Mutagenetix > Incidental Mutation

Incidental Mutation 'R5976:Rgma'

471766

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

044158-MU

Accession Numbers

Essential gene?

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

Stock #

R5976 (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 73059216 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 13 (S13P)

Ref Sequence

ENSEMBL: ENSMUSP00000112599 (fasta)

Gene Model

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

AlphaFold

Q6PCX7

Predicted Effect

probably damaging
Transcript: ENSMUST00000094312
AA Change: S123P

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000091870
Gene: ENSMUSG00000070509
AA Change: S123P

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: S13P

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000112599
Gene: ENSMUSG00000070509
AA Change: S13P

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: ENSMUST00000128471

SMART Domains

Protein: ENSMUSP00000116552
Gene: ENSMUSG00000070509

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: S107P

PolyPhen 2 Score 0.969 (Sensitivity: 0.77; Specificity: 0.95)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000206096

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.0%
20x: 94.2%

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ankar	T	C	1: 72,682,450 (GRCm39)	T1154A	probably benign	Het
Ankrd26	A	T	6: 118,494,855 (GRCm39)		probably null	Het
Arih2	A	T	9: 108,485,172 (GRCm39)	*54R	probably null	Het
AW146154	T	G	7: 41,129,721 (GRCm39)	K465T	probably damaging	Het
Bend3	A	G	10: 43,386,540 (GRCm39)	Y311C	probably benign	Het
Bltp2	G	A	11: 78,174,955 (GRCm39)	A1697T	probably benign	Het
Ccdc110	A	T	8: 46,396,536 (GRCm39)	Y809F	possibly damaging	Het
Ccnh	C	T	13: 85,338,982 (GRCm39)	P76L	probably damaging	Het
Chaf1a	T	A	17: 56,371,115 (GRCm39)	C667S	probably damaging	Het
Clca3a1	A	T	3: 144,452,636 (GRCm39)	Y616N	probably damaging	Het
Cldn4	A	G	5: 134,975,410 (GRCm39)	C64R	probably damaging	Het
Crybg2	TGGAGGAGGAGGAGGAGGAG	TGGAGGAGGAGGAGGAG	4: 133,801,837 (GRCm39)		probably benign	Het
Dclk2	C	A	3: 86,694,532 (GRCm39)	R752L	possibly damaging	Het
Dzank1	C	A	2: 144,343,409 (GRCm39)	G318W	probably damaging	Het
Edem1	T	A	6: 108,819,923 (GRCm39)	I236K	probably damaging	Het
Eif4e1b	T	C	13: 54,932,635 (GRCm39)	F75L	probably damaging	Het
Elmo3	A	G	8: 106,034,279 (GRCm39)	Y266C	probably damaging	Het
Enpep	A	G	3: 129,092,773 (GRCm39)	S509P	probably damaging	Het
Exoc8	A	G	8: 125,623,392 (GRCm39)	M325T	probably benign	Het
Fah	A	G	7: 84,243,949 (GRCm39)	M270T	probably benign	Het
Gabbr1	T	C	17: 37,378,754 (GRCm39)	L532P	probably damaging	Het
Gm10770	T	A	2: 150,021,320 (GRCm39)	K66*	probably null	Het
Gprc5c	A	T	11: 114,755,313 (GRCm39)	Q330L	possibly damaging	Het
Grin3a	T	A	4: 49,792,602 (GRCm39)	H377L	probably damaging	Het
Hipk3	T	C	2: 104,301,529 (GRCm39)	E221G	probably damaging	Het
Hsd17b6	T	A	10: 127,827,308 (GRCm39)	M255L	probably benign	Het
Ighv1-7	T	A	12: 114,502,379 (GRCm39)	E29D	probably benign	Het
Ing3	T	A	6: 21,971,173 (GRCm39)	S326T	probably benign	Het
Ipo7	T	C	7: 109,648,014 (GRCm39)	L632P	probably damaging	Het
Kdm6b	A	G	11: 69,294,614 (GRCm39)		probably null	Het
Kif21a	T	G	15: 90,820,015 (GRCm39)	D1583A	probably damaging	Het
Lama2	C	T	10: 27,066,672 (GRCm39)	V1070I	probably benign	Het
Lrp1	A	T	10: 127,419,770 (GRCm39)	S946R	probably damaging	Het
Lrrc37a	A	G	11: 103,389,897 (GRCm39)	S1843P	possibly damaging	Het
Ltbp1	T	C	17: 75,597,078 (GRCm39)	Y517H	probably damaging	Het
Map2k4	T	A	11: 65,600,778 (GRCm39)	N51I	probably benign	Het
Mfsd2b	G	T	12: 4,916,522 (GRCm39)	A216D	probably damaging	Het
Nbea	T	C	3: 55,761,268 (GRCm39)	T2025A	probably benign	Het
Neb	A	G	2: 52,106,928 (GRCm39)	V4162A	possibly damaging	Het
Nr3c1	A	T	18: 39,554,602 (GRCm39)	F599I	probably damaging	Het
Nsun2	T	G	13: 69,771,271 (GRCm39)		probably null	Het
Or10ab4	T	A	7: 107,655,005 (GRCm39)	M272K	possibly damaging	Het
Or8b37	G	T	9: 37,958,997 (GRCm39)	V160F	possibly damaging	Het
Otoa	T	A	7: 120,726,936 (GRCm39)	W524R	probably benign	Het
Paip1	T	A	13: 119,593,533 (GRCm39)	D182E	probably damaging	Het
Pde1a	G	A	2: 79,698,586 (GRCm39)	Q415*	probably null	Het
Pfkfb2	T	A	1: 130,635,816 (GRCm39)	K72*	probably null	Het
Pigg	A	G	5: 108,480,057 (GRCm39)	E444G	probably null	Het
Plec	T	C	15: 76,073,237 (GRCm39)	Y669C	probably damaging	Het
Ptp4a3	T	C	15: 73,627,885 (GRCm39)	V94A	possibly damaging	Het
Ptprg	A	G	14: 12,211,625 (GRCm38)	E969G	probably damaging	Het
R3hcc1l	T	A	19: 42,551,789 (GRCm39)	V262E	probably benign	Het
Ranbp3l	T	G	15: 9,030,916 (GRCm39)	F65C	possibly damaging	Het
Rbm19	T	A	5: 120,278,372 (GRCm39)	S718R	probably benign	Het
Recql4	C	A	15: 76,593,624 (GRCm39)	R162L	probably benign	Het
Rest	T	C	5: 77,416,119 (GRCm39)	L111P	probably benign	Het
Rogdi	T	A	16: 4,831,175 (GRCm39)	I31F	probably benign	Het
Serpinb9e	T	A	13: 33,439,112 (GRCm39)	D179E	probably benign	Het
Slc1a5	T	C	7: 16,529,807 (GRCm39)	C409R	probably damaging	Het
Slc25a38	A	G	9: 119,945,613 (GRCm39)	T38A	probably damaging	Het
Spag17	C	T	3: 100,003,107 (GRCm39)	Q1897*	probably null	Het
St7	C	A	6: 17,694,221 (GRCm39)	A4E	possibly damaging	Het
Tbcel	T	A	9: 42,350,499 (GRCm39)	I263F	possibly damaging	Het
Tmtc3	A	G	10: 100,312,534 (GRCm39)	V103A	probably benign	Het
Tnc	G	A	4: 63,936,403 (GRCm39)	P178S	probably benign	Het
Vwf	A	G	6: 125,580,426 (GRCm39)	D558G		Het
Zfp541	A	G	7: 15,810,344 (GRCm39)	K127R	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
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
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'- TCAAGTGCAACTCTGAGTTCTGG -3'
(R):5'- ACCTTGCATGTCTGGAAGTGG -3'

Sequencing Primer
(F):5'- AACTCTGAGTTCTGGAGCGC -3'
(R):5'- AAGTGGTCTGTGAAAGTCCTGAG -3'

Posted On

2017-03-31