Mutagenetix > Incidental Mutation

Incidental Mutation 'R1731:Rgma'

199317

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

039763-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.158) question?

Stock #

R1731 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

73025268-73069647 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 73059160 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 88 (V88A)

Ref Sequence

ENSEMBL: ENSMUSP00000145758 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000094312] [ENSMUST00000119206] [ENSMUST00000128471] [ENSMUST00000139780]

AlphaFold

Q6PCX7

Predicted Effect

probably damaging
Transcript: ENSMUST00000094312
AA Change: V104A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000091870
Gene: ENSMUSG00000070509
AA Change: V104A

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 benign
Transcript: ENSMUST00000119206

SMART Domains

Protein: ENSMUSP00000112599
Gene: ENSMUSG00000070509

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

probably damaging
Transcript: ENSMUST00000128471
AA Change: V88A

PolyPhen 2 Score 0.985 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000116552
Gene: ENSMUSG00000070509
AA Change: V88A

Domain	Start	End	E-Value	Type
signal peptide	1	31	N/A	INTRINSIC
Pfam:RGM_N	32	101	7.5e-27	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000139780
AA Change: V88A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206096

Meta Mutation Damage Score

0.7236

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.3%
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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam7	T	A	14: 68,762,805 (GRCm39)	Y140F	probably damaging	Het
Adgrl4	T	G	3: 151,246,623 (GRCm39)	I641S	possibly damaging	Het
Aqp9	A	G	9: 71,030,250 (GRCm39)	I205T	possibly damaging	Het
Arap3	C	T	18: 38,122,965 (GRCm39)	V512I	probably benign	Het
Atf2	C	T	2: 73,675,853 (GRCm39)	G123E	probably damaging	Het
Baz1a	T	C	12: 54,965,330 (GRCm39)	D708G	possibly damaging	Het
Calcrl	A	G	2: 84,175,512 (GRCm39)		probably null	Het
Capzb	T	A	4: 139,007,341 (GRCm39)	W110R	probably damaging	Het
Casp8ap2	A	T	4: 32,641,442 (GRCm39)	N832I	possibly damaging	Het
Cecr2	T	A	6: 120,735,141 (GRCm39)	H764Q	possibly damaging	Het
Cep131	T	C	11: 119,967,742 (GRCm39)		probably null	Het
Ces2e	T	C	8: 105,656,208 (GRCm39)	V173A	probably damaging	Het
Clstn3	T	C	6: 124,408,591 (GRCm39)	D944G	probably benign	Het
Cyb5rl	C	A	4: 106,938,110 (GRCm39)	A189E	probably damaging	Het
Cyp2c40	A	G	19: 39,801,133 (GRCm39)	S41P	probably damaging	Het
Dscam	A	G	16: 96,621,076 (GRCm39)	L544P	probably damaging	Het
Epha2	A	G	4: 141,049,063 (GRCm39)	K640E	possibly damaging	Het
Erap1	T	A	13: 74,814,241 (GRCm39)	C8*	probably null	Het
Fat3	A	G	9: 15,907,233 (GRCm39)	V2923A	probably benign	Het
Fat4	A	T	3: 38,945,459 (GRCm39)	I1451F	probably damaging	Het
Fcsk	A	T	8: 111,621,455 (GRCm39)	I163N	probably damaging	Het
Fzd6	G	A	15: 38,894,722 (GRCm39)	G296D	probably damaging	Het
Gm3486	T	A	14: 41,206,492 (GRCm39)	M194L	probably benign	Het
Gm5592	C	T	7: 40,937,837 (GRCm39)	A373V	probably damaging	Het
Hectd3	T	A	4: 116,853,652 (GRCm39)		probably null	Het
Hira	T	A	16: 18,751,764 (GRCm39)	V521E	probably benign	Het
Hsd17b6	A	G	10: 127,830,348 (GRCm39)	L141S	possibly damaging	Het
Idua	A	G	5: 108,829,538 (GRCm39)	D467G	probably benign	Het
Ikzf4	G	A	10: 128,470,401 (GRCm39)	P373L	probably benign	Het
Kcng1	T	C	2: 168,110,609 (GRCm39)	E185G	probably benign	Het
Krt84	G	A	15: 101,434,398 (GRCm39)	S523F	possibly damaging	Het
Lpcat4	T	C	2: 112,074,188 (GRCm39)	L250P	probably damaging	Het
Lrrc49	A	G	9: 60,528,914 (GRCm39)	Y281H	probably damaging	Het
Mta2	C	A	19: 8,925,088 (GRCm39)		probably null	Het
Myo15b	T	C	11: 115,782,386 (GRCm39)	I372T	possibly damaging	Het
Myocd	T	A	11: 65,091,714 (GRCm39)	N76I	probably benign	Het
Nav2	T	A	7: 49,197,922 (GRCm39)	Y1123N	probably damaging	Het
Otogl	A	T	10: 107,652,972 (GRCm39)	C1127S	probably damaging	Het
Pcdhb8	A	G	18: 37,488,891 (GRCm39)	K190E	probably damaging	Het
Pcnx1	A	G	12: 82,037,478 (GRCm39)	H1918R	probably damaging	Het
Pde2a	T	A	7: 101,150,867 (GRCm39)	Y272N	probably damaging	Het
Phldb3	T	C	7: 24,318,660 (GRCm39)	V313A	probably benign	Het
Plch2	C	T	4: 155,091,451 (GRCm39)	V116I	possibly damaging	Het
Plod2	G	A	9: 92,466,657 (GRCm39)		probably null	Het
Ppfibp2	T	C	7: 107,339,796 (GRCm39)	Y730H	probably damaging	Het
Ptprh	T	C	7: 4,604,912 (GRCm39)	E44G	probably benign	Het
Rab11fip1	T	C	8: 27,642,438 (GRCm39)	E787G	probably damaging	Het
Rabep2	T	A	7: 126,043,444 (GRCm39)	L448Q	probably damaging	Het
Rbfox3	A	G	11: 118,387,762 (GRCm39)		probably null	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rnf125	A	G	18: 21,110,873 (GRCm39)	T44A	probably benign	Het
Rusc2	G	T	4: 43,426,046 (GRCm39)	A1384S	probably benign	Het
Selp	T	A	1: 163,969,009 (GRCm39)	C536*	probably null	Het
Serpinb3c	G	A	1: 107,199,504 (GRCm39)	T339I	probably damaging	Het
Slc4a5	C	T	6: 83,273,617 (GRCm39)	R986C	probably damaging	Het
Slc8b1	T	C	5: 120,659,180 (GRCm39)	I208T	probably benign	Het
Sp3	G	A	2: 72,776,999 (GRCm39)	H533Y	probably damaging	Het
Speer1e	T	A	5: 11,233,080 (GRCm39)	N14K	probably damaging	Het
Tiam2	A	G	17: 3,568,698 (GRCm39)	R1615G	probably damaging	Het
Tie1	T	C	4: 118,333,460 (GRCm39)	E802G	probably damaging	Het
Tinagl1	A	G	4: 130,061,842 (GRCm39)	V164A	probably benign	Het
Vmn1r68	A	G	7: 10,261,802 (GRCm39)	Y99H	probably damaging	Het
Vmn1r87	T	A	7: 12,865,703 (GRCm39)	T195S	possibly damaging	Het
Vmn2r56	T	C	7: 12,466,972 (GRCm39)	T21A	probably benign	Het
Zfp108	C	A	7: 23,957,964 (GRCm39)	H34Q	possibly damaging	Het
Zfp267	T	A	3: 36,218,620 (GRCm39)	F214L	probably benign	Het
Zfp456	C	T	13: 67,514,674 (GRCm39)	S344N	probably benign	Het
Zscan22	T	C	7: 12,640,907 (GRCm39)	C384R	probably 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
R1707:Rgma	UTSW	7	73,067,707 (GRCm39)	missense	unknown
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'- CCTCAAGTGCAACTCTGAGTTCTGG -3'
(R):5'- AGAATAGGGTCTCGCAACTCTCTCC -3'

Sequencing Primer
(F):5'- GAGCGCCACGTCATCAG -3'
(R):5'- GCACCTTGCATGTCTGGAAG -3'

Posted On

2014-05-23