Cdx2	C	T	5: 147,243,470 (GRCm39)	S108N	probably benign	Het
Cenpf	A	T	1: 189,386,936 (GRCm39)	N1781K	probably damaging	Het
Cgref1	T	A	5: 31,093,338 (GRCm39)		probably benign	Het
Clcn4	C	T	7: 7,299,763 (GRCm39)	W22*	probably null	Het
Cntn2	A	G	1: 132,448,875 (GRCm39)		probably null	Het
Cntn5	C	T	9: 9,673,801 (GRCm39)		probably null	Het
Cpeb3	A	G	19: 37,116,500 (GRCm39)	M377T	probably benign	Het
Cryge	T	A	1: 65,087,997 (GRCm39)	R135*	probably null	Het
Ctdsp2	C	A	10: 126,829,790 (GRCm39)		probably benign	Het
Ctsll3	G	A	13: 60,949,089 (GRCm39)		probably benign	Het
Cuzd1	C	A	7: 130,918,371 (GRCm39)	G189C	probably damaging	Het
Dmbt1	T	A	7: 130,711,366 (GRCm39)		probably null	Het
Dnai4	T	A	4: 102,944,615 (GRCm39)	L245F	possibly damaging	Het
Dnajc13	A	T	9: 104,056,139 (GRCm39)	S1587R	probably damaging	Het
Dock4	GCTCAGTGTATC	GC	12: 40,866,324 (GRCm39)		probably null	Het
Dock6	T	C	9: 21,743,202 (GRCm39)	H701R	probably damaging	Het
Esrra	A	C	19: 6,889,823 (GRCm39)	D160E	probably benign	Het
Fbn2	T	C	18: 58,143,452 (GRCm39)	T2868A	probably benign	Het
Galnt7	T	A	8: 58,105,892 (GRCm39)	M41L	probably benign	Het
Gbf1	T	C	19: 46,259,984 (GRCm39)		probably benign	Het
Glyat	A	G	19: 12,625,467 (GRCm39)	N63S	probably damaging	Het
Gm9376	A	T	14: 118,504,894 (GRCm39)	M109L	probably benign	Het
H2-M10.3	A	G	17: 36,677,612 (GRCm39)	V222A	probably damaging	Het
Ifna12	T	G	4: 88,521,193 (GRCm39)	D118A	possibly damaging	Het
Inpp5j	T	C	11: 3,451,147 (GRCm39)	M501V	probably benign	Het
Itpr3	C	T	17: 27,336,128 (GRCm39)		probably benign	Het
Ivns1abp	A	G	1: 151,237,291 (GRCm39)	N527S	probably benign	Het
Kif13a	T	C	13: 47,083,088 (GRCm39)	T4A	possibly damaging	Het
Kif3b	T	C	2: 153,172,073 (GRCm39)	*748Q	probably null	Het
Klf8	C	T	X: 152,167,677 (GRCm39)	Q241*	probably null	Het
Kras	A	T	6: 145,170,787 (GRCm39)		probably benign	Het
Lamc3	C	A	2: 31,777,423 (GRCm39)	T23K	probably benign	Het
Lrrc74b	T	A	16: 17,377,737 (GRCm39)	H47L	probably benign	Het
Ly75	A	G	2: 60,199,101 (GRCm39)		probably null	Het
Map3k21	G	A	8: 126,668,876 (GRCm39)	G821S	probably benign	Het
Mettl14	A	G	3: 123,167,722 (GRCm39)		probably benign	Het
Mettl5	T	C	2: 69,715,590 (GRCm39)		probably benign	Het
Mier3	A	G	13: 111,848,289 (GRCm39)	D301G	probably damaging	Het
Mipep	T	C	14: 61,025,595 (GRCm39)		probably benign	Het
Mmp21	T	C	7: 133,277,588 (GRCm39)		probably null	Het
Msh4	A	G	3: 153,563,207 (GRCm39)	L723P	probably damaging	Het
Muc5b	T	C	7: 141,412,817 (GRCm39)	V1921A	unknown	Het
Myo1e	G	A	9: 70,246,038 (GRCm39)	E410K	possibly damaging	Het
Nav2	T	G	7: 49,185,710 (GRCm39)	I951S	probably damaging	Het
Npc1	G	A	18: 12,324,887 (GRCm39)	T1202I	probably damaging	Het
Or10j3	A	G	1: 173,030,934 (GRCm39)	K4E	probably benign	Het
Or2ab1	A	G	11: 58,488,947 (GRCm39)	R242G	probably damaging	Het
Or5a3	C	T	19: 12,400,252 (GRCm39)	T193I	probably benign	Het
Pacc1	T	C	1: 191,060,486 (GRCm39)		probably benign	Het
Patl2	C	T	2: 121,954,216 (GRCm39)	V452M	probably benign	Het
Pcdh18	A	G	3: 49,709,854 (GRCm39)	V487A	probably damaging	Het
Pdzph1	C	T	17: 59,239,440 (GRCm39)	A963T	probably damaging	Het
Pkd1l1	C	T	11: 8,866,302 (GRCm39)	V518M	probably damaging	Het
Plcd3	A	G	11: 102,969,199 (GRCm39)	F256S	probably damaging	Het
Proc	T	C	18: 32,266,491 (GRCm39)	D112G	possibly damaging	Het
Ptges2	T	A	2: 32,290,874 (GRCm39)		probably null	Het
Pth2r	A	T	1: 65,402,436 (GRCm39)	R312W	probably damaging	Het
Pttg1ip2	C	A	5: 5,502,073 (GRCm39)		probably benign	Het
Rbbp6	C	T	7: 122,591,676 (GRCm39)	H546Y	possibly damaging	Het
Retreg2	A	G	1: 75,123,164 (GRCm39)	E364G	probably damaging	Het
Rxrb	G	A	17: 34,253,134 (GRCm39)	C185Y	probably damaging	Het
Septin2	T	A	1: 93,427,037 (GRCm39)	N133K	possibly damaging	Het
Serpina3b	T	A	12: 104,104,969 (GRCm39)	S382T	probably benign	Het
Serpinb9e	T	C	13: 33,439,099 (GRCm39)	F175S	probably benign	Het
Slc19a2	C	T	1: 164,084,766 (GRCm39)	H219Y	probably damaging	Het
Slfn9	A	T	11: 82,872,524 (GRCm39)	D737E	possibly damaging	Het
Snx31	T	C	15: 36,539,444 (GRCm39)	E144G	probably null	Het
Sp2	A	G	11: 96,854,282 (GRCm39)		probably benign	Het
Spag9	C	T	11: 94,007,663 (GRCm39)	L1117F	probably damaging	Het
Spata31e2	G	T	1: 26,721,222 (GRCm39)	Y1319*	probably null	Het
Syndig1l	A	T	12: 84,727,137 (GRCm39)		probably benign	Het
Sypl1	A	T	12: 33,024,332 (GRCm39)		probably benign	Het
Tmem169	T	C	1: 72,339,855 (GRCm39)	M95T	probably benign	Het
Tnfrsf17	A	G	16: 11,133,066 (GRCm39)	Y48C	possibly damaging	Het
Ttn	A	T	2: 76,657,859 (GRCm39)		probably benign	Het
Uap1	G	C	1: 169,977,952 (GRCm39)	H366Q	probably benign	Het
Ulbp1	A	G	10: 7,396,557 (GRCm39)		probably benign	Het
Urb2	T	C	8: 124,757,647 (GRCm39)	V1118A	probably benign	Het
Usp54	T	C	14: 20,600,258 (GRCm39)	N1493S	probably benign	Het
Vmn1r129	C	A	7: 21,094,655 (GRCm39)	V188F	probably benign	Het
Vmn1r226	A	T	17: 20,907,994 (GRCm39)	L75F	probably benign	Het
Yes1	T	A	5: 32,809,046 (GRCm39)	S137R	probably benign	Het
Zfp804b	A	G	5: 7,229,372 (GRCm39)		probably benign	Het

Other mutations in Edem3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00503:Edem3	APN	1	151,694,264 (GRCm39)	missense	probably benign
IGL01065:Edem3	APN	1	151,653,302 (GRCm39)	missense	probably damaging	1.00
IGL01351:Edem3	APN	1	151,668,136 (GRCm39)	missense	possibly damaging	0.95
IGL01451:Edem3	APN	1	151,694,379 (GRCm39)	missense	probably benign	0.21
IGL01831:Edem3	APN	1	151,671,833 (GRCm39)	missense	probably damaging	0.97
IGL02096:Edem3	APN	1	151,680,470 (GRCm39)	missense	probably benign	0.00
IGL02207:Edem3	APN	1	151,684,111 (GRCm39)	missense	possibly damaging	0.77
IGL02507:Edem3	APN	1	151,687,407 (GRCm39)	missense	probably benign	0.20
IGL02690:Edem3	APN	1	151,680,550 (GRCm39)	missense	probably damaging	1.00
Abel	UTSW	1	151,687,270 (GRCm39)	missense	probably damaging	1.00
adam	UTSW	1	151,687,347 (GRCm39)	nonsense	probably null
eve	UTSW	1	151,688,365 (GRCm39)	splice site	probably null
R0421:Edem3	UTSW	1	151,668,189 (GRCm39)	splice site	probably benign
R1934:Edem3	UTSW	1	151,680,034 (GRCm39)	missense	probably damaging	1.00
R1958:Edem3	UTSW	1	151,680,076 (GRCm39)	missense	probably damaging	1.00
R2090:Edem3	UTSW	1	151,680,577 (GRCm39)	splice site	probably benign
R2126:Edem3	UTSW	1	151,670,482 (GRCm39)	missense	possibly damaging	0.76
R2191:Edem3	UTSW	1	151,672,634 (GRCm39)	missense	probably damaging	1.00
R2211:Edem3	UTSW	1	151,680,453 (GRCm39)	missense	possibly damaging	0.74
R4005:Edem3	UTSW	1	151,635,506 (GRCm39)	missense	probably damaging	1.00
R4018:Edem3	UTSW	1	151,680,577 (GRCm39)	splice site	probably benign
R4723:Edem3	UTSW	1	151,680,449 (GRCm39)	missense	possibly damaging	0.95
R4818:Edem3	UTSW	1	151,668,136 (GRCm39)	missense	possibly damaging	0.95
R4871:Edem3	UTSW	1	151,679,982 (GRCm39)	splice site	probably null
R5205:Edem3	UTSW	1	151,687,270 (GRCm39)	missense	probably damaging	1.00
R5347:Edem3	UTSW	1	151,683,202 (GRCm39)	missense	probably damaging	0.97
R5910:Edem3	UTSW	1	151,646,578 (GRCm39)	splice site	probably null
R7021:Edem3	UTSW	1	151,631,423 (GRCm39)	missense	probably benign	0.01
R7366:Edem3	UTSW	1	151,688,365 (GRCm39)	splice site	probably null
R7481:Edem3	UTSW	1	151,683,974 (GRCm39)	missense	possibly damaging	0.46
R7481:Edem3	UTSW	1	151,683,973 (GRCm39)	missense	probably damaging	0.98
R7734:Edem3	UTSW	1	151,694,336 (GRCm39)	missense	probably benign	0.00
R7773:Edem3	UTSW	1	151,687,347 (GRCm39)	nonsense	probably null
R7828:Edem3	UTSW	1	151,687,386 (GRCm39)	missense	possibly damaging	0.51
R8556:Edem3	UTSW	1	151,660,586 (GRCm39)	missense	possibly damaging	0.77
R8559:Edem3	UTSW	1	151,694,169 (GRCm39)	missense	probably benign	0.27
R8724:Edem3	UTSW	1	151,651,624 (GRCm39)	missense	possibly damaging	0.79
R9193:Edem3	UTSW	1	151,694,270 (GRCm39)	missense	probably benign	0.00
R9201:Edem3	UTSW	1	151,694,324 (GRCm39)	missense	probably benign
X0028:Edem3	UTSW	1	151,694,313 (GRCm39)	missense	probably benign	0.24

Predicted Primers

PCR Primer
(F):5'- CTAAACCCGCCTTCAGTATCTCAGC -3'
(R):5'- GTATGTGTTTCCACCACTGAGTCCC -3'

Sequencing Primer
(F):5'- TTTCCTTCAAAGGGGAAGCC -3'
(R):5'- ACTGAGTCCCCCAACTTCTAC -3'

Posted On

2014-03-14