Incidental Mutation 'R6458:Rgma'
ID |
517434 |
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 |
044593-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.158)
|
Stock # |
R6458 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
7 |
Chromosomal Location |
73025268-73069647 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to A
at 73059442 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Glutamic Acid
at position 88
(V88E)
|
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: V198E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000091870 Gene: ENSMUSG00000070509 AA Change: V198E
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: V88E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000112599 Gene: ENSMUSG00000070509 AA Change: V88E
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: V182E
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000206096
|
Meta Mutation Damage Score |
0.9186 |
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 97.8%
- 20x: 92.3%
|
Validation Efficiency |
100% (56/56) |
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: 53 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acot8 |
A |
G |
2: 164,646,655 (GRCm39) |
V28A |
possibly damaging |
Het |
Ak1 |
T |
A |
2: 32,520,385 (GRCm39) |
M61K |
probably damaging |
Het |
Akap12 |
T |
C |
10: 4,305,148 (GRCm39) |
S653P |
probably damaging |
Het |
Anapc4 |
G |
A |
5: 53,021,895 (GRCm39) |
R659H |
possibly damaging |
Het |
Arel1 |
T |
C |
12: 84,987,159 (GRCm39) |
N86D |
possibly damaging |
Het |
Bco1 |
A |
G |
8: 117,854,245 (GRCm39) |
D390G |
possibly damaging |
Het |
Ccr1l1 |
A |
T |
9: 123,778,203 (GRCm39) |
D81E |
probably damaging |
Het |
Chd1 |
A |
T |
17: 15,950,864 (GRCm39) |
N185I |
probably benign |
Het |
Clca4b |
T |
G |
3: 144,617,088 (GRCm39) |
N854T |
possibly damaging |
Het |
Col4a4 |
T |
C |
1: 82,433,546 (GRCm39) |
T1466A |
unknown |
Het |
Cxcr4 |
T |
C |
1: 128,516,831 (GRCm39) |
I277V |
probably benign |
Het |
Dgkq |
A |
G |
5: 108,802,242 (GRCm39) |
V441A |
possibly damaging |
Het |
Dnah10 |
G |
T |
5: 124,886,333 (GRCm39) |
L3030F |
probably damaging |
Het |
Epg5 |
T |
A |
18: 77,991,469 (GRCm39) |
D55E |
probably benign |
Het |
Ermap |
A |
T |
4: 119,035,337 (GRCm39) |
N550K |
probably damaging |
Het |
Fnbp1l |
A |
T |
3: 122,350,089 (GRCm39) |
I374N |
probably damaging |
Het |
Gadl1 |
T |
A |
9: 115,870,070 (GRCm39) |
*479K |
probably null |
Het |
Gm5591 |
T |
A |
7: 38,218,459 (GRCm39) |
T805S |
probably damaging |
Het |
H2-T3 |
A |
T |
17: 36,497,911 (GRCm39) |
M334K |
possibly damaging |
Het |
Ihh |
C |
T |
1: 74,985,601 (GRCm39) |
A295T |
probably damaging |
Het |
Il18r1 |
T |
A |
1: 40,530,342 (GRCm39) |
Y356* |
probably null |
Het |
Lingo3 |
A |
G |
10: 80,671,150 (GRCm39) |
V260A |
probably damaging |
Het |
Lrp2 |
T |
G |
2: 69,335,500 (GRCm39) |
M1408L |
probably benign |
Het |
Mical1 |
C |
A |
10: 41,360,731 (GRCm39) |
H657N |
probably benign |
Het |
Mpp2 |
T |
A |
11: 101,971,595 (GRCm39) |
M12L |
probably benign |
Het |
Muc16 |
A |
T |
9: 18,553,017 (GRCm39) |
D4425E |
probably benign |
Het |
Muc4 |
T |
A |
16: 32,579,694 (GRCm39) |
|
probably null |
Het |
Myt1l |
T |
A |
12: 29,945,298 (GRCm39) |
F1021Y |
unknown |
Het |
Nbas |
T |
C |
12: 13,338,750 (GRCm39) |
S197P |
probably damaging |
Het |
Nckap1 |
T |
C |
2: 80,342,893 (GRCm39) |
|
probably null |
Het |
Nek1 |
T |
G |
8: 61,553,046 (GRCm39) |
V903G |
probably benign |
Het |
Or14c43 |
A |
G |
7: 86,114,888 (GRCm39) |
I90V |
probably damaging |
Het |
Or1e18-ps1 |
T |
G |
11: 73,279,517 (GRCm39) |
S112R |
probably damaging |
Het |
Or4p22 |
T |
A |
2: 88,317,562 (GRCm39) |
I162N |
possibly damaging |
Het |
Or8b40 |
T |
C |
9: 38,027,350 (GRCm39) |
V91A |
possibly damaging |
Het |
Ppm1j |
T |
C |
3: 104,688,560 (GRCm39) |
V53A |
probably benign |
Het |
Ralgapb |
T |
A |
2: 158,286,540 (GRCm39) |
D328E |
probably damaging |
Het |
Slc30a6 |
A |
G |
17: 74,730,108 (GRCm39) |
T333A |
probably damaging |
Het |
Spr |
T |
C |
6: 85,114,039 (GRCm39) |
|
probably null |
Het |
Srek1 |
A |
T |
13: 103,880,076 (GRCm39) |
V494E |
probably benign |
Het |
Ston1 |
A |
T |
17: 88,942,731 (GRCm39) |
T46S |
probably benign |
Het |
Stox2 |
T |
C |
8: 47,645,079 (GRCm39) |
K858E |
possibly damaging |
Het |
Thoc1 |
G |
A |
18: 9,993,333 (GRCm39) |
R564Q |
probably benign |
Het |
Thoc2l |
A |
T |
5: 104,670,169 (GRCm39) |
I1564L |
probably benign |
Het |
Tmc5 |
T |
A |
7: 118,244,539 (GRCm39) |
N472K |
probably damaging |
Het |
Ttc41 |
A |
G |
10: 86,594,134 (GRCm39) |
T856A |
possibly damaging |
Het |
Ttn |
A |
T |
2: 76,608,854 (GRCm39) |
W17721R |
probably damaging |
Het |
Vmn1r69 |
A |
G |
7: 10,314,365 (GRCm39) |
I43T |
probably benign |
Het |
Vmn2r56 |
T |
A |
7: 12,427,984 (GRCm39) |
I761F |
probably damaging |
Het |
Zfp109 |
T |
C |
7: 23,927,870 (GRCm39) |
D521G |
probably benign |
Het |
Zfp516 |
A |
G |
18: 83,005,475 (GRCm39) |
H793R |
probably benign |
Het |
Zfp800 |
A |
T |
6: 28,244,215 (GRCm39) |
I250N |
probably damaging |
Het |
Zpbp |
T |
A |
11: 11,358,538 (GRCm39) |
Y243F |
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 |
|
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 |
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'- TTATGAGCCAGCACAACTGC -3'
(R):5'- GTTGGTTTATATCCCGACAAGGAATC -3'
Sequencing Primer
(F):5'- AACTGCTCCAAGGACGGC -3'
(R):5'- TTATATCCCGACAAGGAATCTCTAC -3'
|
Posted On |
2018-05-21 |