Mutagenetix > Incidental Mutation

Incidental Mutation 'R7365:Rag2'

571679

Institutional Source

Beutler Lab

Gene Symbol

Rag2

Ensembl Gene

ENSMUSG00000032864

Gene Name

recombination activating gene 2

Synonyms

Rag-2

MMRRC Submission

045449-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7365 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

101455063-101462874 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 101461118 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 476 (Y476C)

Ref Sequence

ENSEMBL: ENSMUSP00000038204 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000044031] [ENSMUST00000099682] [ENSMUST00000111227] [ENSMUST00000111231] [ENSMUST00000128898] [ENSMUST00000160037] [ENSMUST00000160722]

AlphaFold

P21784

PDB Structure

A PHD finger motif in the C-terminus of RAG2 modulates recombination activity [SOLUTION NMR]
Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME1K4ME3 PEPTIDE [X-RAY DIFFRACTION]
Crystal structure of RAG2-PHD finger in complex with H3R2me2aK4me3 peptide [X-RAY DIFFRACTION]
Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me3 peptide [X-RAY DIFFRACTION]
Crystal structure of RAG2-PHD finger in complex with H3R2me2sK4me2 peptide [X-RAY DIFFRACTION]
Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution [X-RAY DIFFRACTION]
Crystal structure of the core RAG1/2 recombinase [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000044031
AA Change: Y476C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000038204
Gene: ENSMUSG00000032864
AA Change: Y476C

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: Y476C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000106858
Gene: ENSMUSG00000032864
AA Change: Y476C

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

Meta Mutation Damage Score

0.3177

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

100% (96/96)

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: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700123K08Rik	T	C	5: 138,561,198 (GRCm39)	S155G	probably benign	Het
Abcc4	T	C	14: 118,865,066 (GRCm39)	N320S	probably damaging	Het
Akr1c19	G	A	13: 4,287,069 (GRCm39)	R96H	probably benign	Het
Ankrd17	T	C	5: 90,439,010 (GRCm39)	D451G	possibly damaging	Het
Ano8	T	A	8: 71,937,754 (GRCm39)	D36V	probably damaging	Het
Aqp3	A	G	4: 41,098,003 (GRCm39)	V36A	probably benign	Het
Atf7ip	A	G	6: 136,537,708 (GRCm39)	T314A	probably benign	Het
Atp2c1	A	T	9: 105,300,198 (GRCm39)	D700E	probably damaging	Het
Axin2	G	A	11: 108,830,202 (GRCm39)	V341M	possibly damaging	Het
Bin3	A	G	14: 70,371,976 (GRCm39)	Q139R	probably damaging	Het
Brca2	A	G	5: 150,455,802 (GRCm39)	D181G	probably damaging	Het
Capn3	A	G	2: 120,325,295 (GRCm39)	E466G	probably damaging	Het
Ccdc14	T	A	16: 34,543,989 (GRCm39)	Y830*	probably null	Het
Cdk12	T	C	11: 98,111,910 (GRCm39)	F723L	unknown	Het
Cep89	G	A	7: 35,129,353 (GRCm39)	R630H	probably damaging	Het
Cip2a	T	A	16: 48,822,016 (GRCm39)	S215T	probably benign	Het
Clca3a2	T	A	3: 144,804,545 (GRCm39)	I61F	probably damaging	Het
Clca4b	T	C	3: 144,628,529 (GRCm39)	T393A	not run	Het
Cldn5	G	A	16: 18,595,845 (GRCm39)	A34T	probably damaging	Het
Cobll1	A	T	2: 64,928,717 (GRCm39)	S870T	probably damaging	Het
Col12a1	T	C	9: 79,613,642 (GRCm39)	K68E	probably damaging	Het
Crnn	A	T	3: 93,055,841 (GRCm39)	Q209L	probably damaging	Het
Cwf19l1	A	T	19: 44,120,579 (GRCm39)	F45I	probably damaging	Het
Cyfip2	T	A	11: 46,098,267 (GRCm39)	K1052*	probably null	Het
D930020B18Rik	G	A	10: 121,503,716 (GRCm39)		probably null	Het
Dcc	G	A	18: 71,959,194 (GRCm39)	P193S	probably damaging	Het
Dda1	T	A	8: 71,927,137 (GRCm39)	C48S	probably benign	Het
Disc1	A	G	8: 125,881,780 (GRCm39)	R572G	probably damaging	Het
Dnah7a	A	T	1: 53,536,297 (GRCm39)	M2582K	probably benign	Het
Dsel	C	T	1: 111,789,303 (GRCm39)	G411S	probably damaging	Het
Dynlrb2	T	C	8: 117,241,696 (GRCm39)	V80A	probably benign	Het
Eif3a	A	T	19: 60,755,082 (GRCm39)	D1033E	unknown	Het
Enam	C	A	5: 88,649,347 (GRCm39)	H285Q	possibly damaging	Het
Ep400	T	C	5: 110,867,480 (GRCm39)	D980G	unknown	Het
Epha7	C	T	4: 28,871,937 (GRCm39)	S422L	probably benign	Het
Erc2	A	C	14: 27,762,346 (GRCm39)	D703A	probably damaging	Het
Ezh2	G	T	6: 47,510,692 (GRCm39)	S639*	probably null	Het
Fbn1	G	A	2: 125,193,969 (GRCm39)	H1333Y	probably damaging	Het
Flad1	A	G	3: 89,315,972 (GRCm39)	S197P	possibly damaging	Het
Foxl3	A	G	5: 138,806,736 (GRCm39)	H82R	probably damaging	Het
Gfm2	G	T	13: 97,279,529 (GRCm39)	C26F	probably benign	Het
Golga2	C	T	2: 32,193,013 (GRCm39)	Q444*	probably null	Het
Gp5	A	T	16: 30,127,426 (GRCm39)	V416D	probably damaging	Het
Gpat2	A	G	2: 127,268,901 (GRCm39)		probably null	Het
Gpr137c	A	G	14: 45,516,471 (GRCm39)	D353G	probably damaging	Het
Hoxa13	A	C	6: 52,236,862 (GRCm39)	W133G	probably damaging	Het
Hydin	A	T	8: 111,327,905 (GRCm39)	K4804M	probably damaging	Het
Hydin	A	T	8: 111,284,294 (GRCm39)	I3189F	probably damaging	Het
Ice2	T	C	9: 69,307,794 (GRCm39)	F26S	probably damaging	Het
Ints11	T	C	4: 155,956,687 (GRCm39)		probably null	Het
Ipo5	A	G	14: 121,157,497 (GRCm39)	I112V	probably benign	Het
Itgax	T	A	7: 127,734,481 (GRCm39)	S346R	probably damaging	Het
Kcnj13	T	A	1: 87,316,739 (GRCm39)	M125L	probably damaging	Het
Lmbrd1	T	A	1: 24,783,948 (GRCm39)	V359E	possibly damaging	Het
Lrrc7	T	G	3: 157,903,798 (GRCm39)	K287N	probably damaging	Het
Mau2	C	T	8: 70,481,884 (GRCm39)	A191T	possibly damaging	Het
Mkx	C	A	18: 7,000,747 (GRCm39)	R65L	possibly damaging	Het
Mroh4	T	A	15: 74,482,220 (GRCm39)	K746*	probably null	Het
Myh4	A	G	11: 67,133,674 (GRCm39)	T238A	probably damaging	Het
Nlrp9c	T	A	7: 26,070,822 (GRCm39)	N920Y	possibly damaging	Het
Nr4a3	T	G	4: 48,051,290 (GRCm39)	S15A	possibly damaging	Het
Ntn4	T	C	10: 93,480,666 (GRCm39)	L130P	probably damaging	Het
Or2ag13	A	G	7: 106,313,171 (GRCm39)	V239A	probably benign	Het
Or4a68	A	G	2: 89,270,542 (GRCm39)	V27A	probably benign	Het
Or4f59	A	T	2: 111,873,359 (GRCm39)	V6E	possibly damaging	Het
Or56a42-ps1	T	A	7: 104,777,552 (GRCm39)	I21F	probably benign	Het
Or8d23	A	T	9: 38,842,072 (GRCm39)	I202F	probably damaging	Het
Otog	T	C	7: 45,947,732 (GRCm39)	L110P	probably damaging	Het
Platr25	G	A	13: 62,848,719 (GRCm39)	H48Y	probably benign	Het
Plcxd2	T	C	16: 45,800,789 (GRCm39)	E145G	probably damaging	Het
Pltp	A	T	2: 164,696,242 (GRCm39)	N143K	probably damaging	Het
Pnpt1	T	C	11: 29,111,334 (GRCm39)	Y735H	probably damaging	Het
Prom1	A	G	5: 44,178,173 (GRCm39)	Y520H	probably damaging	Het
Rdh16f2	A	G	10: 127,712,893 (GRCm39)	Y297C	probably damaging	Het
Ryr1	T	C	7: 28,785,180 (GRCm39)	E1844G	probably benign	Het
Ryr2	A	G	13: 11,655,161 (GRCm39)	C3679R	probably damaging	Het
Sirt1	A	G	10: 63,157,782 (GRCm39)	I544T	probably benign	Het
Slc26a10	A	T	10: 127,012,716 (GRCm39)	I382N	possibly damaging	Het
Sox2	C	A	3: 34,705,121 (GRCm39)	P186Q	possibly damaging	Het
Spata31e5	A	T	1: 28,819,233 (GRCm39)	M16K	probably benign	Het
Tnpo3	A	G	6: 29,556,995 (GRCm39)	L752P	probably damaging	Het
Top2b	T	A	14: 16,416,649 (GRCm38)	N1136K	probably benign	Het
Tpsg1	G	T	17: 25,592,184 (GRCm39)	G86V	probably damaging	Het
Ttf2	C	A	3: 100,870,618 (GRCm39)	D152Y	possibly damaging	Het
Txndc15	T	C	13: 55,862,601 (GRCm39)	L4P	unknown	Het
Unc5a	T	C	13: 55,144,386 (GRCm39)	V237A	possibly damaging	Het
Urb1	CACTTAC	CAC	16: 90,569,461 (GRCm39)		probably benign	Het
Vav3	C	A	3: 109,535,415 (GRCm39)	P616T	possibly damaging	Het
Vmn2r15	T	A	5: 109,441,105 (GRCm39)	D251V	probably benign	Het
Vmn2r15	A	G	5: 109,445,388 (GRCm39)	L12S	probably benign	Het
Wfs1	A	C	5: 37,125,076 (GRCm39)	I605S	probably benign	Het
Wif1	G	A	10: 120,919,814 (GRCm39)	R187Q	possibly damaging	Het
Yipf1	A	G	4: 107,207,738 (GRCm39)		probably null	Het
Zdhhc20	G	T	14: 58,111,377 (GRCm39)	F74L	possibly damaging	Het
Zfp507	T	C	7: 35,475,843 (GRCm39)	T303A	unknown	Het
Zfp763	A	T	17: 33,252,352 (GRCm39)		probably benign	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
R0266:Rag2	UTSW	2	101,460,948 (GRCm39)	missense	probably damaging	1.00
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
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'- TGAAGATGACGAGTCTGTAACCG -3'
(R):5'- CAATATACCTGAGTCTGAGGGGC -3'

Sequencing Primer
(F):5'- GTCTGTAACCGGCTACTGGATAAC -3'
(R):5'- CTGAGGGGCTTTTGCTAAATTAATC -3'

Posted On

2019-09-13