Mutagenetix > Incidental Mutation

Incidental Mutation 'R2327:Rgma'

245697

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

040318-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.146) question?

Stock #

R2327 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

73025268-73069647 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 73067574 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 276 (D276E)

Ref Sequence

ENSEMBL: ENSMUSP00000112599 (fasta)

Gene Model

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

AlphaFold

Q6PCX7

Predicted Effect

probably damaging
Transcript: ENSMUST00000094312
AA Change: D386E

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000091870
Gene: ENSMUSG00000070509
AA Change: D386E

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: D276E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000112599
Gene: ENSMUSG00000070509
AA Change: D276E

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: D370E

PolyPhen 2 Score 0.893 (Sensitivity: 0.82; Specificity: 0.94)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205492

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.2%
20x: 94.7%

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930578I06Rik	A	T	14: 64,208,569 (GRCm39)		probably null	Het
Agbl4	T	G	4: 111,383,798 (GRCm39)	S218A	probably benign	Het
Apol11b	T	C	15: 77,522,153 (GRCm39)	E48G	probably damaging	Het
Atp4a	T	A	7: 30,419,666 (GRCm39)	N676K	probably benign	Het
Capn5	T	A	7: 97,775,574 (GRCm39)	S456C	probably benign	Het
Ccar1	T	C	10: 62,600,161 (GRCm39)	Y590C	probably damaging	Het
Ccdc188	G	T	16: 18,037,070 (GRCm39)	G283W	probably damaging	Het
Cd69	A	G	6: 129,248,351 (GRCm39)	V45A	probably damaging	Het
Col3a1	G	T	1: 45,377,771 (GRCm39)		probably benign	Het
Cyb561a3	A	T	19: 10,564,166 (GRCm39)	T169S	probably benign	Het
Cyp2c39	A	T	19: 39,527,397 (GRCm39)	I248L	probably benign	Het
Cyp2j13	T	C	4: 95,947,344 (GRCm39)	T236A	possibly damaging	Het
Efs	A	G	14: 55,154,961 (GRCm39)	V426A	probably benign	Het
Eme2	A	G	17: 25,113,157 (GRCm39)	L136S	probably damaging	Het
Fastkd1	T	A	2: 69,535,872 (GRCm39)	K312*	probably null	Het
Fbxl12	A	G	9: 20,553,530 (GRCm39)	L19P	probably damaging	Het
Flg2	T	A	3: 93,110,913 (GRCm39)	Y980*	probably null	Het
Fscn2	T	A	11: 120,257,527 (GRCm39)	I296N	probably damaging	Het
Gabrg3	A	G	7: 56,384,835 (GRCm39)	V242A	probably benign	Het
Galk2	A	G	2: 125,817,315 (GRCm39)	H368R	probably damaging	Het
Gm12695	C	T	4: 96,657,893 (GRCm39)	S92N	probably benign	Het
Gpalpp1	A	T	14: 76,336,031 (GRCm39)	S196T	probably benign	Het
Gpld1	A	T	13: 25,168,804 (GRCm39)	M773L	probably benign	Het
Haus8	A	G	8: 71,708,289 (GRCm39)		probably null	Het
Hirip3	A	G	7: 126,462,038 (GRCm39)	R19G	probably damaging	Het
Inpp4a	A	G	1: 37,405,247 (GRCm39)	T92A	probably damaging	Het
Irgm2	A	G	11: 58,111,218 (GRCm39)	D303G	probably damaging	Het
Kpna2rt	C	A	17: 90,217,697 (GRCm39)	R16S	probably benign	Het
Krtap5-2	T	G	7: 141,728,748 (GRCm39)	S311R	unknown	Het
Krtdap	T	A	7: 30,489,185 (GRCm39)		probably null	Het
Lce1g	G	T	3: 92,658,140 (GRCm39)	S56Y	unknown	Het
Lrrn1	G	A	6: 107,545,794 (GRCm39)	V531I	probably benign	Het
Mctp2	T	C	7: 71,861,358 (GRCm39)	E429G	probably damaging	Het
Mrgpra2b	T	G	7: 47,113,793 (GRCm39)	D287A	probably damaging	Het
Mterf3	T	C	13: 67,076,258 (GRCm39)	T150A	probably damaging	Het
Mtus2	A	G	5: 148,014,725 (GRCm39)	N506S	probably benign	Het
Myh15	G	T	16: 48,963,313 (GRCm39)	V1085L	probably benign	Het
Myo9a	A	G	9: 59,687,048 (GRCm39)	N51S	probably benign	Het
Nlrc3	A	T	16: 3,771,304 (GRCm39)	L196Q	probably damaging	Het
Nlrp9c	T	A	7: 26,074,747 (GRCm39)	N816I	probably damaging	Het
Nsun2	T	C	13: 69,767,700 (GRCm39)	V218A	probably benign	Het
Nt5dc1	T	C	10: 34,189,673 (GRCm39)	E339G	possibly damaging	Het
Or10ak14	C	T	4: 118,611,331 (GRCm39)	V135I	probably benign	Het
Or51b6b	A	G	7: 103,309,779 (GRCm39)	V226A	probably damaging	Het
Or8j3c	A	T	2: 86,253,165 (GRCm39)	L285*	probably null	Het
Pik3ap1	A	G	19: 41,284,828 (GRCm39)	I619T	probably damaging	Het
Plk1	A	G	7: 121,759,118 (GRCm39)	D118G	probably benign	Het
Ppat	T	C	5: 77,070,314 (GRCm39)	D168G	possibly damaging	Het
Preb	T	C	5: 31,115,849 (GRCm39)	E198G	probably damaging	Het
Psg21	T	C	7: 18,386,378 (GRCm39)	T203A	possibly damaging	Het
Rbm17	A	G	2: 11,602,942 (GRCm39)	V54A	probably damaging	Het
Ric8a	T	C	7: 140,439,471 (GRCm39)	L77P	probably damaging	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Scarf1	A	C	11: 75,416,854 (GRCm39)	E765D	probably damaging	Het
Scart1	A	T	7: 139,803,890 (GRCm39)	N363Y	possibly damaging	Het
Sec14l4	G	A	11: 3,990,041 (GRCm39)	M113I	probably benign	Het
Senp1	C	T	15: 97,980,165 (GRCm39)	C60Y	probably damaging	Het
Slc22a21	T	A	11: 53,842,130 (GRCm39)	K549N	probably benign	Het
Slc39a10	T	C	1: 46,875,156 (GRCm39)	S49G	probably damaging	Het
Spata13	T	C	14: 60,947,004 (GRCm39)	M684T	probably damaging	Het
Spns1	T	C	7: 125,969,958 (GRCm39)	T481A	probably damaging	Het
Stag1	A	G	9: 100,668,666 (GRCm39)	Y198C	possibly damaging	Het
Tgfbr1	T	A	4: 47,402,833 (GRCm39)	V210E	probably damaging	Het
Tnc	C	T	4: 63,893,475 (GRCm39)	E1604K	possibly damaging	Het
Tspan31	T	C	10: 126,904,365 (GRCm39)	D143G	probably benign	Het
Tspan5	T	A	3: 138,603,903 (GRCm39)	Y131*	probably null	Het
Ttc21a	A	G	9: 119,795,189 (GRCm39)	D1070G	probably damaging	Het
Vmn2r26	C	T	6: 124,016,708 (GRCm39)	P391S	probably benign	Het
Vmn2r72	A	G	7: 85,387,464 (GRCm39)	I700T	probably damaging	Het
Vps13c	A	C	9: 67,821,102 (GRCm39)	N1204T	probably damaging	Het
Zfhx4	C	T	3: 5,468,418 (GRCm39)	P2859S	probably benign	Het

Other mutations in Rgma

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01069:Rgma	APN	7	73,067,239 (GRCm39)	missense	probably damaging	1.00
IGL01089:Rgma	APN	7	73,059,462 (GRCm39)	missense	possibly damaging	0.79
IGL01336:Rgma	APN	7	73,059,066 (GRCm39)	missense	possibly damaging	0.61
IGL01339:Rgma	APN	7	73,067,231 (GRCm39)	missense	probably damaging	1.00
IGL01340:Rgma	APN	7	73,067,078 (GRCm39)	missense	probably damaging	1.00
IGL02034:Rgma	APN	7	73,067,181 (GRCm39)	missense	probably damaging	0.99
IGL03003:Rgma	APN	7	73,067,188 (GRCm39)	missense	probably damaging	0.97
IGL03050:Rgma	UTSW	7	73,067,263 (GRCm39)	missense	probably damaging	1.00
R0173:Rgma	UTSW	7	73,067,302 (GRCm39)	missense	probably damaging	1.00
R0630:Rgma	UTSW	7	73,067,366 (GRCm39)	missense	probably damaging	1.00
R0691:Rgma	UTSW	7	73,059,160 (GRCm39)	missense	probably damaging	0.99
R0696:Rgma	UTSW	7	73,059,160 (GRCm39)	missense	probably damaging	0.99
R0971:Rgma	UTSW	7	73,041,246 (GRCm39)	critical splice donor site	probably null
R1394:Rgma	UTSW	7	73,067,542 (GRCm39)	missense	probably benign	0.06
R1395:Rgma	UTSW	7	73,067,542 (GRCm39)	missense	probably benign	0.06
R1707:Rgma	UTSW	7	73,067,707 (GRCm39)	missense	unknown
R1731:Rgma	UTSW	7	73,059,160 (GRCm39)	missense	probably damaging	0.99
R1792:Rgma	UTSW	7	73,067,585 (GRCm39)	missense	probably damaging	0.97
R2068:Rgma	UTSW	7	73,059,379 (GRCm39)	missense	probably damaging	0.98
R4707:Rgma	UTSW	7	73,067,564 (GRCm39)	missense	probably damaging	1.00
R5976:Rgma	UTSW	7	73,059,216 (GRCm39)	missense	probably damaging	0.97
R6458:Rgma	UTSW	7	73,059,442 (GRCm39)	missense	probably damaging	1.00
R6702:Rgma	UTSW	7	73,067,068 (GRCm39)	missense	probably damaging	1.00
R7123:Rgma	UTSW	7	73,059,139 (GRCm39)	missense	probably damaging	1.00
R7767:Rgma	UTSW	7	73,067,752 (GRCm39)	missense	unknown
R8169:Rgma	UTSW	7	73,025,630 (GRCm39)	missense	probably benign	0.25
R8733:Rgma	UTSW	7	73,059,036 (GRCm39)	missense	possibly damaging	0.81
R8794:Rgma	UTSW	7	73,067,648 (GRCm39)	missense	probably damaging	1.00
V7732:Rgma	UTSW	7	73,067,068 (GRCm39)	missense	probably damaging	1.00
Z1177:Rgma	UTSW	7	73,059,423 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATCGACTTCCAGGCTTTCCG -3'
(R):5'- TACATGGCCAACTGTCTACCAC -3'

Sequencing Primer
(F):5'- GTGCCAACGCTGAAAGC -3'
(R):5'- CCAGAAGTGGGATGGTGCC -3'

Posted On

2014-10-30