Mutagenetix > Incidental Mutations

Incidental Mutation 'R6259:Rag1'

506526

Institutional Source

Beutler Lab

Gene Symbol

Rag1

Ensembl Gene

ENSMUSG00000061311

Gene Name

recombination activating gene 1

Synonyms

Rag-1

MMRRC Submission

044376-MU

Accession Numbers

MGI:97848

Is this an essential gene?

Possibly essential (E-score: 0.573) question?

Stock #

R6259 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

101638282-101649501 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 101644452 bp

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Isoleucine at position 115 (N115I)

Ref Sequence

ENSEMBL: ENSMUSP00000077584 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000078494] [ENSMUST00000160037] [ENSMUST00000160722]

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

possibly damaging
Transcript: ENSMUST00000078494
AA Change: N115I

PolyPhen 2 Score 0.826 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000077584
Gene: ENSMUSG00000061311
AA Change: N115I

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

0.1080

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 96.0%

Validation Efficiency

99% (74/75)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700061G19Rik	A	G	17: 56,877,513	Y96C	probably benign	Het
5730507C01Rik	C	A	12: 18,534,119	N393K	probably benign	Het
Acap3	A	T	4: 155,896,118	I19F	possibly damaging	Het
Adamts5	C	T	16: 85,899,753	R172H	probably benign	Het
Adgra3	A	G	5: 49,999,141	F416L	possibly damaging	Het
Amy1	T	C	3: 113,569,410	D96G	possibly damaging	Het
Ank2	A	G	3: 127,016,986	S484P	probably benign	Het
Arsa	A	G	15: 89,475,521	C68R	probably damaging	Het
Asprv1	A	G	6: 86,628,379	Y69C	probably benign	Het
Ass1	A	G	2: 31,488,642	E162G	possibly damaging	Het
Atf7	G	T	15: 102,547,238	N230K	probably damaging	Het
Atp10b	A	G	11: 43,201,238	M367V	probably benign	Het
Atp11b	A	G	3: 35,806,901	Y179C	probably damaging	Het
BC004004	A	T	17: 29,298,712	Q300L	possibly damaging	Het
Bglap3	A	T	3: 88,368,760	I95N	probably damaging	Het
Cacna1h	T	C	17: 25,397,656		probably null	Het
Caskin2	C	T	11: 115,800,453	G1141D	probably damaging	Het
Clcn4	G	A	7: 7,291,530	R351W	possibly damaging	Het
Col11a1	T	C	3: 114,138,447	C89R	probably benign	Het
Csrp1	T	G	1: 135,739,514		probably null	Het
Cwf19l2	T	C	9: 3,458,879	I776T	probably damaging	Het
Cyp2b19	A	T	7: 26,771,392	Q486L	possibly damaging	Het
Cyp2j9	T	A	4: 96,584,006	Y165F	probably benign	Het
Dab1	C	T	4: 104,731,751	A524V	probably benign	Het
Dennd1c	G	A	17: 57,067,104	R522C	probably damaging	Het
Dmgdh	T	C	13: 93,752,308	V818A	probably benign	Het
Dst	T	A	1: 34,182,396	V2427E	probably benign	Het
Duox1	C	T	2: 122,344,783	T1354M	probably benign	Het
Ehbp1	A	G	11: 22,285,684		probably benign	Het
Epc2	T	A	2: 49,488,854		probably null	Het
Eya2	T	C	2: 165,716,099	V205A	probably benign	Het
Fam84a	T	A	12: 14,150,645	D27V	probably damaging	Het
Fat4	A	G	3: 39,007,246	H4326R	probably benign	Het
Gaa	C	A	11: 119,281,171	A700D	probably benign	Het
Gm10100	G	T	10: 77,726,664	C60F	possibly damaging	Het
Hhip	T	A	8: 79,972,404	R678W	probably damaging	Het
Il21r	T	A	7: 125,630,719	I266K	possibly damaging	Het
Itgb4	C	T	11: 115,984,157	R447W	probably benign	Het
Kif26b	T	C	1: 178,917,405	S1689P	probably damaging	Het
L3mbtl2	A	G	15: 81,681,927	E317G	probably damaging	Het
Lgr6	C	T	1: 134,994,010	A199T	probably damaging	Het
Lrr1	A	G	12: 69,174,815	N244D	probably damaging	Het
Lrrk2	A	T	15: 91,702,247	H422L	probably benign	Het
Map4k5	A	G	12: 69,852,740	S46P	probably damaging	Het
Ngf	A	G	3: 102,509,797		probably benign	Het
Nploc4	T	C	11: 120,385,865	I452V	probably benign	Het
Oas1d	T	A	5: 120,919,181	Y283*	probably null	Het
Olfr1156	T	C	2: 87,949,435	N266S	probably benign	Het
Olfr1463	A	G	19: 13,234,421	H57R	probably damaging	Het
Olfr648	A	T	7: 104,180,054	M118K	possibly damaging	Het
Olfr689	A	T	7: 105,314,057	I18F	probably benign	Het
Pdzrn4	A	T	15: 92,757,681	E485V	probably damaging	Het
Peg3	A	G	7: 6,709,811	V804A	probably damaging	Het
Piezo2	T	A	18: 63,117,678	Y450F	possibly damaging	Het
Pprc1	T	A	19: 46,064,410	V789E	probably damaging	Het
Prcc	A	G	3: 87,862,147	M436T	possibly damaging	Het
Prepl	A	T	17: 85,070,431	V507D	probably damaging	Het
Rap1gap	T	C	4: 137,681,757		probably null	Het
Reln	A	C	5: 22,060,333	F454V	probably damaging	Het
Slc39a11	A	T	11: 113,463,954	S150T	probably benign	Het
Slc45a1	T	A	4: 150,638,360	I356F	possibly damaging	Het
Snrnp200	G	A	2: 127,218,423	G529D	possibly damaging	Het
Stkld1	A	T	2: 26,949,381	D353V	possibly damaging	Het
Susd2	T	C	10: 75,638,046	S572G	probably damaging	Het
Synrg	T	A	11: 84,008,658	D563E	probably damaging	Het
Tmem131	C	T	1: 36,819,128	V713I	probably benign	Het
Tnfrsf8	A	G	4: 145,277,524		probably null	Het
Trim26	C	T	17: 36,856,218	A267V	probably benign	Het
Trpm1	T	G	7: 64,268,478	F522C	possibly damaging	Het
Uggt1	T	C	1: 36,234,916	I29V	probably benign	Het
Unc5d	C	T	8: 28,666,792	M808I	probably benign	Het
Vmn2r108	T	A	17: 20,463,109	D611V	possibly damaging	Het
Vps13a	A	C	19: 16,687,170	Y1436*	probably null	Het
Wdfy3	C	T	5: 101,872,965	R2491Q	possibly damaging	Het
Zfp518a	G	T	19: 40,912,781	V385F	probably benign	Het
Zfp541	C	T	7: 16,095,526	A1222V	probably benign	Het
Zfp709	TCGACG	TCG	8: 71,890,708		probably benign	Het

Other mutations in Rag1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00940:Rag1	APN	2	101642388	missense	probably damaging	1.00
IGL01125:Rag1	APN	2	101642001	missense	probably damaging	0.99
IGL01836:Rag1	APN	2	101641894	missense	probably damaging	1.00
IGL02216:Rag1	APN	2	101643381	missense	possibly damaging	0.91
IGL02271:Rag1	APN	2	101643388	missense	probably damaging	0.99
IGL02293:Rag1	APN	2	101643046	missense	probably benign	0.39
IGL02601:Rag1	APN	2	101642673	missense	probably damaging	1.00
anne	UTSW	2	101643516	missense	probably damaging	0.99
busted	UTSW	2	101641947	missense	probably damaging	1.00
defective	UTSW	2	101642710	missense	probably damaging	1.00
doll	UTSW	2	101642070	missense	probably damaging	1.00
dysfunctional	UTSW	2	101644284	missense	probably damaging	1.00
huckle	UTSW	2	101641223	intron	probably benign
maladaptive	UTSW	2	101645647	intron	probably benign
scarecrow	UTSW	2	101642507	missense	probably damaging	1.00
R0658:Rag1	UTSW	2	101642683	missense	probably damaging	0.99
R1126:Rag1	UTSW	2	101642689	missense	probably damaging	1.00
R1177:Rag1	UTSW	2	101642278	missense	probably benign	0.10
R1319:Rag1	UTSW	2	101643192	missense	probably damaging	1.00
R1513:Rag1	UTSW	2	101642991	missense	possibly damaging	0.95
R1859:Rag1	UTSW	2	101644062	missense	probably benign	0.03
R2218:Rag1	UTSW	2	101644146	missense	probably benign
R3932:Rag1	UTSW	2	101643039	missense	probably damaging	1.00
R4127:Rag1	UTSW	2	101642071	missense	probably damaging	1.00
R4365:Rag1	UTSW	2	101642943	missense	probably damaging	1.00
R4620:Rag1	UTSW	2	101643680	missense	probably damaging	1.00
R4815:Rag1	UTSW	2	101643516	missense	probably damaging	0.99
R5070:Rag1	UTSW	2	101642311	missense	probably damaging	1.00
R5209:Rag1	UTSW	2	101644215	missense	probably benign	0.01
R5239:Rag1	UTSW	2	101642955	missense	possibly damaging	0.91
R5390:Rag1	UTSW	2	101642734	missense	probably benign
R5607:Rag1	UTSW	2	101643792	missense	probably damaging	1.00
R6412:Rag1	UTSW	2	101642520	missense	probably damaging	0.99
R6633:Rag1	UTSW	2	101642710	missense	probably damaging	1.00
R6679:Rag1	UTSW	2	101644284	missense	probably damaging	1.00
R6723:Rag1	UTSW	2	101643645	missense	probably damaging	0.99
R6853:Rag1	UTSW	2	101642221	missense	probably damaging	0.99
R6867:Rag1	UTSW	2	101641947	missense	probably damaging	1.00
R6974:Rag1	UTSW	2	101641792	missense	probably damaging	0.99
R7071:Rag1	UTSW	2	101643462	missense	probably damaging	0.99
R7124:Rag1	UTSW	2	101643783	missense	probably damaging	0.99
R7248:Rag1	UTSW	2	101641778	missense	probably damaging	0.99
R7256:Rag1	UTSW	2	101642070	missense	probably damaging	1.00
R7567:Rag1	UTSW	2	101643661	missense	probably damaging	0.98
R7581:Rag1	UTSW	2	101643304	missense	possibly damaging	0.95
R7830:Rag1	UTSW	2	101642059	missense	probably damaging	1.00
R7941:Rag1	UTSW	2	101642346	missense	probably benign	0.24
R8024:Rag1	UTSW	2	101642507	missense	probably damaging	1.00
R8434:Rag1	UTSW	2	101642664	missense	probably damaging	1.00
X0018:Rag1	UTSW	2	101643597	missense	probably damaging	1.00
X0018:Rag1	UTSW	2	101644547	missense	probably damaging	0.99
Z1176:Rag1	UTSW	2	101643259	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CATGATGCTCCAACAGTCATGG -3'
(R):5'- GGATTCCTCAGAGGGGAAAC -3'

Sequencing Primer
(F):5'- AGTCATGGCAGAATTCCGTC -3'
(R):5'- CCTTACCTAGAACAGTCTCCAGTAG -3'

Posted On

2018-03-15