Mutagenetix > Incidental Mutation

Incidental Mutation 'R6702:Rgma'

528815

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

044820-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.207) question?

Stock #

R6702 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

73375509-73419899 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 73417320 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 108 (T108S)

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: T218S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000091870
Gene: ENSMUSG00000070509
AA Change: T218S

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: T108S

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

SMART Domains

Protein: ENSMUSP00000112599
Gene: ENSMUSG00000070509
AA Change: T108S

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: ENSMUST00000139780
AA Change: T202S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000205492

Meta Mutation Damage Score

0.7976

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.5%

Validation Efficiency

97% (59/61)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700020N01Rik	T	A	10: 21,621,659 (GRCm38)	Y66*	probably null	Het
2810474O19Rik	T	A	6: 149,327,878 (GRCm38)	N807K	probably damaging	Het
Ak3	A	G	19: 29,026,227 (GRCm38)	V183A	probably damaging	Het
Ano10	G	T	9: 122,259,564 (GRCm38)	Q397K	possibly damaging	Het
Atg7	C	A	6: 114,671,097 (GRCm38)		probably null	Het
Brpf3	A	C	17: 28,810,659 (GRCm38)	N531T	probably benign	Het
Casp2	T	C	6: 42,268,051 (GRCm38)	V128A	probably benign	Het
Cdcp2	T	C	4: 107,107,086 (GRCm38)	C378R	probably benign	Het
Cfap54	T	A	10: 92,868,734 (GRCm38)	D2828V	unknown	Het
Col6a3	T	C	1: 90,779,439 (GRCm38)	D1984G	unknown	Het
Csnk2a1	A	G	2: 152,258,688 (GRCm38)	T93A	probably benign	Het
Ddx54	T	A	5: 120,626,503 (GRCm38)	D758E	possibly damaging	Het
Dlx2	A	G	2: 71,546,227 (GRCm38)	S56P	probably damaging	Het
Dna2	T	A	10: 62,973,294 (GRCm38)	I1055N	possibly damaging	Het
Dnah10	A	G	5: 124,805,805 (GRCm38)	Y2909C	probably damaging	Het
Dnm3	A	G	1: 162,318,687 (GRCm38)	F296L	probably benign	Het
Fat1	A	G	8: 44,953,046 (GRCm38)	T945A	probably benign	Het
Herpud1	T	C	8: 94,392,526 (GRCm38)		probably null	Het
Iqub	T	A	6: 24,449,745 (GRCm38)	N707I	probably damaging	Het
Kif26b	C	G	1: 178,917,287 (GRCm38)	S1649R	possibly damaging	Het
Lamp5	C	G	2: 136,059,563 (GRCm38)	N102K	possibly damaging	Het
Ltbr	A	G	6: 125,308,068 (GRCm38)	S290P	probably benign	Het
Map4k1	T	G	7: 29,002,396 (GRCm38)	S803A	possibly damaging	Het
Mef2c	T	A	13: 83,625,406 (GRCm38)	C134S	possibly damaging	Het
Myo15	A	G	11: 60,492,992 (GRCm38)	I1622V	probably benign	Het
Nbea	A	G	3: 56,005,502 (GRCm38)	Y955H	probably benign	Het
Ndor1	A	G	2: 25,249,890 (GRCm38)	F142S	possibly damaging	Het
Nynrin	A	G	14: 55,864,478 (GRCm38)	T535A	possibly damaging	Het
Olfr1176	G	A	2: 88,340,242 (GRCm38)	V226I	probably benign	Het
Olfr1290	T	A	2: 111,490,109 (GRCm38)		probably null	Het
Olfr205	C	T	16: 59,328,598 (GRCm38)	V304I	probably benign	Het
Olfr727	A	G	14: 50,127,231 (GRCm38)	Y218C	probably damaging	Het
Olfr916	A	T	9: 38,657,777 (GRCm38)	I205N	possibly damaging	Het
Pcdhb13	T	G	18: 37,444,775 (GRCm38)	H735Q	probably benign	Het
Pcdhb7	A	T	18: 37,341,906 (GRCm38)	M32L	probably benign	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm38)		probably benign	Het
Per2	C	T	1: 91,427,949 (GRCm38)	E696K	probably damaging	Het
Pld4	T	C	12: 112,765,051 (GRCm38)	S213P	probably damaging	Het
Prkg1	T	A	19: 30,993,084 (GRCm38)	H209L	probably benign	Het
Psg16	T	C	7: 17,090,396 (GRCm38)	L35P	probably damaging	Het
Pxn	C	T	5: 115,551,896 (GRCm38)	L160F	probably benign	Het
Rab3a	A	G	8: 70,756,448 (GRCm38)	D77G	probably damaging	Het
Rxrg	A	G	1: 167,613,805 (GRCm38)	S51G	probably benign	Het
S1pr3	A	T	13: 51,419,439 (GRCm38)	I219F	probably damaging	Het
Sec23b	A	T	2: 144,559,189 (GRCm38)		probably null	Het
Sfrp5	G	T	19: 42,201,827 (GRCm38)	T62K	probably benign	Het
Slco1a6	T	A	6: 142,103,100 (GRCm38)	Y318F	probably damaging	Het
Slit1	A	C	19: 41,614,870 (GRCm38)	S931A	possibly damaging	Het
Sorl1	A	T	9: 42,071,201 (GRCm38)	V361E	probably damaging	Het
St6galnac2	A	G	11: 116,684,387 (GRCm38)	S209P	probably benign	Het
Supt6	C	A	11: 78,231,800 (GRCm38)	R199L	possibly damaging	Het
Tas2r107	A	C	6: 131,659,384 (GRCm38)	M234R	probably benign	Het
Tmem72	C	G	6: 116,698,349 (GRCm38)	V61L	probably benign	Het
Trpm5	C	A	7: 143,069,318 (GRCm38)		probably benign	Het
Ttn	T	G	2: 76,720,112 (GRCm38)	T23282P	probably damaging	Het
Ubap2	GCCCGCTTGCCCCGCT	GCCCGCTTGCCCCGCTTGCCCCGCT	4: 41,227,210 (GRCm38)		probably benign	Het
Ubr3	A	T	2: 69,956,049 (GRCm38)	R836W	probably benign	Het
Umodl1	A	G	17: 30,986,299 (GRCm38)		probably null	Het
Ythdf1	A	G	2: 180,919,133 (GRCm38)		probably null	Het
Zfp780b	T	C	7: 27,971,641 (GRCm38)	T81A	possibly damaging	Het
Zfp811	T	C	17: 32,797,842 (GRCm38)	E407G	probably damaging	Het

Other mutations in Rgma

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01069:Rgma	APN	7	73,417,491 (GRCm38)	missense	probably damaging	1.00
IGL01089:Rgma	APN	7	73,409,714 (GRCm38)	missense	possibly damaging	0.79
IGL01336:Rgma	APN	7	73,409,318 (GRCm38)	missense	possibly damaging	0.61
IGL01339:Rgma	APN	7	73,417,483 (GRCm38)	missense	probably damaging	1.00
IGL01340:Rgma	APN	7	73,417,330 (GRCm38)	missense	probably damaging	1.00
IGL02034:Rgma	APN	7	73,417,433 (GRCm38)	missense	probably damaging	0.99
IGL03003:Rgma	APN	7	73,417,440 (GRCm38)	missense	probably damaging	0.97
IGL03050:Rgma	UTSW	7	73,417,515 (GRCm38)	missense	probably damaging	1.00
R0173:Rgma	UTSW	7	73,417,554 (GRCm38)	missense	probably damaging	1.00
R0630:Rgma	UTSW	7	73,417,618 (GRCm38)	missense	probably damaging	1.00
R0691:Rgma	UTSW	7	73,409,412 (GRCm38)	missense	probably damaging	0.99
R0696:Rgma	UTSW	7	73,409,412 (GRCm38)	missense	probably damaging	0.99
R0971:Rgma	UTSW	7	73,391,498 (GRCm38)	critical splice donor site	probably null
R1394:Rgma	UTSW	7	73,417,794 (GRCm38)	missense	probably benign	0.06
R1395:Rgma	UTSW	7	73,417,794 (GRCm38)	missense	probably benign	0.06
R1707:Rgma	UTSW	7	73,417,959 (GRCm38)	missense	unknown
R1731:Rgma	UTSW	7	73,409,412 (GRCm38)	missense	probably damaging	0.99
R1792:Rgma	UTSW	7	73,417,837 (GRCm38)	missense	probably damaging	0.97
R2068:Rgma	UTSW	7	73,409,631 (GRCm38)	missense	probably damaging	0.98
R2327:Rgma	UTSW	7	73,417,826 (GRCm38)	missense	probably damaging	1.00
R4707:Rgma	UTSW	7	73,417,816 (GRCm38)	missense	probably damaging	1.00
R5976:Rgma	UTSW	7	73,409,468 (GRCm38)	missense	probably damaging	0.97
R6458:Rgma	UTSW	7	73,409,694 (GRCm38)	missense	probably damaging	1.00
R7123:Rgma	UTSW	7	73,409,391 (GRCm38)	missense	probably damaging	1.00
R7767:Rgma	UTSW	7	73,418,004 (GRCm38)	missense	unknown
R8169:Rgma	UTSW	7	73,375,882 (GRCm38)	missense	probably benign	0.25
R8733:Rgma	UTSW	7	73,409,288 (GRCm38)	missense	possibly damaging	0.81
R8794:Rgma	UTSW	7	73,417,900 (GRCm38)	missense	probably damaging	1.00
V7732:Rgma	UTSW	7	73,417,320 (GRCm38)	missense	probably damaging	1.00
Z1177:Rgma	UTSW	7	73,409,675 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGTTATGGTAGTGAGCGAACGTTTAAG -3'
(R):5'- TACTTGGCCTGGATCTCCAC -3'

Sequencing Primer
(F):5'- GTGAGCGAACGTTTAAGTAATTTTAG -3'
(R):5'- TGGATCTCCACGTGCTGG -3'

Posted On

2018-07-24