Incidental Mutation 'R5209:Rag1'
| ID |
403028 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rag1
|
| Ensembl Gene |
ENSMUSG00000061311 |
| Gene Name |
recombination activating 1 |
| Synonyms |
Rag-1 |
| MMRRC Submission |
042784-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.429)
|
| Stock # |
R5209 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
101468627-101479846 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 101474560 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 194
(Y194C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000077584
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000078494]
[ENSMUST00000160037]
[ENSMUST00000160722]
|
| AlphaFold |
P15919 |
| PDB Structure |
RAG1 DIMERIZATION DOMAIN [X-RAY DIFFRACTION]
Crystal structure of the RAG1 nonamer-binding domain with DNA [X-RAY DIFFRACTION]
Crystal structure of the RAG1 nonamer-binding domain with DNA [X-RAY DIFFRACTION]
Crystal structure of the core RAG1/2 recombinase [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000078494
AA Change: Y194C
PolyPhen 2
Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
|
| SMART Domains |
Protein: ENSMUSP00000077584
Gene: ENSMUSG00000061311
AA Change: Y194C
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RAG1_imp_bd
|
11 |
288 |
5.7e-120 |
PFAM |
|
RING
|
290 |
328 |
1.39e-3 |
SMART |
|
ZnF_C2H2
|
353 |
376 |
2.61e1 |
SMART |
|
PDB:3GNB|A
|
389 |
464 |
3e-44 |
PDB |
|
ZnF_C2H2
|
725 |
750 |
7e1 |
SMART |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160037
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160722
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177171
|
| Meta Mutation Damage Score |
0.2143 |
| Coding Region Coverage |
- 1x: 99.3%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.0%
|
| Validation Efficiency |
100% (57/57) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is involved in activation of immunoglobulin V-D-J recombination. The encoded protein is involved in recognition of the DNA substrate, but stable binding and cleavage activity also requires RAG2. Defects in this gene can be the cause of several diseases. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit arrested development of T and B cell maturation at the CD4-8- thymocyte or B220+/CD43+pro-B cell stage due to inability to undergo V(D)J recombination. [provided by MGI curators]
|
| Allele List at MGI |
All alleles(13) : Targeted(10) Chemically induced(3)
|
| Other mutations in this stock |
Total: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca14 |
T |
C |
7: 119,832,130 (GRCm39) |
V500A |
probably benign |
Het |
| Abcg4 |
A |
G |
9: 44,186,672 (GRCm39) |
Y491H |
probably damaging |
Het |
| Adgb |
C |
A |
10: 10,274,681 (GRCm39) |
V759L |
possibly damaging |
Het |
| Adprhl1 |
T |
A |
8: 13,292,563 (GRCm39) |
K243* |
probably null |
Het |
| Arhgap24 |
T |
A |
5: 103,040,015 (GRCm39) |
D317E |
probably benign |
Het |
| Arhgef5 |
A |
T |
6: 43,250,634 (GRCm39) |
I462F |
probably benign |
Het |
| Birc6 |
A |
C |
17: 74,977,369 (GRCm39) |
N4388T |
probably damaging |
Het |
| Btbd18 |
A |
G |
2: 84,498,443 (GRCm39) |
T694A |
possibly damaging |
Het |
| Ces1d |
A |
T |
8: 93,901,816 (GRCm39) |
|
probably benign |
Het |
| Chmp2a |
C |
A |
7: 12,766,601 (GRCm39) |
V106F |
probably damaging |
Het |
| Cinp |
T |
C |
12: 110,840,494 (GRCm39) |
E219G |
probably benign |
Het |
| Col5a3 |
C |
T |
9: 20,689,939 (GRCm39) |
|
probably benign |
Het |
| Dnhd1 |
T |
G |
7: 105,345,667 (GRCm39) |
S2271A |
probably benign |
Het |
| Epg5 |
T |
A |
18: 77,994,497 (GRCm39) |
L376H |
probably damaging |
Het |
| Fam81a |
T |
C |
9: 70,032,442 (GRCm39) |
T17A |
probably benign |
Het |
| Fgd2 |
T |
A |
17: 29,587,350 (GRCm39) |
|
probably null |
Het |
| Gjc3 |
C |
T |
5: 137,955,533 (GRCm39) |
V251I |
probably benign |
Het |
| Gnaz |
T |
G |
10: 74,827,823 (GRCm39) |
F192V |
probably benign |
Het |
| Hmgcr |
T |
C |
13: 96,803,020 (GRCm39) |
|
probably benign |
Het |
| Mamdc4 |
G |
T |
2: 25,456,935 (GRCm39) |
A614E |
probably damaging |
Het |
| Mapk8ip2 |
A |
T |
15: 89,343,490 (GRCm39) |
Q713L |
probably damaging |
Het |
| Mettl1 |
T |
C |
10: 126,881,203 (GRCm39) |
V238A |
possibly damaging |
Het |
| Ms4a4c |
G |
A |
19: 11,393,802 (GRCm39) |
G74E |
probably damaging |
Het |
| Msh3 |
A |
G |
13: 92,481,462 (GRCm39) |
|
probably null |
Het |
| Mtmr14 |
T |
A |
6: 113,230,736 (GRCm39) |
Y113* |
probably null |
Het |
| Mylk |
T |
C |
16: 34,742,995 (GRCm39) |
L1169P |
possibly damaging |
Het |
| Npr3 |
A |
G |
15: 11,848,689 (GRCm39) |
V426A |
possibly damaging |
Het |
| Or12d15 |
T |
C |
17: 37,693,721 (GRCm39) |
S88P |
probably damaging |
Het |
| Or5au1 |
T |
C |
14: 52,273,410 (GRCm39) |
T53A |
probably benign |
Het |
| Or6c202 |
A |
C |
10: 128,996,801 (GRCm39) |
D17E |
possibly damaging |
Het |
| Or8b1c |
T |
A |
9: 38,384,817 (GRCm39) |
M258K |
possibly damaging |
Het |
| Pcdhb17 |
T |
C |
18: 37,620,514 (GRCm39) |
F768S |
probably damaging |
Het |
| Piezo2 |
T |
C |
18: 63,166,000 (GRCm39) |
N2077S |
probably damaging |
Het |
| Pkd1l2 |
G |
A |
8: 117,783,181 (GRCm39) |
P713L |
probably benign |
Het |
| Primpol |
T |
C |
8: 47,043,295 (GRCm39) |
T333A |
probably benign |
Het |
| Pth2r |
A |
T |
1: 65,427,856 (GRCm39) |
T510S |
probably benign |
Het |
| Ptprr |
A |
T |
10: 115,998,514 (GRCm39) |
E208V |
probably damaging |
Het |
| Reep5 |
A |
T |
18: 34,490,293 (GRCm39) |
|
probably null |
Het |
| Rexo5 |
T |
A |
7: 119,433,522 (GRCm39) |
Y493* |
probably null |
Het |
| Rgs9 |
T |
C |
11: 109,130,420 (GRCm39) |
|
probably null |
Het |
| Rps6ka1 |
A |
T |
4: 133,593,129 (GRCm39) |
V218D |
probably damaging |
Het |
| Satb1 |
A |
T |
17: 52,116,235 (GRCm39) |
M16K |
probably benign |
Het |
| Slc45a2 |
C |
T |
15: 11,027,871 (GRCm39) |
T480I |
probably damaging |
Het |
| Slfn14 |
A |
G |
11: 83,170,459 (GRCm39) |
F395S |
possibly damaging |
Het |
| Spata31h1 |
T |
C |
10: 82,119,652 (GRCm39) |
T4453A |
possibly damaging |
Het |
| Sptbn5 |
T |
A |
2: 119,902,483 (GRCm39) |
I82F |
probably benign |
Het |
| Stam |
T |
A |
2: 14,151,158 (GRCm39) |
I505K |
probably benign |
Het |
| Tesk2 |
G |
A |
4: 116,581,895 (GRCm39) |
|
probably benign |
Het |
| Trappc12 |
T |
C |
12: 28,787,793 (GRCm39) |
K430R |
probably benign |
Het |
| Trmo |
T |
C |
4: 46,387,740 (GRCm39) |
N34D |
probably damaging |
Het |
| Ubr2 |
C |
A |
17: 47,279,350 (GRCm39) |
C686F |
probably damaging |
Het |
| Vdac1 |
C |
T |
11: 52,267,279 (GRCm39) |
T60I |
probably damaging |
Het |
| Zfp652 |
G |
C |
11: 95,654,491 (GRCm39) |
R478P |
possibly damaging |
Het |
|
| Other mutations in Rag1 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00940:Rag1
|
APN |
2 |
101,472,733 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01125:Rag1
|
APN |
2 |
101,472,346 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL01836:Rag1
|
APN |
2 |
101,472,239 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02216:Rag1
|
APN |
2 |
101,473,726 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
IGL02271:Rag1
|
APN |
2 |
101,473,733 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02293:Rag1
|
APN |
2 |
101,473,391 (GRCm39) |
missense |
probably benign |
0.39 |
|
IGL02601:Rag1
|
APN |
2 |
101,473,018 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Anne
|
UTSW |
2 |
101,473,861 (GRCm39) |
missense |
probably damaging |
0.99 |
|
busted
|
UTSW |
2 |
101,472,292 (GRCm39) |
missense |
probably damaging |
1.00 |
|
cloth
|
UTSW |
2 |
101,473,009 (GRCm39) |
missense |
probably damaging |
1.00 |
|
defective
|
UTSW |
2 |
101,473,055 (GRCm39) |
missense |
probably damaging |
1.00 |
|
doll
|
UTSW |
2 |
101,472,415 (GRCm39) |
missense |
probably damaging |
1.00 |
|
dysfunctional
|
UTSW |
2 |
101,474,629 (GRCm39) |
missense |
probably damaging |
1.00 |
|
furchte
|
UTSW |
2 |
101,474,852 (GRCm39) |
missense |
probably benign |
0.05 |
|
horrorshow
|
UTSW |
2 |
101,472,968 (GRCm39) |
missense |
probably damaging |
1.00 |
|
huckle
|
UTSW |
2 |
101,471,568 (GRCm39) |
intron |
probably benign |
|
|
maladaptive
|
UTSW |
2 |
101,645,647 (GRCm38) |
intron |
probably benign |
|
|
scarecrow
|
UTSW |
2 |
101,472,852 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0658:Rag1
|
UTSW |
2 |
101,473,028 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1126:Rag1
|
UTSW |
2 |
101,473,034 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1177:Rag1
|
UTSW |
2 |
101,472,623 (GRCm39) |
missense |
probably benign |
0.10 |
|
R1319:Rag1
|
UTSW |
2 |
101,473,537 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R1513:Rag1
|
UTSW |
2 |
101,473,336 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R1859:Rag1
|
UTSW |
2 |
101,474,407 (GRCm39) |
missense |
probably benign |
0.03 |
|
R2218:Rag1
|
UTSW |
2 |
101,474,491 (GRCm39) |
missense |
probably benign |
|
|
R3932:Rag1
|
UTSW |
2 |
101,473,384 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4127:Rag1
|
UTSW |
2 |
101,472,416 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4365:Rag1
|
UTSW |
2 |
101,473,288 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4620:Rag1
|
UTSW |
2 |
101,474,025 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4815:Rag1
|
UTSW |
2 |
101,473,861 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R5070:Rag1
|
UTSW |
2 |
101,472,656 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5239:Rag1
|
UTSW |
2 |
101,473,300 (GRCm39) |
missense |
possibly damaging |
0.91 |
|
R5390:Rag1
|
UTSW |
2 |
101,473,079 (GRCm39) |
missense |
probably benign |
|
|
R5607:Rag1
|
UTSW |
2 |
101,474,137 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6259:Rag1
|
UTSW |
2 |
101,474,797 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R6412:Rag1
|
UTSW |
2 |
101,472,865 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6633:Rag1
|
UTSW |
2 |
101,473,055 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6679:Rag1
|
UTSW |
2 |
101,474,629 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6723:Rag1
|
UTSW |
2 |
101,473,990 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6853:Rag1
|
UTSW |
2 |
101,472,566 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6867:Rag1
|
UTSW |
2 |
101,472,292 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6974:Rag1
|
UTSW |
2 |
101,472,137 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7071:Rag1
|
UTSW |
2 |
101,473,807 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7124:Rag1
|
UTSW |
2 |
101,474,128 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7248:Rag1
|
UTSW |
2 |
101,472,123 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7256:Rag1
|
UTSW |
2 |
101,472,415 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7567:Rag1
|
UTSW |
2 |
101,474,006 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R7581:Rag1
|
UTSW |
2 |
101,473,649 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
R7830:Rag1
|
UTSW |
2 |
101,472,404 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7941:Rag1
|
UTSW |
2 |
101,472,691 (GRCm39) |
missense |
probably benign |
0.24 |
|
R8024:Rag1
|
UTSW |
2 |
101,472,852 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8434:Rag1
|
UTSW |
2 |
101,473,009 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8688:Rag1
|
UTSW |
2 |
101,472,968 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8918:Rag1
|
UTSW |
2 |
101,472,098 (GRCm39) |
missense |
probably benign |
|
|
R9116:Rag1
|
UTSW |
2 |
101,475,137 (GRCm39) |
missense |
probably benign |
0.38 |
|
R9116:Rag1
|
UTSW |
2 |
101,472,820 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9210:Rag1
|
UTSW |
2 |
101,474,852 (GRCm39) |
missense |
probably benign |
0.05 |
|
R9409:Rag1
|
UTSW |
2 |
101,473,192 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9562:Rag1
|
UTSW |
2 |
101,473,327 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9565:Rag1
|
UTSW |
2 |
101,473,327 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9594:Rag1
|
UTSW |
2 |
101,474,701 (GRCm39) |
missense |
probably benign |
|
|
R9658:Rag1
|
UTSW |
2 |
101,473,229 (GRCm39) |
missense |
possibly damaging |
0.83 |
|
R9779:Rag1
|
UTSW |
2 |
101,474,153 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0018:Rag1
|
UTSW |
2 |
101,474,892 (GRCm39) |
missense |
probably damaging |
0.99 |
|
X0018:Rag1
|
UTSW |
2 |
101,473,942 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z1176:Rag1
|
UTSW |
2 |
101,473,604 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TGAGTTCTCTTGCGACGGTC -3'
(R):5'- ATCGTTTCAAGAGTGACGGG -3'
Sequencing Primer
(F):5'- TCCCGTCTCGCGTGGTTG -3'
(R):5'- TGGACGCTAAAACCCAAAGTCTTTTC -3'
|
| Posted On |
2016-07-22 |
Incidental Mutation