Mutagenetix > Incidental Mutation

Incidental Mutation 'R0266:Rag2'

34903

Institutional Source

Beutler Lab

Gene Symbol

Rag2

Ensembl Gene

ENSMUSG00000032864

Gene Name

recombination activating gene 2

Synonyms

Rag-2

MMRRC Submission

038492-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0266 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

101455063-101462874 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 101460948 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Tryptophan at position 419 (C419W)

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: C419W

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

SMART Domains

Protein: ENSMUSP00000038204
Gene: ENSMUSG00000032864
AA Change: C419W

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: C419W

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

SMART Domains

Protein: ENSMUSP00000106858
Gene: ENSMUSG00000032864
AA Change: C419W

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: ENSMUST00000177007

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177171

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 98.3%
3x: 97.2%
10x: 94.9%
20x: 89.8%

Validation Efficiency

100% (79/79)

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001K19Rik	A	G	12: 110,635,188 (GRCm39)	S117P	possibly damaging	Het
Aars2	T	C	17: 45,818,436 (GRCm39)		probably benign	Het
Acot11	T	C	4: 106,607,185 (GRCm39)	D466G	probably damaging	Het
Adgrd1	G	A	5: 129,216,658 (GRCm39)	A342T	probably benign	Het
Apbb2	A	T	5: 66,459,954 (GRCm39)	N714K	probably benign	Het
Aqp12	C	A	1: 92,934,572 (GRCm39)	H150N	possibly damaging	Het
Brinp3	T	A	1: 146,558,418 (GRCm39)	L114*	probably null	Het
Ccng2	T	C	5: 93,419,148 (GRCm39)		probably benign	Het
Cd36	T	A	5: 18,003,250 (GRCm39)	R265S	probably benign	Het
Ces4a	T	C	8: 105,868,598 (GRCm39)	L104S	probably benign	Het
Clca4b	T	C	3: 144,628,547 (GRCm39)	I387V	probably damaging	Het
Cul7	T	A	17: 46,965,521 (GRCm39)	H566Q	probably benign	Het
Ddx60	A	T	8: 62,486,527 (GRCm39)	H1646L	possibly damaging	Het
Dntt	T	C	19: 41,047,566 (GRCm39)	I503T	probably damaging	Het
Dynlt1a	T	G	17: 6,367,670 (GRCm39)	E2D	probably benign	Het
Efemp2	G	T	19: 5,528,027 (GRCm39)	C78F	probably damaging	Het
Esco1	T	C	18: 10,594,605 (GRCm39)	E227G	probably benign	Het
Fezf2	T	A	14: 12,342,607 (GRCm38)	K419N	probably damaging	Het
Gm17541	A	T	12: 4,739,487 (GRCm39)		probably benign	Het
Gm2381	G	A	7: 42,469,372 (GRCm39)	Q251*	probably null	Het
Gm4782	T	G	6: 50,587,674 (GRCm39)	S686R	probably damaging	Het
Grin3a	G	A	4: 49,665,501 (GRCm39)	R1045*	probably null	Het
Grm8	T	C	6: 27,285,895 (GRCm39)	Y839C	probably damaging	Het
Gtf3c1	G	A	7: 125,243,306 (GRCm39)	P1766L	possibly damaging	Het
Herc2	T	A	7: 55,856,326 (GRCm39)	H3921Q	probably damaging	Het
Hes6	A	T	1: 91,340,026 (GRCm39)	D143E	possibly damaging	Het
Hmcn2	A	G	2: 31,284,839 (GRCm39)	E2055G	probably benign	Het
Hmcn2	G	A	2: 31,335,365 (GRCm39)		probably benign	Het
Ikzf3	A	G	11: 98,358,143 (GRCm39)	L398P	probably benign	Het
Il10ra	A	T	9: 45,176,950 (GRCm39)	I125N	probably benign	Het
Kcnb2	G	A	1: 15,783,137 (GRCm39)		probably benign	Het
Krt77	T	C	15: 101,777,813 (GRCm39)	R81G	possibly damaging	Het
Lrrc40	T	A	3: 157,747,298 (GRCm39)		probably null	Het
Man1a2	C	T	3: 100,489,350 (GRCm39)	R543Q	probably damaging	Het
Mansc1	T	C	6: 134,587,670 (GRCm39)	D169G	probably benign	Het
Mdn1	T	A	4: 32,741,835 (GRCm39)	S3869T	probably damaging	Het
Mettl14	A	T	3: 123,176,475 (GRCm39)	S58T	probably benign	Het
Mrpl4	T	C	9: 20,914,610 (GRCm39)	V62A	probably benign	Het
Myh3	A	G	11: 66,984,498 (GRCm39)	D1085G	possibly damaging	Het
Myo5c	C	A	9: 75,191,498 (GRCm39)		probably benign	Het
Naalad2	G	T	9: 18,262,239 (GRCm39)		probably benign	Het
Nat3	A	G	8: 68,000,432 (GRCm39)	T104A	probably benign	Het
Nek4	A	G	14: 30,679,253 (GRCm39)	E198G	probably damaging	Het
Olfm1	A	G	2: 28,119,619 (GRCm39)	Y403C	probably damaging	Het
Or5w11	C	A	2: 87,459,626 (GRCm39)	T273K	possibly damaging	Het
Or7e177	A	T	9: 20,212,454 (GRCm39)	R320S	probably benign	Het
Osbpl1a	T	A	18: 13,004,220 (GRCm39)		probably null	Het
Pax7	G	A	4: 139,507,047 (GRCm39)	S330L	possibly damaging	Het
Pcdhb15	C	A	18: 37,608,329 (GRCm39)	D520E	probably damaging	Het
Pgm3	T	C	9: 86,449,586 (GRCm39)	T145A	probably benign	Het
Phox2b	G	A	5: 67,253,968 (GRCm39)		probably null	Het
Pik3r6	A	T	11: 68,417,234 (GRCm39)	R59*	probably null	Het
Pold1	A	G	7: 44,190,449 (GRCm39)		probably benign	Het
Ppp1r21	T	C	17: 88,876,500 (GRCm39)		probably benign	Het
Prl5a1	A	G	13: 28,333,970 (GRCm39)	K158E	possibly damaging	Het
Reln	A	G	5: 22,193,774 (GRCm39)	S1395P	probably damaging	Het
Retnlb	T	G	16: 48,639,022 (GRCm39)	Y74*	probably null	Het
Robo3	A	G	9: 37,333,936 (GRCm39)	S633P	probably damaging	Het
Ryr1	A	G	7: 28,740,104 (GRCm39)	S3941P	probably damaging	Het
Scnn1b	A	G	7: 121,511,698 (GRCm39)	N370S	probably damaging	Het
Slc6a5	C	A	7: 49,588,156 (GRCm39)		probably benign	Het
Sort1	T	A	3: 108,252,247 (GRCm39)	N481K	probably benign	Het
Sptlc3	T	A	2: 139,437,957 (GRCm39)	I417K	possibly damaging	Het
Svil	T	A	18: 5,099,063 (GRCm39)		probably benign	Het
Taf4b	T	C	18: 14,946,134 (GRCm39)		probably benign	Het
Tchp	T	C	5: 114,847,394 (GRCm39)	M71T	possibly damaging	Het
Thsd4	T	A	9: 59,904,417 (GRCm39)	H233L	probably benign	Het
Tmem217	G	T	17: 29,745,573 (GRCm39)	N52K	possibly damaging	Het
Tmem38b	T	C	4: 53,840,765 (GRCm39)	L60S	probably damaging	Het
Uqcrfs1	A	C	13: 30,725,146 (GRCm39)	N131K	probably benign	Het
Vars1	T	A	17: 35,232,845 (GRCm39)	S896R	probably benign	Het
Vmn1r170	A	T	7: 23,305,906 (GRCm39)	M103L	probably benign	Het
Vmn2r22	T	C	6: 123,614,363 (GRCm39)	Y409C	probably damaging	Het
Vmn2r92	C	T	17: 18,388,219 (GRCm39)	A408V	probably damaging	Het
Wdr49	A	T	3: 75,359,103 (GRCm39)	I8N	possibly damaging	Het
Zfp648	T	A	1: 154,080,632 (GRCm39)	Y264N	probably damaging	Het
Zmym1	A	C	4: 126,941,818 (GRCm39)	F857V	possibly damaging	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
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
R3752:Rag2	UTSW	2	101,461,121 (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'- AGGAGGAATCTCTGTCTCCAGTGC -3'
(R):5'- AGGAGTCAAGACTTTCCCAGAGCC -3'

Posted On

2013-05-09