Mutagenetix > Incidental Mutation

Incidental Mutation 'R9409:Rag1'

711701

Institutional Source

Beutler Lab

Gene Symbol

Rag1

Ensembl Gene

ENSMUSG00000061311

Gene Name

recombination activating 1

Synonyms

Rag-1

MMRRC Submission

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.391) question?

Stock #

R9409 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

101468627-101479846 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 101473192 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 650 (L650Q)

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: L650Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000077584
Gene: ENSMUSG00000061311
AA Change: L650Q

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

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: 32 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030K09Rik	A	T	8: 73,211,888 (GRCm39)	I538F	possibly damaging	Het
Arih2	C	G	9: 108,488,938 (GRCm39)	R260P	probably damaging	Het
Ccdc138	A	G	10: 58,374,135 (GRCm39)	H385R	probably damaging	Het
Cep43	T	C	17: 8,411,088 (GRCm39)	V367A	probably benign	Het
Cfhr1	T	C	1: 139,478,704 (GRCm39)	D222G	probably benign	Het
Cpb2	A	T	14: 75,505,522 (GRCm39)	I173F	probably damaging	Het
Creb3l1	C	T	2: 91,822,231 (GRCm39)		probably null	Het
Ebf2	T	C	14: 67,472,665 (GRCm39)	S28P	probably damaging	Het
Eomes	A	T	9: 118,314,069 (GRCm39)	T705S	probably benign	Het
Fbxo15	T	A	18: 84,977,246 (GRCm39)	W98R	possibly damaging	Het
Gm12258	T	C	11: 58,745,119 (GRCm39)	F17L		Het
Grin2c	C	T	11: 115,144,106 (GRCm39)	R697H	probably benign	Het
Ighmbp2	C	A	19: 3,318,832 (GRCm39)	A415S	possibly damaging	Het
Il6st	C	G	13: 112,640,872 (GRCm39)	Q883E	probably benign	Het
Med17	T	C	9: 15,176,695 (GRCm39)	M511V	probably benign	Het
Or2n1d	A	T	17: 38,646,320 (GRCm39)	T91S	possibly damaging	Het
Or8b39	G	A	9: 37,996,584 (GRCm39)	G151R	probably damaging	Het
Pacrg	A	T	17: 10,996,065 (GRCm39)	I67N	probably damaging	Het
Pam	A	G	1: 97,749,585 (GRCm39)	S964P	probably damaging	Het
Pcdh15	A	G	10: 74,160,190 (GRCm39)	T436A	probably damaging	Het
Pgap4	T	A	4: 49,586,043 (GRCm39)	E375V	probably damaging	Het
Rhobtb1	A	T	10: 69,106,217 (GRCm39)	T323S	probably benign	Het
Rhot2	T	C	17: 26,060,085 (GRCm39)	T299A	probably benign	Het
Rnf180	CGAGG	CGAGGAGG	13: 105,386,781 (GRCm39)		probably benign	Het
Ryr2	C	A	13: 11,695,973 (GRCm39)	V2965F	probably damaging	Het
Serpina1b	A	T	12: 103,694,607 (GRCm39)	M379K	probably benign	Het
Serpinb9	A	G	13: 33,192,797 (GRCm39)	Q118R	probably benign	Het
Slc16a14	G	A	1: 84,907,116 (GRCm39)	Q53*	probably null	Het
Tas2r130	T	A	6: 131,607,660 (GRCm39)	D45V	probably damaging	Het
Tie1	T	C	4: 118,339,945 (GRCm39)	N361D	probably damaging	Het
Tmtc2	G	T	10: 105,159,419 (GRCm39)	L560M	probably damaging	Het
Trav13-5	G	T	14: 54,033,277 (GRCm39)	R62L	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
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
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'- ATCCAGTGCCCCTGAAGATG -3'
(R):5'- ATCTTGGAAGGCATGAGATCCC -3'

Sequencing Primer
(F):5'- GAATTTAAAAGTCCTGGGGATGCCTC -3'
(R):5'- CCCTTCACAGTGGTGGTAAAG -3'

Posted On

2022-05-16