Mutagenetix > Incidental Mutations

Incidental Mutation 'R1792:Rgma'

201825

Institutional Source

Beutler Lab

Gene Symbol

Rgma

Ensembl Gene

ENSMUSG00000070509

Gene Name

repulsive guidance molecule family member A

Synonyms

RGM domain family, member A

MMRRC Submission

039822-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.171) question?

Stock #

R1792 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

73375509-73419899 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 73417837 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Methionine at position 280 (T280M)

Ref Sequence

ENSEMBL: ENSMUSP00000112599 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000094312] [ENSMUST00000119206] [ENSMUST00000139780]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000094312
AA Change: T390M

PolyPhen 2 Score 0.647 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000091870
Gene: ENSMUSG00000070509
AA Change: T390M

Domain	Start	End	E-Value	Type
low complexity region	12	31	N/A	INTRINSIC
Pfam:RGM_N	48	223	6.6e-74	PFAM
Pfam:RGM_C	227	410	1.5e-75	PFAM
low complexity region	422	430	N/A	INTRINSIC
low complexity region	439	453	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000119206
AA Change: T280M

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000112599
Gene: ENSMUSG00000070509
AA Change: T280M

Domain	Start	End	E-Value	Type
Pfam:RGM_N	1	113	3.8e-45	PFAM
Pfam:RGM_C	117	302	1.8e-76	PFAM
low complexity region	312	320	N/A	INTRINSIC
low complexity region	329	343	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000139780
AA Change: T374M

PolyPhen 2 Score 0.647 (Sensitivity: 0.87; Specificity: 0.91)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205492

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.2%
20x: 92.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the repulsive guidance molecule family. The encoded protein is a glycosylphosphatidylinositol-anchored glycoprotein that functions as an axon guidance protein in the developing and adult central nervous system. This protein may also function as a tumor suppressor in some cancers. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
PHENOTYPE: Inactivation of this locus results in impaired cephalic closure and subsequent exencephaly, both with incomplete penetrance. The retinal topography of the visual system is normal in homozygous mutant mice. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca6	C	T	11: 110,184,044	V1398I	probably benign	Het
Ackr3	A	T	1: 90,214,898	N360Y	probably benign	Het
Acr	T	G	15: 89,573,143	M198R	probably benign	Het
Adamts14	A	T	10: 61,218,498	M585K	probably benign	Het
Adgrb3	A	T	1: 25,228,471	C853S	probably damaging	Het
Arhgef28	G	T	13: 97,931,186	S1410R	probably benign	Het
Armc4	T	C	18: 7,286,743	T163A	probably benign	Het
Asprv1	T	A	6: 86,628,372	F67I	possibly damaging	Het
Atp8b4	T	A	2: 126,325,294	Y1095F	probably benign	Het
Cadps	A	G	14: 12,449,802	S1136P	possibly damaging	Het
Ccdc36	A	C	9: 108,404,912	S526A	possibly damaging	Het
Ccdc57	T	C	11: 120,897,881	Q380R	possibly damaging	Het
Cdc45	A	T	16: 18,807,340	D142E	probably benign	Het
Cs	A	T	10: 128,360,079	N386Y	possibly damaging	Het
Dsc3	A	T	18: 19,986,998	V201E	probably damaging	Het
Dusp26	G	T	8: 31,091,935	R19L	probably benign	Het
Esyt3	C	A	9: 99,358,116	E92*	probably null	Het
Ext2	T	C	2: 93,704,545	N625D	probably damaging	Het
Fam208b	T	C	13: 3,590,559	K193E	possibly damaging	Het
Flvcr2	A	T	12: 85,747,155	K102*	probably null	Het
Fmnl2	T	A	2: 53,042,317	S103T	possibly damaging	Het
Fmo4	T	A	1: 162,794,290	I451F	probably benign	Het
Gak	A	T	5: 108,585,531	Y47*	probably null	Het
Gbp10	A	T	5: 105,224,300	L198Q	probably damaging	Het
Gm11559	T	A	11: 99,864,929	S135T	unknown	Het
Gm14496	A	T	2: 181,996,153	D340V	probably benign	Het
Grin2a	T	C	16: 9,992,395	T47A	possibly damaging	Het
Gtf2ird1	A	T	5: 134,366,936		probably null	Het
Herc4	T	A	10: 63,245,901	M1K	probably null	Het
Hirip3	T	A	7: 126,862,620	V29E	probably damaging	Het
Hs3st5	A	G	10: 36,832,724	D85G	probably benign	Het
Htt	T	A	5: 34,907,199	S2981T	probably damaging	Het
Il20ra	G	A	10: 19,759,636	V542I	probably damaging	Het
Itgb2l	C	A	16: 96,425,082	C603F	probably damaging	Het
Klhl41	A	C	2: 69,670,802	K202N	probably benign	Het
Lct	G	A	1: 128,327,942	S121F	possibly damaging	Het
Lhx6	C	T	2: 36,087,375	G355D	probably damaging	Het
Limk2	A	G	11: 3,358,236	V121A	probably benign	Het
Med1	T	G	11: 98,157,283	K896Q	probably damaging	Het
Muc6	A	G	7: 141,634,458	F2789S	probably benign	Het
Nemf	T	A	12: 69,312,569	Y997F	probably damaging	Het
Nrap	A	G	19: 56,379,158	S296P	probably benign	Het
Nrxn1	T	C	17: 90,588,824	N961D	probably damaging	Het
Olfr220	T	C	1: 174,448,737	V38A	probably benign	Het
Olfr398	A	C	11: 73,983,847	S254A	probably benign	Het
Olfr777	A	T	10: 129,269,243	F27I	probably benign	Het
Parp14	G	A	16: 35,856,760	A946V	probably benign	Het
Pdk4	T	A	6: 5,489,166	H247L	probably damaging	Het
Pkd1l3	T	A	8: 109,632,605	V866E	probably damaging	Het
Pla2g4e	G	A	2: 120,168,474	P803L	probably damaging	Het
Pnisr	T	C	4: 21,860,968	V217A	possibly damaging	Het
Pole4	G	A	6: 82,652,739	P34L	unknown	Het
Pole4	G	T	6: 82,652,740	P34T	unknown	Het
Ptchd3	G	A	11: 121,841,551	W422*	probably null	Het
Rab1b	C	T	19: 5,100,485	A167T	probably benign	Het
Rasal1	T	C	5: 120,664,756	M359T	probably benign	Het
Rexo4	T	C	2: 26,960,236	N310D	probably benign	Het
Rnaset2a	A	T	17: 8,145,576	I43N	probably damaging	Het
Rtcb	A	T	10: 85,942,582	V399E	probably damaging	Het
Scd4	T	G	19: 44,337,574	Y122*	probably null	Het
Sirt6	T	C	10: 81,626,521	I15V	possibly damaging	Het
Slamf8	A	T	1: 172,587,959	V104E	possibly damaging	Het
Slc12a4	A	G	8: 105,951,843	I285T	possibly damaging	Het
Slc25a13	G	A	6: 6,115,104	A207V	possibly damaging	Het
Slc6a21	T	C	7: 45,280,731	S185P	probably benign	Het
Smarcc2	A	C	10: 128,463,871	N135T	probably damaging	Het
Susd6	T	C	12: 80,874,291	S221P	probably damaging	Het
Syne1	C	T	10: 5,040,975	G8418D	probably damaging	Het
Tbc1d7	C	T	13: 43,165,377	V95I	probably benign	Het
Tcerg1l	T	C	7: 138,361,866	D225G	probably benign	Het
Tfip11	A	T	5: 112,329,397	I82F	possibly damaging	Het
Tmem41a	C	T	16: 21,936,981	G192S	probably null	Het
Trrap	G	A	5: 144,853,586	A3619T	possibly damaging	Het
Tspoap1	G	A	11: 87,765,881		probably null	Het
Wfdc21	T	C	11: 83,747,057	S11P	probably benign	Het
Zc2hc1b	A	T	10: 13,168,730	V63E	probably damaging	Het

Other mutations in Rgma

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01069:Rgma	APN	7	73417491	missense	probably damaging	1.00
IGL01089:Rgma	APN	7	73409714	missense	possibly damaging	0.79
IGL01336:Rgma	APN	7	73409318	missense	possibly damaging	0.61
IGL01339:Rgma	APN	7	73417483	missense	probably damaging	1.00
IGL01340:Rgma	APN	7	73417330	missense	probably damaging	1.00
IGL02034:Rgma	APN	7	73417433	missense	probably damaging	0.99
IGL03003:Rgma	APN	7	73417440	missense	probably damaging	0.97
IGL03050:Rgma	UTSW	7	73417515	missense	probably damaging	1.00
R0173:Rgma	UTSW	7	73417554	missense	probably damaging	1.00
R0630:Rgma	UTSW	7	73417618	missense	probably damaging	1.00
R0691:Rgma	UTSW	7	73409412	missense	probably damaging	0.99
R0696:Rgma	UTSW	7	73409412	missense	probably damaging	0.99
R0971:Rgma	UTSW	7	73391498	critical splice donor site	probably null
R1394:Rgma	UTSW	7	73417794	missense	probably benign	0.06
R1395:Rgma	UTSW	7	73417794	missense	probably benign	0.06
R1707:Rgma	UTSW	7	73417959	missense	unknown
R1731:Rgma	UTSW	7	73409412	missense	probably damaging	0.99
R2068:Rgma	UTSW	7	73409631	missense	probably damaging	0.98
R2327:Rgma	UTSW	7	73417826	missense	probably damaging	1.00
R4707:Rgma	UTSW	7	73417816	missense	probably damaging	1.00
R5976:Rgma	UTSW	7	73409468	missense	probably damaging	0.97
R6458:Rgma	UTSW	7	73409694	missense	probably damaging	1.00
R6702:Rgma	UTSW	7	73417320	missense	probably damaging	1.00
R7123:Rgma	UTSW	7	73409391	missense	probably damaging	1.00
R7767:Rgma	UTSW	7	73418004	missense	unknown
R8169:Rgma	UTSW	7	73375882	missense	probably benign	0.25
V7732:Rgma	UTSW	7	73417320	missense	probably damaging	1.00
Z1177:Rgma	UTSW	7	73409675	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGATCGACTTCCAGGCTTTC -3'
(R):5'- CATGGCCAACTGTCTACCAC -3'

Sequencing Primer
(F):5'- GACTTCCAGGCTTTCCGTGC -3'
(R):5'- TGTCTACCACAACACAGGCAGG -3'

Posted On

2014-06-23