Mutagenetix > Incidental Mutation

Incidental Mutation 'R1707:Rgma'

190152

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

039740-MU

Accession Numbers

Essential gene?

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

Stock #

R1707 (G1)

Quality Score

203

Status

Validated

Chromosome

Chromosomal Location

73025268-73069647 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 73067707 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 415 (T415S)

Ref Sequence

ENSEMBL: ENSMUSP00000145758 (fasta)

Gene Model

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

AlphaFold

Q6PCX7

Predicted Effect

unknown
Transcript: ENSMUST00000094312
AA Change: T431S

SMART Domains

Protein: ENSMUSP00000091870
Gene: ENSMUSG00000070509
AA Change: T431S

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

unknown
Transcript: ENSMUST00000119206
AA Change: T321S

SMART Domains

Protein: ENSMUSP00000112599
Gene: ENSMUSG00000070509
AA Change: T321S

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

unknown
Transcript: ENSMUST00000139780
AA Change: T415S

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205492

Meta Mutation Damage Score

0.0869

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.9%

Validation Efficiency

96% (82/85)

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930523C07Rik	A	T	1: 159,898,372 (GRCm39)		probably benign	Het
4931429P17Rik	A	G	13: 48,114,481 (GRCm39)		noncoding transcript	Het
Acox3	T	A	5: 35,758,908 (GRCm39)	I373N	possibly damaging	Het
Adgrb1	G	T	15: 74,401,192 (GRCm39)	A63S	probably damaging	Het
Alkbh2	C	T	5: 114,262,287 (GRCm39)	E148K	probably damaging	Het
Aplp2	A	T	9: 31,062,215 (GRCm39)	H692Q	probably damaging	Het
Arhgap24	T	C	5: 103,039,953 (GRCm39)	S297P	probably benign	Het
Arhgap9	C	T	10: 127,164,758 (GRCm39)	P561S	probably benign	Het
Arhgef10l	T	G	4: 140,291,600 (GRCm39)	D62A	probably damaging	Het
Asb14	T	G	14: 26,623,079 (GRCm39)	F150L	probably benign	Het
Atp8b3	A	T	10: 80,357,635 (GRCm39)		probably null	Het
Atrnl1	A	G	19: 57,675,169 (GRCm39)	D686G	probably benign	Het
Bmpr1a	A	T	14: 34,147,098 (GRCm39)		probably benign	Het
Cc2d2a	T	A	5: 43,881,030 (GRCm39)		probably null	Het
Ccin	T	A	4: 43,983,947 (GRCm39)	I118N	probably benign	Het
Cd8b1	G	A	6: 71,303,168 (GRCm39)	G81D	probably damaging	Het
Cep126	G	A	9: 8,100,383 (GRCm39)	S717L	probably benign	Het
Cip2a	A	C	16: 48,838,767 (GRCm39)	Q861H	probably damaging	Het
Colgalt2	C	T	1: 152,276,114 (GRCm39)	R76W	probably damaging	Het
Copg1	A	T	6: 87,882,192 (GRCm39)	T596S	probably benign	Het
Cpb1	G	A	3: 20,329,655 (GRCm39)	R24W	probably damaging	Het
Csad	T	A	15: 102,088,407 (GRCm39)	D134V	probably damaging	Het
Dchs2	A	G	3: 83,034,912 (GRCm39)		probably benign	Het
Ddb2	A	G	2: 91,064,554 (GRCm39)	W119R	probably damaging	Het
Dhx57	A	T	17: 80,582,655 (GRCm39)	S317T	probably damaging	Het
Dlc1	A	G	8: 37,404,763 (GRCm39)	V342A	probably benign	Het
Dpp4	G	A	2: 62,189,679 (GRCm39)		probably benign	Het
Dst	G	T	1: 34,206,727 (GRCm39)	W1005L	probably damaging	Het
Ehmt1	T	C	2: 24,695,150 (GRCm39)	M989V	probably benign	Het
Entr1	T	A	2: 26,277,618 (GRCm39)	N69Y	probably damaging	Het
Gm5422	G	A	10: 31,124,458 (GRCm39)		noncoding transcript	Het
Gm9944	A	G	4: 144,179,833 (GRCm39)		probably benign	Het
Gtf2ird2	T	C	5: 134,245,829 (GRCm39)	Y696H	probably damaging	Het
H2-M11	T	G	17: 36,859,658 (GRCm39)	V217G	probably damaging	Het
Hunk	C	T	16: 90,183,295 (GRCm39)		probably benign	Het
Impg1	T	C	9: 80,285,799 (GRCm39)		probably null	Het
Ints11	T	G	4: 155,959,655 (GRCm39)	D87E	probably benign	Het
Intu	T	A	3: 40,595,073 (GRCm39)	S21T	probably benign	Het
Intu	C	A	3: 40,637,931 (GRCm39)	D472E	possibly damaging	Het
Kbtbd3	T	A	9: 4,316,985 (GRCm39)	N45K	probably benign	Het
Kif1c	C	T	11: 70,619,223 (GRCm39)	L953F	probably damaging	Het
Klrg2	C	G	6: 38,613,729 (GRCm39)	E91D	possibly damaging	Het
Lamc3	T	C	2: 31,802,141 (GRCm39)		probably null	Het
Magi2	T	G	5: 20,420,491 (GRCm39)	M309R	probably damaging	Het
Magohb	G	A	6: 131,261,600 (GRCm39)	P147S	probably damaging	Het
Mdn1	A	G	4: 32,693,504 (GRCm39)	D1043G	probably damaging	Het
Mtmr3	T	C	11: 4,454,095 (GRCm39)	D203G	probably damaging	Het
Mvp	C	T	7: 126,600,744 (GRCm39)	V86I	probably benign	Het
Naip5	A	T	13: 100,379,363 (GRCm39)	F226I	probably damaging	Het
Nasp	T	A	4: 116,476,133 (GRCm39)	Q51L	probably damaging	Het
Nf1	T	A	11: 79,426,430 (GRCm39)	F1594I	probably damaging	Het
Nod2	A	C	8: 89,397,104 (GRCm39)	E816A	possibly damaging	Het
Nom1	G	A	5: 29,640,316 (GRCm39)	S214N	probably damaging	Het
Or2l13b	T	C	16: 19,348,927 (GRCm39)	T248A	probably benign	Het
Or8c9	T	A	9: 38,241,197 (GRCm39)	F105I	probably damaging	Het
Parp14	A	C	16: 35,678,219 (GRCm39)	L583R	probably damaging	Het
Pclo	T	C	5: 14,763,238 (GRCm39)	S3904P	unknown	Het
Pkhd1	T	A	1: 20,621,064 (GRCm39)		probably benign	Het
Plaat1	A	G	16: 29,046,978 (GRCm39)	K166E	probably damaging	Het
Polr1e	A	C	4: 45,027,469 (GRCm39)	D233A	probably damaging	Het
Prr29	T	C	11: 106,267,509 (GRCm39)	V124A	probably damaging	Het
Rasgrp1	A	T	2: 117,129,028 (GRCm39)	V197E	probably damaging	Het
Sacs	G	T	14: 61,447,211 (GRCm39)	V3086L	probably benign	Het
Sash1	A	G	10: 8,606,141 (GRCm39)	S750P	probably benign	Het
Scpppq1	T	A	5: 104,222,099 (GRCm39)		probably benign	Het
Sema6a	A	T	18: 47,416,512 (GRCm39)	S372T	probably benign	Het
Sis	A	G	3: 72,816,420 (GRCm39)		probably benign	Het
Skint8	T	A	4: 111,796,769 (GRCm39)	V291D	probably damaging	Het
Slc12a8	A	G	16: 33,371,377 (GRCm39)	N171S	probably damaging	Het
Slc25a40	G	A	5: 8,490,793 (GRCm39)		probably null	Het
Spag6l	A	T	16: 16,598,492 (GRCm39)	I333N	probably benign	Het
Sspo	T	A	6: 48,454,811 (GRCm39)	F2999L	probably damaging	Het
Stambpl1	A	C	19: 34,216,221 (GRCm39)	T363P	probably damaging	Het
Tenm4	A	T	7: 96,537,892 (GRCm39)	N1785Y	probably damaging	Het
Tln2	C	T	9: 67,283,089 (GRCm39)	S293N	probably benign	Het
Tmed3	G	A	9: 89,584,833 (GRCm39)	L141F	probably damaging	Het
Tmem30c	G	T	16: 57,086,843 (GRCm39)	T320K	possibly damaging	Het
Tnn	T	C	1: 159,972,714 (GRCm39)	Y296C	probably damaging	Het
Ttn	C	T	2: 76,620,430 (GRCm39)	A15802T	probably damaging	Het
Usp53	T	C	3: 122,741,049 (GRCm39)	M734V	probably benign	Het
Vmn1r24	A	G	6: 57,933,497 (GRCm39)	I7T	probably benign	Het
Vmn1r74	T	A	7: 11,581,504 (GRCm39)	V268E	probably damaging	Het
Xirp1	A	T	9: 119,847,841 (GRCm39)	H347Q	possibly damaging	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
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
R2327:Rgma	UTSW	7	73,067,574 (GRCm39)	missense	probably damaging	1.00
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'- AGACATTCCCCTATGAGACAGCCG -3'
(R):5'- GCTGACTTGAGCCCTCAGACAAAAG -3'

Sequencing Primer
(F):5'- GTAGAAGACCTGTACTACCAGGC -3'
(R):5'- GCCCTCAGACAAAAGGAGAAG -3'

Posted On

2014-05-14