Mutagenetix > Incidental Mutation

Incidental Mutation 'R1395:Rgma'

162804

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

039457-MU

Accession Numbers

Essential gene?

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

Stock #

R1395 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

73025268-73069647 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 73067542 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Serine at position 360 (A360S)

Ref Sequence

ENSEMBL: ENSMUSP00000145758 (fasta)

Gene Model

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

AlphaFold

Q6PCX7

Predicted Effect

probably benign
Transcript: ENSMUST00000094312
AA Change: A376S

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000091870
Gene: ENSMUSG00000070509
AA Change: A376S

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
AA Change: A266S

PolyPhen 2 Score 0.056 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000112599
Gene: ENSMUSG00000070509
AA Change: A266S

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 benign
Transcript: ENSMUST00000139780
AA Change: A360S

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205492

Meta Mutation Damage Score

0.1067

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 96.0%
20x: 92.0%

Validation Efficiency

99% (70/71)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900026A02Rik	A	G	5: 113,249,362 (GRCm39)	Y122H	probably damaging	Het
A330070K13Rik	A	G	5: 130,407,982 (GRCm39)		probably benign	Het
Abcc2	A	G	19: 43,822,379 (GRCm39)	R1406G	probably benign	Het
Adgrv1	G	T	13: 81,534,907 (GRCm39)	T5786K	probably benign	Het
Ankrd27	T	C	7: 35,315,294 (GRCm39)	F481S	possibly damaging	Het
Arhgap11a	C	T	2: 113,663,467 (GRCm39)	V939I	probably benign	Het
Arhgap12	T	C	18: 6,037,058 (GRCm39)	N561S	probably benign	Het
Arhgef12	T	C	9: 42,917,166 (GRCm39)	H391R	probably damaging	Het
Asb3	T	C	11: 31,051,032 (GRCm39)		probably benign	Het
C2cd5	T	C	6: 143,007,464 (GRCm39)		probably benign	Het
Ccdc85a	T	C	11: 28,533,412 (GRCm39)	K44R	possibly damaging	Het
Cep128	C	T	12: 91,233,754 (GRCm39)	R438Q	probably benign	Het
Cep192	A	G	18: 67,991,992 (GRCm39)	T1957A	probably damaging	Het
Col20a1	T	A	2: 180,640,400 (GRCm39)	V519E	probably damaging	Het
Cylc2	A	G	4: 51,228,366 (GRCm39)	K146E	possibly damaging	Het
Drgx	C	T	14: 32,330,326 (GRCm39)	P148S	probably benign	Het
Dst	T	C	1: 34,204,236 (GRCm39)		probably null	Het
Eef1a1	C	T	9: 78,386,300 (GRCm39)	V402I	probably benign	Het
Esyt3	T	C	9: 99,198,835 (GRCm39)		probably benign	Het
Extl3	A	G	14: 65,314,945 (GRCm39)	V79A	possibly damaging	Het
Fat3	C	T	9: 16,158,212 (GRCm39)	V1133I	probably benign	Het
Fcgbp	A	G	7: 27,792,804 (GRCm39)	H936R	probably damaging	Het
Fdxacb1	TAGAC	T	9: 50,683,796 (GRCm39)		probably null	Het
Fryl	T	C	5: 73,230,255 (GRCm39)	H1634R	probably damaging	Het
Gm44511	G	A	6: 128,797,293 (GRCm39)	S32L	possibly damaging	Het
Gm8374	G	T	14: 18,537,058 (GRCm39)	N55K	probably benign	Het
Gria1	T	A	11: 57,174,392 (GRCm39)	I558N	probably damaging	Het
Gse1	G	T	8: 121,301,738 (GRCm39)		probably benign	Het
Gtf3c3	C	T	1: 54,456,937 (GRCm39)	A488T	probably damaging	Het
Hectd4	T	C	5: 121,466,576 (GRCm39)		probably null	Het
Herc1	T	C	9: 66,346,463 (GRCm39)	I1943T	probably benign	Het
Ift172	T	C	5: 31,442,582 (GRCm39)		probably benign	Het
Ift81	G	T	5: 122,706,986 (GRCm39)	D485E	probably benign	Het
Lactb	T	C	9: 66,878,661 (GRCm39)		probably benign	Het
Map1a	C	T	2: 121,134,406 (GRCm39)	H1741Y	probably benign	Het
Map1lc3b	T	C	8: 122,323,459 (GRCm39)	Y110H	probably benign	Het
Mlh1	T	C	9: 111,076,445 (GRCm39)	D304G	probably damaging	Het
Myo1f	A	G	17: 33,802,714 (GRCm39)	D386G	probably damaging	Het
Ncoa4	T	A	14: 31,894,798 (GRCm39)		probably null	Het
Neto1	T	C	18: 86,416,144 (GRCm39)		probably benign	Het
Nf1	T	C	11: 79,426,809 (GRCm39)	V1741A	possibly damaging	Het
Nkain2	C	A	10: 32,766,185 (GRCm39)		probably benign	Het
Obsl1	T	C	1: 75,469,309 (GRCm39)	S109G	probably damaging	Het
Or51ah3	T	C	7: 103,210,326 (GRCm39)	L214P	possibly damaging	Het
Or51f23	G	A	7: 102,453,414 (GRCm39)	C243Y	possibly damaging	Het
Or6z6	T	A	7: 6,491,361 (GRCm39)	T171S	probably damaging	Het
Or9s13	T	A	1: 92,548,267 (GRCm39)	I213N	probably benign	Het
Phlpp1	T	C	1: 106,278,348 (GRCm39)	V920A	possibly damaging	Het
Psen1	G	A	12: 83,771,346 (GRCm39)	G209R	probably damaging	Het
Ralgapa2	T	G	2: 146,230,420 (GRCm39)	K963N	probably damaging	Het
Rdh12	A	G	12: 79,255,839 (GRCm39)	T9A	probably benign	Het
Sag	G	A	1: 87,756,163 (GRCm39)	V257I	probably benign	Het
Scaf1	T	C	7: 44,657,721 (GRCm39)	E386G	probably damaging	Het
Slc4a10	A	G	2: 62,143,630 (GRCm39)	E1055G	probably benign	Het
Sned1	G	A	1: 93,209,376 (GRCm39)	V830M	possibly damaging	Het
Spata31e5	T	C	1: 28,815,890 (GRCm39)	E714G	possibly damaging	Het
Spata46	A	G	1: 170,139,573 (GRCm39)	T191A	probably benign	Het
Tgm2	T	A	2: 157,966,172 (GRCm39)	H494L	probably benign	Het
Tub	C	T	7: 108,620,161 (GRCm39)	R102*	probably null	Het
Ugt3a1	T	G	15: 9,306,378 (GRCm39)	L176V	possibly damaging	Het
Vmn2r15	T	A	5: 109,442,014 (GRCm39)	I140L	probably benign	Het
Wdr44	T	G	X: 23,662,298 (GRCm39)	C645G	probably damaging	Het
Wdr87-ps	T	A	7: 29,230,812 (GRCm39)		noncoding transcript	Het
Zfp322a	C	T	13: 23,540,945 (GRCm39)	V266I	probably benign	Het
Zfp663	T	C	2: 165,194,492 (GRCm39)	R576G	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
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
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'- TGGAGATCCAGGCCAAGTACATCG -3'
(R):5'- TGTCTACCACAACACAGGCAGGAG -3'

Sequencing Primer
(F):5'- ATGCCCGAGGAGGTAGTC -3'
(R):5'- GCCAAGGGGAATgtggtg -3'

Posted On

2014-03-17