Mutagenetix > Incidental Mutations

Incidental Mutation 'R1539:Magel2'

171555

Institutional Source

Beutler Lab

Gene Symbol

Magel2

Ensembl Gene

ENSMUSG00000056972

Gene Name

melanoma antigen, family L, 2

Synonyms

nM15, ns7, NDNL1, Mage-l2

MMRRC Submission

039578-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R1539 (G1)

Quality Score

200

Status

Not validated

Chromosome

Chromosomal Location

62377010-62381640 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 62378809 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 487 (R487H)

Ref Sequence

ENSEMBL: ENSMUSP00000079265 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000080403]

AlphaFold

Q9QZ04

Predicted Effect

possibly damaging
Transcript: ENSMUST00000080403
AA Change: R487H

PolyPhen 2 Score 0.906 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000079265
Gene: ENSMUSG00000056972
AA Change: R487H

Domain	Start	End	E-Value	Type
low complexity region	30	49	N/A	INTRINSIC
low complexity region	51	84	N/A	INTRINSIC
internal_repeat_1	85	131	2.45e-10	PROSPERO
low complexity region	134	205	N/A	INTRINSIC
internal_repeat_1	222	298	2.45e-10	PROSPERO
internal_repeat_2	289	332	6.32e-5	PROSPERO
low complexity region	347	363	N/A	INTRINSIC
low complexity region	467	492	N/A	INTRINSIC
internal_repeat_2	494	535	6.32e-5	PROSPERO
low complexity region	560	648	N/A	INTRINSIC
low complexity region	675	686	N/A	INTRINSIC
low complexity region	761	785	N/A	INTRINSIC
low complexity region	903	920	N/A	INTRINSIC
MAGE	1059	1229	6.82e-65	SMART
low complexity region	1262	1284	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000207232

Coding Region Coverage

1x: 99.0%
3x: 97.9%
10x: 94.9%
20x: 88.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Prader-Willi syndrome (PWS) is caused by the loss of expression of imprinted genes in chromosome 15q11-q13 region. Affected individuals exhibit neonatal hypotonia, developmental delay, and childhood-onset obesity. Necdin (NDN), a gene involved in the terminal differentiation of neurons, localizes to this region of the genome and has been implicated as one of the genes responsible for the etiology of PWS. This gene is structurally similar to NDN, is also localized to the PWS chromosomal region, and is paternally imprinted, suggesting a possible role for it in PWS. [provided by RefSeq, Oct 2010]
PHENOTYPE: Mice heterozygous for a null allele that is inherited paternally exhibit some postnatal lethality, reduced male fertility, abnormal circadian rhythm, and hypoactivity. Mice heterozygous for another paternal knock-out allele exhibit 50% neonatal lethalityassociated with weak suckling activity. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 99 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1520401A03Rik	T	A	17: 23,717,144		probably benign	Het
Adgrv1	T	A	13: 81,503,978		probably null	Het
Adh7	A	C	3: 138,223,955	T131P	possibly damaging	Het
Agxt	G	A	1: 93,137,979	G190D	probably damaging	Het
AI182371	A	G	2: 35,088,803	I193T	probably damaging	Het
Akna	T	A	4: 63,379,310	T836S	probably benign	Het
Alox12	T	C	11: 70,253,243		probably null	Het
Anapc2	C	A	2: 25,273,063	T104K	probably benign	Het
Ank1	T	C	8: 23,093,919	L346P	probably damaging	Het
Ankfn1	A	T	11: 89,441,391	I443N	probably damaging	Het
Arhgef17	G	A	7: 100,890,473	T1066I	probably damaging	Het
Atg2a	C	A	19: 6,246,771		probably null	Het
Atp5s	G	A	12: 69,741,071	D94N	probably benign	Het
Bpifb5	T	A	2: 154,223,856	H24Q	probably benign	Het
Brd9	A	G	13: 73,944,743	E283G	probably damaging	Het
Cadm2	C	A	16: 66,784,840	V184F	probably damaging	Het
Casr	A	G	16: 36,495,137	V857A	probably benign	Het
Ccdc18	A	T	5: 108,191,977	Q796L	probably damaging	Het
Cep290	T	C	10: 100,496,828	V263A	probably benign	Het
Clec10a	A	T	11: 70,169,819	N167Y	probably damaging	Het
Cog1	A	G	11: 113,652,232	I189V	possibly damaging	Het
Commd2	A	G	3: 57,646,848	I144T	probably benign	Het
Cse1l	A	G	2: 166,926,372	T197A	probably benign	Het
Csmd3	A	T	15: 47,820,398	S1783R	probably benign	Het
Cxxc1	T	C	18: 74,219,207	V334A	possibly damaging	Het
Dennd2d	A	G	3: 106,486,920	I39V	probably benign	Het
Dgkz	G	A	2: 91,938,060	P734S	probably damaging	Het
Diaph3	T	C	14: 86,656,480	D31G	probably damaging	Het
Dlec1	T	C	9: 119,127,450	S731P	probably benign	Het
Dnah11	T	C	12: 117,931,256	R3619G	probably benign	Het
Doc2b	A	G	11: 75,771,957	L405P	probably damaging	Het
Dock3	A	T	9: 106,952,364	I1117N	probably damaging	Het
Dock3	G	A	9: 106,996,913	A453V	probably benign	Het
Ece2	T	A	16: 20,642,513	I474N	probably damaging	Het
Etv4	A	T	11: 101,771,687		probably null	Het
Fam171b	A	T	2: 83,880,098	M705L	probably benign	Het
Frem2	T	C	3: 53,654,210	K959E	probably benign	Het
Fyn	T	C	10: 39,532,070	M251T	possibly damaging	Het
Galnt13	G	A	2: 54,857,857	G250E	probably damaging	Het
Ggh	T	C	4: 20,054,204		probably null	Het
Glcci1	A	G	6: 8,591,620	E222G	probably damaging	Het
Gm1968	G	A	16: 29,958,841		noncoding transcript	Het
Gm3604	T	A	13: 62,371,600	I52F	possibly damaging	Het
Gm43302	T	C	5: 105,274,769	I466V	probably benign	Het
Gm9789	T	C	16: 89,158,146	S48P	unknown	Het
Gpat3	A	T	5: 100,883,388	Y136F	probably benign	Het
Gpr171	T	C	3: 59,097,721	D211G	possibly damaging	Het
Hs3st1	T	C	5: 39,614,448	K284R	probably benign	Het
Htr2a	C	T	14: 74,645,168	A198V	possibly damaging	Het
Ice1	C	A	13: 70,605,904	D688Y	probably damaging	Het
Jade1	T	C	3: 41,604,996	M504T	probably benign	Het
Lrp1	T	C	10: 127,584,381		probably null	Het
Lsr	A	T	7: 30,972,092	I72N	possibly damaging	Het
Mertk	A	G	2: 128,782,526	D619G	probably benign	Het
Myo1b	A	T	1: 51,799,563	V245E	probably damaging	Het
Myrip	T	A	9: 120,424,623	L254Q	probably benign	Het
Nav3	A	G	10: 109,767,170	S1173P	probably damaging	Het
Ncoa7	T	C	10: 30,771,729	Y17C	probably damaging	Het
Ncor2	T	C	5: 125,109,939	E7G	probably benign	Het
Ninl	A	G	2: 150,975,947	V99A	probably damaging	Het
Noct	G	T	3: 51,247,912	E34*	probably null	Het
Notch1	A	T	2: 26,472,113	Y1043*	probably null	Het
Olfr1420	T	C	19: 11,896,491	S157P	possibly damaging	Het
Olfr532	T	A	7: 140,419,413	Y120F	probably benign	Het
Olfr707	A	G	7: 106,891,276	Y278H	probably damaging	Het
Olfr794	G	A	10: 129,570,771	G39R	probably damaging	Het
Pde7b	C	A	10: 20,479,686	R104L	possibly damaging	Het
Pkn1	C	A	8: 83,670,337	R890L	possibly damaging	Het
Podn	A	T	4: 108,021,567	Y368N	probably damaging	Het
Polr1b	G	A	2: 129,118,099		probably null	Het
Ppp1r3c	A	T	19: 36,733,961	F136L	probably benign	Het
Ppp2ca	T	A	11: 52,120,973	F260Y	probably damaging	Het
Prss39	A	G	1: 34,498,535	S27G	possibly damaging	Het
Ptch1	A	G	13: 63,541,287	V340A	probably benign	Het
Ranbp17	T	C	11: 33,297,394	I246V	probably damaging	Het
Rilpl1	T	A	5: 124,515,555	D181V	probably damaging	Het
Sdk1	T	A	5: 142,094,599	V1282D	probably damaging	Het
Sh3rf2	T	C	18: 42,149,822	S514P	probably damaging	Het
Slc35f2	A	T	9: 53,809,708	I252F	possibly damaging	Het
Slc7a1	A	G	5: 148,335,593	Y425H	possibly damaging	Het
Spaca4	G	T	7: 45,725,560		probably benign	Het
Spata31d1b	T	C	13: 59,715,919	S294P	possibly damaging	Het
Ssh1	T	G	5: 113,952,003	T342P	probably damaging	Het
Stk10	T	A	11: 32,533,440	S13T	possibly damaging	Het
Tbx1	G	T	16: 18,584,093	D214E	probably benign	Het
Tdp1	A	G	12: 99,912,312	E453G	probably damaging	Het
Tlr1	T	C	5: 64,926,976	Y86C	probably damaging	Het
Tmem241	A	T	18: 12,043,240	C124S	possibly damaging	Het
Trp63	A	G	16: 25,884,849	M516V	probably benign	Het
Ttc28	T	C	5: 111,100,811	V210A	possibly damaging	Het
Tut1	C	T	19: 8,965,486	R646W	probably benign	Het
Ubald1	C	T	16: 4,876,397	E49K	possibly damaging	Het
Usp28	T	C	9: 49,037,796	Y897H	probably benign	Het
Vmn2r27	A	C	6: 124,191,771	F800C	probably damaging	Het
Vmn2r83	T	A	10: 79,491,925	M789K	probably damaging	Het
Vwa8	A	G	14: 79,062,562	D945G	probably benign	Het
Wdhd1	T	A	14: 47,245,050	K947N	possibly damaging	Het
Wdr12	A	T	1: 60,083,848		probably null	Het
Xrra1	A	T	7: 99,871,357	E57V	probably damaging	Het

Other mutations in Magel2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00948:Magel2	APN	7	62379322	missense	unknown
IGL01391:Magel2	APN	7	62380884	missense	unknown
IGL01876:Magel2	APN	7	62378827	missense	possibly damaging	0.68
IGL02613:Magel2	APN	7	62380198	missense	unknown
IGL02617:Magel2	APN	7	62380198	missense	unknown
IGL03256:Magel2	APN	7	62380414	missense	unknown
IGL03382:Magel2	APN	7	62378713	missense	probably benign	0.00
astroclast2	UTSW	7	62380159	missense	unknown
IGL02837:Magel2	UTSW	7	62378260	missense	possibly damaging	0.93
R0398:Magel2	UTSW	7	62380551	nonsense	probably null
R0463:Magel2	UTSW	7	62378030	missense	possibly damaging	0.53
R1033:Magel2	UTSW	7	62380050	missense	unknown
R1271:Magel2	UTSW	7	62381014	missense	unknown
R1518:Magel2	UTSW	7	62380440	missense	unknown
R1682:Magel2	UTSW	7	62380235	missense	unknown
R1686:Magel2	UTSW	7	62378240	missense	possibly damaging	0.53
R1782:Magel2	UTSW	7	62380857	nonsense	probably null
R1785:Magel2	UTSW	7	62377738	missense	unknown
R1786:Magel2	UTSW	7	62377738	missense	unknown
R1950:Magel2	UTSW	7	62378415	missense	possibly damaging	0.48
R2001:Magel2	UTSW	7	62379096	missense	unknown
R2002:Magel2	UTSW	7	62379096	missense	unknown
R2018:Magel2	UTSW	7	62379096	missense	unknown
R2019:Magel2	UTSW	7	62379096	missense	unknown
R2029:Magel2	UTSW	7	62380594	missense	unknown
R2070:Magel2	UTSW	7	62379096	missense	unknown
R2131:Magel2	UTSW	7	62377738	missense	unknown
R2132:Magel2	UTSW	7	62377738	missense	unknown
R2133:Magel2	UTSW	7	62377738	missense	unknown
R2134:Magel2	UTSW	7	62379096	missense	unknown
R2155:Magel2	UTSW	7	62380792	missense	unknown
R4294:Magel2	UTSW	7	62378767	missense	possibly damaging	0.86
R4591:Magel2	UTSW	7	62381089	missense	unknown
R4621:Magel2	UTSW	7	62377738	missense	unknown
R4816:Magel2	UTSW	7	62381092	missense	unknown
R4931:Magel2	UTSW	7	62380624	missense	unknown
R5031:Magel2	UTSW	7	62380104	missense	unknown
R5034:Magel2	UTSW	7	62379868	missense	unknown
R5042:Magel2	UTSW	7	62379606	missense	unknown
R5600:Magel2	UTSW	7	62379766	missense	unknown
R5769:Magel2	UTSW	7	62378113	missense	probably benign	0.02
R5980:Magel2	UTSW	7	62380596	missense	unknown
R5987:Magel2	UTSW	7	62378767	missense	probably benign	0.33
R6187:Magel2	UTSW	7	62377641	missense	unknown
R6267:Magel2	UTSW	7	62378679	missense	probably damaging	0.98
R6270:Magel2	UTSW	7	62380658	nonsense	probably null
R6316:Magel2	UTSW	7	62378719	missense	possibly damaging	0.68
R6444:Magel2	UTSW	7	62379999	missense	unknown
R6452:Magel2	UTSW	7	62380384	missense	unknown
R6797:Magel2	UTSW	7	62380159	missense	unknown
R6917:Magel2	UTSW	7	62377844	small deletion	probably benign
R7011:Magel2	UTSW	7	62378533	missense	possibly damaging	0.92
R7025:Magel2	UTSW	7	62379787	missense	unknown
R7335:Magel2	UTSW	7	62380776	missense	unknown
R7353:Magel2	UTSW	7	62379331	missense	unknown
R7413:Magel2	UTSW	7	62377844	small deletion	probably benign
R7570:Magel2	UTSW	7	62378910	missense	possibly damaging	0.53
R7714:Magel2	UTSW	7	62378382	missense	probably benign	0.08
R7836:Magel2	UTSW	7	62378368	missense	possibly damaging	0.73
R8289:Magel2	UTSW	7	62379127	missense	unknown
R8717:Magel2	UTSW	7	62377672	missense	unknown
R8903:Magel2	UTSW	7	62379693	missense	unknown
R8911:Magel2	UTSW	7	62379789	missense	unknown
R8971:Magel2	UTSW	7	62380251	missense	unknown
R9096:Magel2	UTSW	7	62380549	missense	unknown
R9264:Magel2	UTSW	7	62378596	missense	possibly damaging	0.95
RF022:Magel2	UTSW	7	62380093	missense	unknown
Z1088:Magel2	UTSW	7	62378977	missense	possibly damaging	0.53
Z1177:Magel2	UTSW	7	62379607	missense	unknown

Predicted Primers

PCR Primer
(F):5'- CCGTCAGATCCAACCTGTGATGAG -3'
(R):5'- TACCTCCTGGAACTCCAATGGCAC -3'

Sequencing Primer
(F):5'- TCCAACCTGTGATGAGGCAAG -3'
(R):5'- GAACCGGGACCTCTTGTG -3'

Posted On

2014-04-13