Mutagenetix > Incidental Mutation

Incidental Mutation 'R1319:Rag1'

157621

Institutional Source

Beutler Lab

Gene Symbol

Rag1

Ensembl Gene

ENSMUSG00000061311

Gene Name

recombination activating 1

Synonyms

Rag-1

MMRRC Submission

039385-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.429) question?

Stock #

R1319 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

101468627-101479846 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 101473537 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 535 (I535N)

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: I535N

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000077584
Gene: ENSMUSG00000061311
AA Change: I535N

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

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.5%
20x: 90.3%

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: 26 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam28	T	C	14: 68,846,578 (GRCm39)	E745G	probably benign	Het
Adamts12	G	T	15: 11,286,877 (GRCm39)	K827N	probably benign	Het
Ang2	T	C	14: 51,433,164 (GRCm39)	T73A	probably benign	Het
Bbs10	T	C	10: 111,134,735 (GRCm39)	L51P	probably damaging	Het
Bean1	T	C	8: 104,943,856 (GRCm39)	I137T	probably benign	Het
Cimip1	A	T	2: 173,369,716 (GRCm39)	S77C	probably damaging	Het
Cttnbp2	T	C	6: 18,434,629 (GRCm39)	T410A	probably benign	Het
Cyp4a10	A	C	4: 115,378,342 (GRCm39)	I143L	probably damaging	Het
Dlg2	A	T	7: 92,087,231 (GRCm39)	Q788L	probably damaging	Het
Epha10	G	A	4: 124,775,707 (GRCm39)	V14I	probably benign	Het
Eprs1	G	A	1: 185,117,159 (GRCm39)	D401N	probably damaging	Het
Fam169a	T	C	13: 97,234,070 (GRCm39)	V114A	probably damaging	Het
Fbn2	G	A	18: 58,333,682 (GRCm39)	P178S	possibly damaging	Het
Fcrl2	A	C	3: 87,169,484 (GRCm39)		probably null	Het
Grm1	G	T	10: 10,565,142 (GRCm39)	H1055Q	probably benign	Het
Mcm6	T	C	1: 128,276,789 (GRCm39)	N267S	probably benign	Het
Or5an1c	T	C	19: 12,218,866 (GRCm39)	D53G	probably damaging	Het
Phc3	T	C	3: 30,984,018 (GRCm39)	I699V	probably damaging	Het
Prl2c2	G	C	13: 13,176,786 (GRCm39)	T47R	probably damaging	Het
Pyroxd1	T	C	6: 142,304,874 (GRCm39)	V367A	probably benign	Het
R3hdm1	G	A	1: 128,159,142 (GRCm39)	R939H	probably benign	Het
Rhot1	T	C	11: 80,136,847 (GRCm39)	C310R	probably damaging	Het
Tnrc6a	G	A	7: 122,783,474 (GRCm39)	V1481M	probably benign	Het
Vmn1r234	A	T	17: 21,449,172 (GRCm39)	M29L	probably benign	Het
Vmn2r68	A	G	7: 84,881,700 (GRCm39)	I460T	probably damaging	Het
Zfhx3	T	A	8: 109,660,465 (GRCm39)	Y1240N	probably 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
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
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'- ACCACTGTGAAGGGACCATTCAGG -3'
(R):5'- TTAGAGGCCATCATGCAAGGCAGG -3'

Sequencing Primer
(F):5'- GGGACCATTCAGGTAGTCATC -3'
(R):5'- GGCCATCCGTGTCAATACC -3'

Posted On

2014-02-18