Incidental Mutation 'R3752:Rag2'
| ID |
271244 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Rag2
|
| Ensembl Gene |
ENSMUSG00000032864 |
| Gene Name |
recombination activating gene 2 |
| Synonyms |
Rag-2 |
| MMRRC Submission |
040737-MU
|
| Accession Numbers |
|
| Essential gene? |
Non essential
(E-score: 0.000)
|
| Stock # |
R3752 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
101455063-101462874 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 101461121 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Phenylalanine
at position 477
(Y477F)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000106858
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000044031]
[ENSMUST00000099682]
[ENSMUST00000111227]
[ENSMUST00000111231]
[ENSMUST00000128898]
[ENSMUST00000160037]
[ENSMUST00000160722]
|
| AlphaFold |
P21784 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000044031
AA Change: Y477F
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000038204
Gene: ENSMUSG00000032864
AA Change: Y477F
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RAG2
|
51 |
389 |
3.5e-179 |
PFAM |
|
Pfam:RAG2_PHD
|
414 |
491 |
7.2e-50 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000099682
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000111227
AA Change: Y477F
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000106858
Gene: ENSMUSG00000032864
AA Change: Y477F
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:RAG2
|
51 |
389 |
6.7e-193 |
PFAM |
|
Pfam:RAG2_PHD
|
414 |
491 |
1.1e-50 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000111231
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000128898
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160037
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000160722
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177171
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000177007
|
| Meta Mutation Damage Score |
0.1985 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
| Validation Efficiency |
100% (49/49) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is involved in the initiation of V(D)J recombination during B and T cell development. This protein forms a complex with the product of the adjacent recombination activating gene 1, and this complex can form double-strand breaks by cleaving DNA at conserved recombination signal sequences. The recombination activating gene 1 component is thought to contain most of the catalytic activity, while the N-terminal of the recombination activating gene 2 component is thought to form a six-bladed propeller in the active core that serves as a binding scaffold for the tight association of the complex with DNA. A C-terminal plant homeodomain finger-like motif in this protein is necessary for interactions with chromatin components, specifically with histone H3 that is trimethylated at lysine 4. Mutations in this gene cause Omenn syndrome, a form of severe combined immunodeficiency associated with autoimmune-like symptoms. [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(14) : Targeted(14)
|
| Other mutations in this stock |
Total: 48 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A830018L16Rik |
T |
A |
1: 11,588,904 (GRCm39) |
I107N |
probably damaging |
Het |
| Adh1 |
G |
A |
3: 137,994,555 (GRCm39) |
V292I |
probably benign |
Het |
| Brd1 |
C |
T |
15: 88,573,821 (GRCm39) |
V1093I |
possibly damaging |
Het |
| Cep170 |
A |
G |
1: 176,610,061 (GRCm39) |
|
probably benign |
Het |
| Col4a4 |
G |
A |
1: 82,458,215 (GRCm39) |
P1120S |
probably damaging |
Het |
| Cramp1 |
A |
T |
17: 25,190,532 (GRCm39) |
N1067K |
probably damaging |
Het |
| Dhrs7c |
A |
G |
11: 67,702,281 (GRCm39) |
T90A |
probably damaging |
Het |
| E2f1 |
C |
G |
2: 154,405,942 (GRCm39) |
G144R |
probably damaging |
Het |
| Eml6 |
C |
A |
11: 29,759,360 (GRCm39) |
V798F |
probably benign |
Het |
| Ext1 |
A |
T |
15: 52,939,306 (GRCm39) |
V581E |
probably damaging |
Het |
| Fbf1 |
C |
T |
11: 116,038,622 (GRCm39) |
R833Q |
probably benign |
Het |
| Fbln1 |
T |
A |
15: 85,111,279 (GRCm39) |
C144* |
probably null |
Het |
| Gm10521 |
A |
G |
1: 171,723,712 (GRCm39) |
T8A |
unknown |
Het |
| Hapln4 |
A |
T |
8: 70,539,615 (GRCm39) |
L215F |
probably damaging |
Het |
| Hmgcr |
T |
C |
13: 96,799,624 (GRCm39) |
I157V |
probably damaging |
Het |
| Irak4 |
T |
C |
15: 94,459,476 (GRCm39) |
I364T |
probably damaging |
Het |
| Lama3 |
T |
A |
18: 12,640,086 (GRCm39) |
C1700S |
probably damaging |
Het |
| Lama5 |
C |
T |
2: 179,829,015 (GRCm39) |
C2042Y |
probably damaging |
Het |
| Lrrc9 |
T |
G |
12: 72,507,580 (GRCm39) |
Y360* |
probably null |
Het |
| Lrrd1 |
T |
A |
5: 3,900,282 (GRCm39) |
S196T |
probably benign |
Het |
| Mdc1 |
C |
T |
17: 36,156,821 (GRCm39) |
A76V |
probably damaging |
Het |
| Mei1 |
C |
T |
15: 81,970,383 (GRCm39) |
T428M |
probably damaging |
Het |
| Mib2 |
A |
G |
4: 155,739,741 (GRCm39) |
F810S |
probably damaging |
Het |
| Nobox |
T |
G |
6: 43,284,167 (GRCm39) |
K126N |
probably damaging |
Het |
| Ogn |
C |
T |
13: 49,776,307 (GRCm39) |
L249F |
probably benign |
Het |
| Or10ag59 |
A |
G |
2: 87,406,057 (GRCm39) |
I210V |
probably benign |
Het |
| Or6a2 |
A |
T |
7: 106,600,682 (GRCm39) |
Y128* |
probably null |
Het |
| Paqr8 |
A |
G |
1: 21,005,856 (GRCm39) |
T337A |
probably benign |
Het |
| Pcdhb15 |
T |
A |
18: 37,606,810 (GRCm39) |
V14E |
probably damaging |
Het |
| Perm1 |
A |
T |
4: 156,302,403 (GRCm39) |
I316L |
probably benign |
Het |
| Plxnb2 |
G |
A |
15: 89,041,458 (GRCm39) |
|
probably benign |
Het |
| Rab3il1 |
A |
T |
19: 10,007,841 (GRCm39) |
T227S |
probably benign |
Het |
| Ralgapa2 |
A |
T |
2: 146,263,551 (GRCm39) |
V722E |
possibly damaging |
Het |
| Rbp3 |
A |
T |
14: 33,677,969 (GRCm39) |
E639V |
probably damaging |
Het |
| Sh2b1 |
A |
G |
7: 126,067,959 (GRCm39) |
V565A |
probably damaging |
Het |
| Skint6 |
T |
C |
4: 112,700,096 (GRCm39) |
|
probably benign |
Het |
| Slc47a1 |
C |
T |
11: 61,235,207 (GRCm39) |
R542Q |
possibly damaging |
Het |
| Slc6a5 |
T |
C |
7: 49,586,062 (GRCm39) |
|
probably null |
Het |
| Slc9a8 |
C |
A |
2: 167,299,272 (GRCm39) |
H215N |
probably benign |
Het |
| Slit1 |
C |
T |
19: 41,635,406 (GRCm39) |
|
probably null |
Het |
| Snx1 |
A |
T |
9: 66,012,933 (GRCm39) |
|
probably null |
Het |
| Tbc1d30 |
T |
A |
10: 121,108,073 (GRCm39) |
N443I |
probably damaging |
Het |
| Tex15 |
T |
A |
8: 34,061,443 (GRCm39) |
M565K |
probably benign |
Het |
| Traf3ip1 |
T |
C |
1: 91,428,639 (GRCm39) |
|
probably benign |
Het |
| Traf3ip1 |
A |
G |
1: 91,446,019 (GRCm39) |
D384G |
probably damaging |
Het |
| Vldlr |
G |
A |
19: 27,215,731 (GRCm39) |
E243K |
probably damaging |
Het |
| Vps35 |
A |
G |
8: 86,001,460 (GRCm39) |
S453P |
probably benign |
Het |
| Zfp644 |
A |
G |
5: 106,784,249 (GRCm39) |
V766A |
probably benign |
Het |
|
| Other mutations in Rag2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00647:Rag2
|
APN |
2 |
101,460,962 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL01358:Rag2
|
APN |
2 |
101,460,365 (GRCm39) |
missense |
possibly damaging |
0.95 |
|
IGL01774:Rag2
|
APN |
2 |
101,460,392 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02267:Rag2
|
APN |
2 |
101,460,376 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02507:Rag2
|
APN |
2 |
101,461,055 (GRCm39) |
missense |
probably damaging |
0.99 |
|
IGL02615:Rag2
|
APN |
2 |
101,459,913 (GRCm39) |
nonsense |
probably null |
|
|
IGL02690:Rag2
|
APN |
2 |
101,459,839 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03087:Rag2
|
APN |
2 |
101,460,559 (GRCm39) |
missense |
probably benign |
0.00 |
|
IGL03261:Rag2
|
APN |
2 |
101,460,608 (GRCm39) |
missense |
probably damaging |
0.96 |
|
billfold
|
UTSW |
2 |
101,461,118 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Brag
|
UTSW |
2 |
101,460,040 (GRCm39) |
missense |
probably damaging |
1.00 |
|
excambiar
|
UTSW |
2 |
101,461,121 (GRCm39) |
missense |
probably damaging |
0.99 |
|
picker
|
UTSW |
2 |
101,460,419 (GRCm39) |
missense |
probably damaging |
1.00 |
|
snowcock
|
UTSW |
2 |
101,460,948 (GRCm39) |
missense |
probably damaging |
1.00 |
|
woodcock
|
UTSW |
2 |
101,460,464 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R0266:Rag2
|
UTSW |
2 |
101,460,948 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0284:Rag2
|
UTSW |
2 |
101,460,464 (GRCm39) |
missense |
probably damaging |
0.98 |
|
R1250:Rag2
|
UTSW |
2 |
101,460,784 (GRCm39) |
missense |
probably damaging |
0.96 |
|
R1520:Rag2
|
UTSW |
2 |
101,460,476 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R1641:Rag2
|
UTSW |
2 |
101,459,960 (GRCm39) |
missense |
probably benign |
0.22 |
|
R2260:Rag2
|
UTSW |
2 |
101,460,583 (GRCm39) |
missense |
probably benign |
0.00 |
|
R2571:Rag2
|
UTSW |
2 |
101,460,312 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R3441:Rag2
|
UTSW |
2 |
101,460,645 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R4894:Rag2
|
UTSW |
2 |
101,460,022 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5197:Rag2
|
UTSW |
2 |
101,461,085 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R5236:Rag2
|
UTSW |
2 |
101,460,005 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6815:Rag2
|
UTSW |
2 |
101,460,900 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R7365:Rag2
|
UTSW |
2 |
101,461,118 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7917:Rag2
|
UTSW |
2 |
101,460,040 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9026:Rag2
|
UTSW |
2 |
101,460,494 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R9243:Rag2
|
UTSW |
2 |
101,460,419 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9280:Rag2
|
UTSW |
2 |
101,460,145 (GRCm39) |
missense |
probably benign |
0.05 |
|
R9333:Rag2
|
UTSW |
2 |
101,460,752 (GRCm39) |
missense |
probably benign |
0.01 |
|
R9500:Rag2
|
UTSW |
2 |
101,461,217 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0027:Rag2
|
UTSW |
2 |
101,460,718 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Z31818:Rag2
|
UTSW |
2 |
101,461,150 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GAAGATGACGAGTCTGTAACCG -3'
(R):5'- GCAATATACCTGAGTCTGAGGGG -3'
Sequencing Primer
(F):5'- GTCTGTAACCGGCTACTGGATAAC -3'
(R):5'- CTGAGGGGCTTTTGCTAAATTAATC -3'
|
| Posted On |
2015-03-18 |
Incidental Mutation