Incidental Mutation 'R4127:Rag1'
ID 315424
Institutional Source Beutler Lab
Gene Symbol Rag1
Ensembl Gene ENSMUSG00000061311
Gene Name recombination activating 1
Synonyms Rag-1
MMRRC Submission 040860-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.391) question?
Stock # R4127 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 101468627-101479846 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 101472416 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 909 (Y909H)
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 damaging
Transcript: ENSMUST00000078494
AA Change: Y909H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000077584
Gene: ENSMUSG00000061311
AA Change: Y909H

DomainStartEndE-ValueType
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
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.5%
Validation Efficiency
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: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 A G 11: 9,141,973 (GRCm39) H3R probably benign Het
Actg2 A T 6: 83,499,866 (GRCm39) F128Y possibly damaging Het
Ankrd6 G A 4: 32,822,241 (GRCm39) T176M probably damaging Het
Atp6ap1l T C 13: 91,046,826 (GRCm39) D117G probably damaging Het
Cd209b A G 8: 3,968,714 (GRCm39) I284T probably damaging Het
Cfl2 C T 12: 54,908,143 (GRCm39) A123T probably benign Het
Cgnl1 T C 9: 71,631,822 (GRCm39) T510A probably benign Het
Chn2 G T 6: 54,249,963 (GRCm39) R24M probably damaging Het
Cyfip2 T C 11: 46,161,474 (GRCm39) I339V probably benign Het
Etl4 C T 2: 20,748,886 (GRCm39) P539L possibly damaging Het
Fras1 A G 5: 96,918,512 (GRCm39) D3516G probably benign Het
Frem2 T C 3: 53,433,317 (GRCm39) Y2669C probably damaging Het
Gga2 G T 7: 121,601,943 (GRCm39) H205N probably damaging Het
Gm5592 G A 7: 40,938,491 (GRCm39) G591D probably benign Het
Gtf3c1 A T 7: 125,246,622 (GRCm39) C1562* probably null Het
Heatr3 T A 8: 88,864,939 (GRCm39) C59S probably damaging Het
Heatr5b A G 17: 79,060,603 (GRCm39) M2024T possibly damaging Het
Jarid2 T C 13: 45,055,732 (GRCm39) S313P probably damaging Het
Lzts3 A G 2: 130,477,285 (GRCm39) S502P probably damaging Het
Or5d36 A G 2: 87,901,579 (GRCm39) V49A probably benign Het
Pcdhb2 A T 18: 37,428,594 (GRCm39) D189V probably damaging Het
Pias3 G T 3: 96,606,982 (GRCm39) G82C probably damaging Het
Polg T C 7: 79,105,285 (GRCm39) E753G probably damaging Het
Pus10 T C 11: 23,668,654 (GRCm39) probably null Het
Pxn A G 5: 115,684,966 (GRCm39) R264G probably damaging Het
Rell2 A G 18: 38,091,267 (GRCm39) H144R probably benign Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Ryr2 C T 13: 11,602,323 (GRCm39) V4520I possibly damaging Het
Scp2 A G 4: 107,921,181 (GRCm39) F10L probably benign Het
Slc9b2 T C 3: 135,035,598 (GRCm39) Y356H probably benign Het
Sorcs1 T C 19: 50,210,597 (GRCm39) D756G probably benign Het
Stra6 T A 9: 58,058,501 (GRCm39) V454E probably damaging Het
Tbc1d8 T C 1: 39,411,512 (GRCm39) N1108S probably benign Het
Tep1 C T 14: 51,081,191 (GRCm39) R1349Q possibly damaging Het
Tmem132d T C 5: 128,345,884 (GRCm39) R213G probably benign Het
Ubash3a T C 17: 31,456,249 (GRCm39) Y506H probably damaging Het
Xcr1 A C 9: 123,685,561 (GRCm39) V67G probably damaging Het
Zranb2 C A 3: 157,243,227 (GRCm39) C74* probably null Het
Other mutations in Rag1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
R5209:Rag1 UTSW 2 101,474,560 (GRCm39) missense probably benign 0.01
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'- GGACTGCCTGGCATTCATTTTC -3'
(R):5'- TCATGAGGATGAATGGCAACTTTG -3'

Sequencing Primer
(F):5'- TTTCCGAAACCGTCTAAACAGCTTG -3'
(R):5'- AACTTTGCCCGGAAGCTTATGAC -3'
Posted On 2015-05-14