Incidental Mutation 'R0691:Rgma'
| ID |
226039 |
| 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 |
038876-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.158)
|
| Stock # |
R0691 (G1)
|
| Quality Score |
50 |
|
Status
|
Validated
|
| Chromosome |
7 |
| 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: 99.3%
- 3x: 98.8%
- 10x: 97.5%
- 20x: 95.4%
|
| Validation Efficiency |
97% (58/60) |
| 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: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc9 |
T |
C |
6: 142,584,979 (GRCm39) |
D865G |
possibly damaging |
Het |
| Acy1 |
A |
T |
9: 106,313,070 (GRCm39) |
|
probably null |
Het |
| Adcy4 |
A |
T |
14: 56,010,104 (GRCm39) |
|
probably benign |
Het |
| Anpep |
T |
G |
7: 79,489,047 (GRCm39) |
D347A |
probably damaging |
Het |
| Arhgap28 |
C |
T |
17: 68,203,159 (GRCm39) |
|
probably null |
Het |
| Ccdc32 |
A |
G |
2: 118,857,610 (GRCm39) |
|
probably benign |
Het |
| Cdc42bpa |
A |
G |
1: 179,972,400 (GRCm39) |
T1401A |
possibly damaging |
Het |
| Celsr2 |
A |
G |
3: 108,319,939 (GRCm39) |
Y958H |
probably damaging |
Het |
| Cenpe |
A |
G |
3: 134,923,066 (GRCm39) |
E137G |
probably damaging |
Het |
| Chd8 |
T |
C |
14: 52,450,890 (GRCm39) |
D1399G |
probably damaging |
Het |
| Cntn3 |
T |
C |
6: 102,145,908 (GRCm39) |
T978A |
possibly damaging |
Het |
| Col10a1 |
A |
G |
10: 34,271,692 (GRCm39) |
T555A |
possibly damaging |
Het |
| Crybg3 |
A |
C |
16: 59,385,574 (GRCm39) |
|
probably null |
Het |
| Cts7 |
A |
G |
13: 61,503,548 (GRCm39) |
F139L |
probably damaging |
Het |
| Dera |
T |
C |
6: 137,773,745 (GRCm39) |
|
probably benign |
Het |
| Dgka |
A |
G |
10: 128,559,129 (GRCm39) |
|
probably benign |
Het |
| Dhrs7 |
T |
A |
12: 72,699,125 (GRCm39) |
I286F |
probably damaging |
Het |
| Dtwd2 |
A |
G |
18: 49,861,424 (GRCm39) |
|
probably benign |
Het |
| Fermt1 |
A |
G |
2: 132,748,653 (GRCm39) |
S657P |
probably damaging |
Het |
| Fhip2b |
T |
C |
14: 70,825,727 (GRCm39) |
D351G |
probably damaging |
Het |
| Flnb |
T |
C |
14: 7,890,810 (GRCm38) |
V564A |
probably benign |
Het |
| Garnl3 |
A |
G |
2: 32,975,919 (GRCm39) |
F16L |
probably damaging |
Het |
| Gck |
T |
C |
11: 5,856,691 (GRCm39) |
R191G |
probably damaging |
Het |
| Gucy1b1 |
A |
T |
3: 81,952,941 (GRCm39) |
|
probably benign |
Het |
| Ifna2 |
A |
C |
4: 88,601,895 (GRCm39) |
L41R |
probably damaging |
Het |
| Krt33a |
T |
G |
11: 99,903,541 (GRCm39) |
E197A |
probably damaging |
Het |
| Lce1e |
G |
A |
3: 92,615,063 (GRCm39) |
R95C |
unknown |
Het |
| Lct |
G |
T |
1: 128,235,971 (GRCm39) |
S345R |
probably benign |
Het |
| Lrp2 |
A |
T |
2: 69,281,724 (GRCm39) |
N3882K |
probably benign |
Het |
| Mcc |
G |
T |
18: 44,578,927 (GRCm39) |
T652K |
possibly damaging |
Het |
| Mier1 |
A |
G |
4: 102,996,699 (GRCm39) |
S109G |
probably benign |
Het |
| Nfat5 |
A |
G |
8: 108,082,237 (GRCm39) |
N469S |
probably damaging |
Het |
| Or1e23 |
C |
A |
11: 73,407,670 (GRCm39) |
M118I |
possibly damaging |
Het |
| Or6c214 |
G |
A |
10: 129,591,271 (GRCm39) |
T16I |
probably damaging |
Het |
| Piwil1 |
G |
T |
5: 128,820,371 (GRCm39) |
R256M |
probably null |
Het |
| Sdk2 |
T |
C |
11: 113,685,746 (GRCm39) |
|
probably null |
Het |
| Sec22b |
A |
G |
3: 97,819,990 (GRCm39) |
E94G |
probably damaging |
Het |
| Snrnp70 |
T |
C |
7: 45,036,669 (GRCm39) |
R131G |
possibly damaging |
Het |
| Spata31d1a |
A |
G |
13: 59,848,199 (GRCm39) |
S1310P |
possibly damaging |
Het |
| Spint1 |
A |
G |
2: 119,076,948 (GRCm39) |
E344G |
probably damaging |
Het |
| Srrm1 |
G |
A |
4: 135,052,302 (GRCm39) |
Q141* |
probably null |
Het |
| Tecta |
A |
T |
9: 42,295,637 (GRCm39) |
L286Q |
probably damaging |
Het |
| Tep1 |
T |
A |
14: 51,104,301 (GRCm39) |
K198* |
probably null |
Het |
| Tk2 |
A |
G |
8: 104,957,824 (GRCm39) |
V174A |
probably benign |
Het |
| Txndc5 |
T |
C |
13: 38,691,872 (GRCm39) |
K165E |
probably damaging |
Het |
| Ubr4 |
G |
A |
4: 139,151,217 (GRCm39) |
R1884Q |
probably damaging |
Het |
| Vmn2r61 |
T |
C |
7: 41,949,844 (GRCm39) |
Y755H |
probably damaging |
Het |
| Xrn1 |
T |
A |
9: 95,855,592 (GRCm39) |
H296Q |
probably damaging |
Het |
| Zar1l |
A |
T |
5: 150,436,407 (GRCm39) |
V223D |
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 |
|
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 |
|
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'- TTCTTCACTGACCACAGTGGTGC -3'
Sequencing Primer
(F):5'- GAGCGCCACGTCATCAG -3'
(R):5'- GCACCTTGCATGTCTGGAAG -3'
|
| Posted On |
2014-09-10 |
Incidental Mutation