Mutagenetix > Incidental Mutation

Incidental Mutation 'R5119:Rxrb'

392876

Institutional Source

Beutler Lab

Gene Symbol

Rxrb

Ensembl Gene

ENSMUSG00000039656

Gene Name

retinoid X receptor beta

Synonyms

Rub, Nr2b2, H-2RIIBP, RCoR-1

MMRRC Submission

042707-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.863) question?

Stock #

R5119 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34250786-34257373 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 34252562 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 50 (S50P)

Ref Sequence

ENSEMBL: ENSMUSP00000112311 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025186] [ENSMUST00000044858] [ENSMUST00000116612] [ENSMUST00000169397] [ENSMUST00000173354] [ENSMUST00000173554] [ENSMUST00000171872]

AlphaFold

P28704

Predicted Effect

probably benign
Transcript: ENSMUST00000025186

SMART Domains

Protein: ENSMUSP00000025186
Gene: ENSMUSG00000024327

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
low complexity region	39	77	N/A	INTRINSIC
low complexity region	80	123	N/A	INTRINSIC
Pfam:Zip	140	473	2.4e-83	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000044858
AA Change: S160P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000036585
Gene: ENSMUSG00000039656
AA Change: S160P

Domain	Start	End	E-Value	Type
low complexity region	66	85	N/A	INTRINSIC
low complexity region	94	121	N/A	INTRINSIC
low complexity region	124	147	N/A	INTRINSIC
low complexity region	179	186	N/A	INTRINSIC
ZnF_C4	189	260	3.98e-39	SMART
low complexity region	269	282	N/A	INTRINSIC
low complexity region	305	316	N/A	INTRINSIC
HOLI	328	491	1.91e-50	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000116612
AA Change: S50P

PolyPhen 2 Score 0.104 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000112311
Gene: ENSMUSG00000039656
AA Change: S50P

Domain	Start	End	E-Value	Type
Pfam:Nuc_recep-AF1	2	76	4.3e-10	PFAM
ZnF_C4	79	150	3.98e-39	SMART
low complexity region	159	172	N/A	INTRINSIC
low complexity region	195	206	N/A	INTRINSIC
HOLI	218	377	1.35e-50	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000167145

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000168978

Predicted Effect

probably benign
Transcript: ENSMUST00000169397

SMART Domains

Protein: ENSMUSP00000130102
Gene: ENSMUSG00000024327

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
low complexity region	39	77	N/A	INTRINSIC
low complexity region	80	123	N/A	INTRINSIC
Pfam:Zip	140	473	1.9e-81	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170491

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174740

Predicted Effect

probably benign
Transcript: ENSMUST00000173354
AA Change: S50P

PolyPhen 2 Score 0.030 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000133661
Gene: ENSMUSG00000039656
AA Change: S50P

Domain	Start	End	E-Value	Type
Pfam:Nuc_recep-AF1	2	76	4.3e-10	PFAM
ZnF_C4	79	150	3.98e-39	SMART
low complexity region	159	172	N/A	INTRINSIC
low complexity region	195	206	N/A	INTRINSIC
HOLI	218	381	1.91e-50	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000173554
AA Change: S50P

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000134299
Gene: ENSMUSG00000039656
AA Change: S50P

Domain	Start	End	E-Value	Type
Pfam:Nuc_recep-AF1	2	76	4.9e-11	PFAM
ZnF_C4	79	150	3.98e-39	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000174299
AA Change: S98P

SMART Domains

Protein: ENSMUSP00000133775
Gene: ENSMUSG00000039656
AA Change: S98P

Domain	Start	End	E-Value	Type
low complexity region	2	16	N/A	INTRINSIC
low complexity region	25	52	N/A	INTRINSIC
low complexity region	55	78	N/A	INTRINSIC
low complexity region	110	117	N/A	INTRINSIC
ZnF_C4	120	191	3.98e-39	SMART
low complexity region	200	213	N/A	INTRINSIC
low complexity region	236	247	N/A	INTRINSIC
HOLI	259	418	1.35e-50	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173810

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174578

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174645

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174033

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174130

Predicted Effect

probably benign
Transcript: ENSMUST00000171872

SMART Domains

Protein: ENSMUSP00000133146
Gene: ENSMUSG00000024327

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
low complexity region	39	77	N/A	INTRINSIC
low complexity region	80	123	N/A	INTRINSIC
Pfam:Zip	140	246	4.7e-25	PFAM

Meta Mutation Damage Score

0.0593

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.1%

Validation Efficiency

100% (127/127)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the retinoid X receptor (RXR) family of nuclear receptors which are involved in mediating the effects of retinoic acid (RA). The encoded protein forms homodimers with the retinoic acid, thyroid hormone, and vitamin D receptors, increasing both DNA binding and transcriptional function on their respective response elements. This gene lies within the major histocompatibility complex (MHC) class II region on chromosome 6. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]
PHENOTYPE: Mutant mice homozygous for a null mutation exhibit partial embryonic and perinatal lethality, and surviving adult males are sterile due to defects in spermatogenesis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 120 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930470P17Rik	C	A	2: 170,421,505 (GRCm39)	G125V	unknown	Het
Actr6	A	T	10: 89,561,717 (GRCm39)	L143Q	probably damaging	Het
Adamts18	A	G	8: 114,425,642 (GRCm39)	Y1207H	probably benign	Het
Adamts5	T	A	16: 85,696,466 (GRCm39)	R230S	probably benign	Het
Adat2	A	T	10: 13,432,650 (GRCm39)	N51Y	probably damaging	Het
Adgrv1	T	C	13: 81,567,546 (GRCm39)	Y5209C	possibly damaging	Het
Ahnak	G	T	19: 8,991,008 (GRCm39)	M4097I	probably benign	Het
Akap13	A	G	7: 75,337,000 (GRCm39)	T820A	probably damaging	Het
Als2cl	C	T	9: 110,719,887 (GRCm39)	R492C	probably damaging	Het
Aox3	G	A	1: 58,227,683 (GRCm39)		probably null	Het
Arid4b	G	A	13: 14,338,866 (GRCm39)	V446M	probably benign	Het
Armc2	A	G	10: 41,798,144 (GRCm39)	L794P	probably damaging	Het
Atp6v0a1	T	A	11: 100,911,341 (GRCm39)	M80K	probably benign	Het
Aup1	T	C	6: 83,032,115 (GRCm39)	V94A	probably damaging	Het
Bank1	A	T	3: 135,940,443 (GRCm39)	I180K	possibly damaging	Het
Becn1	A	G	11: 101,182,221 (GRCm39)	L116P	probably damaging	Het
Bsg	A	G	10: 79,546,057 (GRCm39)		probably benign	Het
Camk2a	A	T	18: 61,076,208 (GRCm39)		probably benign	Het
Ccdc180	A	G	4: 45,914,603 (GRCm39)	E706G	possibly damaging	Het
Cdk8	A	T	5: 146,220,437 (GRCm39)		probably null	Het
Cpne4	A	G	9: 104,778,720 (GRCm39)		probably null	Het
Cspp1	T	A	1: 10,196,688 (GRCm39)	N900K	probably damaging	Het
Cyp2c38	C	A	19: 39,449,065 (GRCm39)	G96V	probably damaging	Het
Dhx40	A	G	11: 86,667,462 (GRCm39)	I261T	probably damaging	Het
Dnah10	T	C	5: 124,856,322 (GRCm39)	F2038L	probably damaging	Het
Dnah7a	A	T	1: 53,737,851 (GRCm39)	D27E	probably benign	Het
Dock10	A	T	1: 80,545,711 (GRCm39)		probably null	Het
Dst	A	T	1: 34,235,050 (GRCm39)	K3710*	probably null	Het
Dtl	G	T	1: 191,273,618 (GRCm39)	A430D	probably damaging	Het
Ece2	T	C	16: 20,437,381 (GRCm39)	L241P	probably damaging	Het
Ecel1	T	A	1: 87,078,861 (GRCm39)	Y526F	probably benign	Het
Enpp2	T	A	15: 54,733,701 (GRCm39)	R420*	probably null	Het
Epb41	A	C	4: 131,664,747 (GRCm39)		probably benign	Het
Eppin	T	C	2: 164,431,371 (GRCm39)	Y85C	probably damaging	Het
Fam171a2	G	A	11: 102,329,559 (GRCm39)	A400V	probably damaging	Het
Fem1c	A	C	18: 46,639,436 (GRCm39)	C189G	probably damaging	Het
Frmd4b	A	G	6: 97,277,275 (GRCm39)	V560A	probably benign	Het
Fsip2	A	T	2: 82,818,535 (GRCm39)	D4756V	probably damaging	Het
Gabbr1	T	C	17: 37,359,330 (GRCm39)	S102P	probably damaging	Het
Garin3	G	A	11: 46,297,863 (GRCm39)	G389D	probably damaging	Het
Gm28042	G	A	2: 119,865,124 (GRCm39)	A250T	probably damaging	Het
Gm30275	T	C	14: 54,312,978 (GRCm39)		probably benign	Het
Gm9762	A	T	3: 78,873,707 (GRCm39)		noncoding transcript	Het
Gpr183	G	T	14: 122,192,275 (GRCm39)	T82N	possibly damaging	Het
Gps2	A	G	11: 69,805,617 (GRCm39)	K45R	probably benign	Het
Gramd2a	A	G	9: 59,621,603 (GRCm39)		probably benign	Het
Grap2	G	A	15: 80,530,345 (GRCm39)	R155Q	possibly damaging	Het
Hsdl1	T	A	8: 120,292,606 (GRCm39)	Y203F	possibly damaging	Het
Ifi204	A	T	1: 173,583,234 (GRCm39)	I328N	probably damaging	Het
Igsf3	T	A	3: 101,346,677 (GRCm39)		probably null	Het
Il1rap	T	C	16: 26,442,949 (GRCm39)	I15T	probably benign	Het
Il23r	A	T	6: 67,443,300 (GRCm39)	C268S	probably damaging	Het
Irx4	A	G	13: 73,417,040 (GRCm39)	T479A	probably benign	Het
Kcnk7	G	A	19: 5,756,352 (GRCm39)	V193I	probably benign	Het
Kcnt1	G	T	2: 25,799,334 (GRCm39)		probably benign	Het
Kif13b	T	G	14: 64,994,902 (GRCm39)	C885G	probably benign	Het
Kif21b	C	A	1: 136,090,838 (GRCm39)	D1215E	probably benign	Het
Klhdc2	A	G	12: 69,343,736 (GRCm39)		probably benign	Het
Kmt2d	G	A	15: 98,745,075 (GRCm39)		probably benign	Het
Lama4	A	G	10: 38,924,050 (GRCm39)	N486S	probably benign	Het
Ldah	G	A	12: 8,277,237 (GRCm39)	A58T	probably benign	Het
Lrrc24	T	C	15: 76,600,200 (GRCm39)	Q313R	probably benign	Het
Luzp1	A	G	4: 136,270,708 (GRCm39)	D977G	possibly damaging	Het
Meak7	A	C	8: 120,494,882 (GRCm39)	L292R	probably damaging	Het
Mrgpra4	A	G	7: 47,631,466 (GRCm39)	L45P	probably damaging	Het
Mrps28	C	T	3: 8,988,756 (GRCm39)	G34D	possibly damaging	Het
Myh8	A	G	11: 67,189,184 (GRCm39)	E1120G	probably damaging	Het
Myt1l	A	G	12: 29,882,302 (GRCm39)	E499G	unknown	Het
Ncan	C	T	8: 70,567,675 (GRCm39)	E146K	probably damaging	Het
Nlgn1	A	T	3: 25,487,958 (GRCm39)	D763E	probably damaging	Het
Or11g26	T	C	14: 50,752,966 (GRCm39)	F102L	probably benign	Het
Or13c7c	G	T	4: 43,836,433 (GRCm39)	A19D	probably benign	Het
Or1e17	A	T	11: 73,831,378 (GRCm39)	Y102F	possibly damaging	Het
Or4c12	A	T	2: 89,774,147 (GRCm39)	I104N	possibly damaging	Het
Or5b118	C	T	19: 13,448,910 (GRCm39)	T192I	probably benign	Het
Or6c8b	T	A	10: 128,882,711 (GRCm39)	I74F	possibly damaging	Het
Pak6	A	T	2: 118,525,029 (GRCm39)	I552F	probably damaging	Het
Pcbp1	G	A	6: 86,501,897 (GRCm39)	A334V	probably damaging	Het
Pclaf	T	C	9: 65,798,062 (GRCm39)	V32A	probably benign	Het
Pga5	T	A	19: 10,654,053 (GRCm39)	H50L	probably benign	Het
Phyhipl	A	T	10: 70,404,904 (GRCm39)	D56E	probably damaging	Het
Pik3ap1	C	T	19: 41,270,415 (GRCm39)	R758H	probably benign	Het
Plekha1	A	G	7: 130,507,094 (GRCm39)		probably benign	Het
Plekhm1	A	T	11: 103,278,141 (GRCm39)	N318K	possibly damaging	Het
Ppargc1b	G	A	18: 61,440,725 (GRCm39)	A731V	probably benign	Het
Pptc7	T	C	5: 122,451,844 (GRCm39)	V100A	possibly damaging	Het
Prl7a1	A	T	13: 27,817,564 (GRCm39)	H233Q	possibly damaging	Het
Prpf40a	A	G	2: 53,034,861 (GRCm39)	F776L	probably damaging	Het
Prrc2c	T	C	1: 162,533,009 (GRCm39)		probably benign	Het
Psmb1	T	C	17: 15,718,524 (GRCm39)	M1V	probably null	Het
Ptpn3	A	G	4: 57,218,513 (GRCm39)	F650S	possibly damaging	Het
Ranbp17	A	T	11: 33,354,181 (GRCm39)	*577R	probably null	Het
Reln	T	A	5: 22,176,868 (GRCm39)	N1933Y	probably benign	Het
Rgl2	T	A	17: 34,156,094 (GRCm39)	H727Q	probably benign	Het
Rhpn2	A	G	7: 35,070,549 (GRCm39)	T160A	probably damaging	Het
Rlf	G	A	4: 121,004,652 (GRCm39)	H1443Y	probably damaging	Het
Rpgrip1l	T	C	8: 92,007,444 (GRCm39)	E382G	probably damaging	Het
Scn4b	A	T	9: 45,059,056 (GRCm39)	E109V	probably damaging	Het
Scrib	C	T	15: 75,923,602 (GRCm39)		probably null	Het
Slc22a29	A	T	19: 8,195,194 (GRCm39)	V147D	probably damaging	Het
Slc4a4	A	T	5: 89,102,721 (GRCm39)	E53V	probably null	Het
Slx4	A	G	16: 3,819,063 (GRCm39)	S37P	possibly damaging	Het
Spag9	G	A	11: 94,013,548 (GRCm39)	G1127D	probably damaging	Het
Srek1	T	A	13: 103,889,064 (GRCm39)		probably benign	Het
Supt5	G	T	7: 28,015,795 (GRCm39)	P849Q	probably damaging	Het
Tex14	T	C	11: 87,324,639 (GRCm39)	S2P	probably damaging	Het
Them7	A	G	2: 105,209,153 (GRCm39)	T158A	probably benign	Het
Tll2	A	G	19: 41,118,948 (GRCm39)	V260A	possibly damaging	Het
Tlr6	A	G	5: 65,111,644 (GRCm39)	V421A	probably benign	Het
Tmc3	T	G	7: 83,264,218 (GRCm39)	C649G	probably damaging	Het
Tnn	A	G	1: 159,948,122 (GRCm39)	W864R	probably damaging	Het
Tsc2	A	C	17: 24,822,254 (GRCm39)	V1095G	probably benign	Het
Vmn1r124	C	T	7: 20,994,172 (GRCm39)	G124D	probably damaging	Het
Vmn2r116	T	C	17: 23,606,138 (GRCm39)	V350A	probably benign	Het
Vps13d	A	G	4: 144,832,468 (GRCm39)	S2813P	possibly damaging	Het
Wrap53	T	A	11: 69,454,758 (GRCm39)	M204L	possibly damaging	Het
Zfp277	A	G	12: 40,378,687 (GRCm39)	V390A	possibly damaging	Het
Zfp687	A	T	3: 94,918,987 (GRCm39)	S262T	probably benign	Het
Zfp831	T	A	2: 174,547,103 (GRCm39)	S1429T	probably benign	Het
Znfx1	G	A	2: 166,907,307 (GRCm39)		probably benign	Het

Other mutations in Rxrb

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00435:Rxrb	APN	17	34,253,049 (GRCm39)	missense	probably damaging	1.00
IGL01337:Rxrb	APN	17	34,255,605 (GRCm39)	missense	probably damaging	1.00
concerned	UTSW	17	34,255,645 (GRCm39)	missense	probably benign	0.03
problematic	UTSW	17	34,253,134 (GRCm39)	missense	probably damaging	1.00
BB006:Rxrb	UTSW	17	34,255,645 (GRCm39)	missense	probably benign	0.03
BB016:Rxrb	UTSW	17	34,255,645 (GRCm39)	missense	probably benign	0.03
I2505:Rxrb	UTSW	17	34,252,523 (GRCm39)	splice site	probably benign
R0571:Rxrb	UTSW	17	34,251,106 (GRCm39)	unclassified	probably benign
R1463:Rxrb	UTSW	17	34,253,134 (GRCm39)	missense	probably damaging	1.00
R2312:Rxrb	UTSW	17	34,251,103 (GRCm39)	unclassified	probably benign
R2395:Rxrb	UTSW	17	34,256,412 (GRCm39)	missense	probably damaging	1.00
R2935:Rxrb	UTSW	17	34,251,106 (GRCm39)	unclassified	probably benign
R3978:Rxrb	UTSW	17	34,255,300 (GRCm39)	missense	possibly damaging	0.92
R5523:Rxrb	UTSW	17	34,255,411 (GRCm39)	missense	probably damaging	1.00
R5638:Rxrb	UTSW	17	34,256,381 (GRCm39)	missense	probably damaging	1.00
R5769:Rxrb	UTSW	17	34,251,821 (GRCm39)	utr 5 prime	probably benign
R5894:Rxrb	UTSW	17	34,254,718 (GRCm39)	missense	probably damaging	1.00
R6373:Rxrb	UTSW	17	34,252,533 (GRCm39)	missense	probably benign	0.08
R7798:Rxrb	UTSW	17	34,252,579 (GRCm39)	missense	probably damaging	1.00
R7929:Rxrb	UTSW	17	34,255,645 (GRCm39)	missense	probably benign	0.03
R8087:Rxrb	UTSW	17	34,254,763 (GRCm39)	missense	probably benign	0.00
R8233:Rxrb	UTSW	17	34,255,879 (GRCm39)	missense	possibly damaging	0.48
R8268:Rxrb	UTSW	17	34,254,750 (GRCm39)	missense	probably benign	0.01
R8886:Rxrb	UTSW	17	34,256,428 (GRCm39)	missense	probably damaging	0.99
R9211:Rxrb	UTSW	17	34,255,626 (GRCm39)	missense	probably damaging	1.00
R9671:Rxrb	UTSW	17	34,252,020 (GRCm39)	critical splice donor site	probably null
Z1177:Rxrb	UTSW	17	34,251,101 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- CTGTAGCACAATTACAGAAGGGTG -3'
(R):5'- CCCATAGGCAGTGGTAAACAG -3'

Sequencing Primer
(F):5'- CACTCTTGGTGTCACGTGCAAG -3'
(R):5'- AGTGGTAAACAGCCCCGACG -3'

Posted On

2016-06-15