Incidental Mutation 'R5523:Rxrb'
ID 431715
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 043265-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.863) question?
Stock # R5523 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 34250786-34257373 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 34255411 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 246 (V246A)
Ref Sequence ENSEMBL: ENSMUSP00000133661 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000025186] [ENSMUST00000044858] [ENSMUST00000087497] [ENSMUST00000114252] [ENSMUST00000114255] [ENSMUST00000116612] [ENSMUST00000173354] [ENSMUST00000173554] [ENSMUST00000169397] [ENSMUST00000131134] [ENSMUST00000171872]
AlphaFold P28704
Predicted Effect probably benign
Transcript: ENSMUST00000025186
SMART Domains Protein: ENSMUSP00000025186
Gene: ENSMUSG00000024327

DomainStartEndE-ValueType
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 possibly damaging
Transcript: ENSMUST00000044858
AA Change: V356A

PolyPhen 2 Score 0.924 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000036585
Gene: ENSMUSG00000039656
AA Change: V356A

DomainStartEndE-ValueType
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: ENSMUST00000087497
SMART Domains Protein: ENSMUSP00000084772
Gene: ENSMUSG00000024330

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
TSPN 31 214 4.25e-72 SMART
LamG 82 213 1.08e-9 SMART
Pfam:Collagen 306 364 2.2e-9 PFAM
Pfam:Collagen 399 460 1e-10 PFAM
Pfam:Collagen 437 520 1.2e-7 PFAM
Pfam:Collagen 479 553 5.7e-9 PFAM
Pfam:Collagen 506 579 1.6e-8 PFAM
internal_repeat_4 584 614 3.98e-5 PROSPERO
internal_repeat_2 584 669 5.49e-20 PROSPERO
internal_repeat_1 587 740 2.58e-22 PROSPERO
Pfam:Collagen 743 814 1.5e-8 PFAM
Pfam:Collagen 767 839 4.8e-7 PFAM
low complexity region 854 872 N/A INTRINSIC
Pfam:Collagen 881 946 4.5e-8 PFAM
Pfam:Collagen 905 976 2e-7 PFAM
Pfam:Collagen 933 1002 2.7e-8 PFAM
low complexity region 1013 1047 N/A INTRINSIC
low complexity region 1064 1112 N/A INTRINSIC
low complexity region 1121 1199 N/A INTRINSIC
low complexity region 1216 1232 N/A INTRINSIC
low complexity region 1289 1320 N/A INTRINSIC
Pfam:Collagen 1358 1417 1.7e-8 PFAM
COLFI 1454 1649 4.42e-117 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000114252
SMART Domains Protein: ENSMUSP00000109890
Gene: ENSMUSG00000024330

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
TSPN 31 214 4.25e-72 SMART
LamG 82 213 1.08e-9 SMART
Pfam:Collagen 311 369 2.3e-9 PFAM
Pfam:Collagen 404 465 1.1e-10 PFAM
Pfam:Collagen 442 525 1.3e-7 PFAM
Pfam:Collagen 484 558 6.4e-9 PFAM
Pfam:Collagen 511 584 1.7e-8 PFAM
internal_repeat_4 589 619 3.69e-5 PROSPERO
internal_repeat_2 589 674 4.46e-20 PROSPERO
internal_repeat_1 592 745 2.05e-22 PROSPERO
internal_repeat_3 636 752 7.84e-10 PROSPERO
Pfam:Collagen 772 844 5.5e-7 PFAM
Pfam:Collagen 800 869 1.9e-8 PFAM
Pfam:Collagen 886 951 5e-8 PFAM
Pfam:Collagen 910 981 2.2e-7 PFAM
Pfam:Collagen 934 1007 6.9e-7 PFAM
low complexity region 1018 1052 N/A INTRINSIC
low complexity region 1069 1117 N/A INTRINSIC
low complexity region 1126 1204 N/A INTRINSIC
low complexity region 1221 1237 N/A INTRINSIC
low complexity region 1294 1325 N/A INTRINSIC
Pfam:Collagen 1363 1422 1.9e-8 PFAM
COLFI 1459 1654 4.42e-117 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000114255
SMART Domains Protein: ENSMUSP00000109893
Gene: ENSMUSG00000024330

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
TSPN 31 214 4.25e-72 SMART
LamG 82 213 1.08e-9 SMART
low complexity region 257 268 N/A INTRINSIC
low complexity region 295 307 N/A INTRINSIC
Pfam:Collagen 345 403 2.1e-9 PFAM
Pfam:Collagen 438 499 1.1e-10 PFAM
Pfam:Collagen 521 593 2.2e-8 PFAM
Pfam:Collagen 545 613 9.1e-10 PFAM
internal_repeat_4 623 653 2.83e-5 PROSPERO
internal_repeat_2 623 708 2.11e-20 PROSPERO
internal_repeat_1 626 779 9e-23 PROSPERO
internal_repeat_3 670 786 5.16e-10 PROSPERO
low complexity region 788 819 N/A INTRINSIC
low complexity region 830 857 N/A INTRINSIC
low complexity region 866 887 N/A INTRINSIC
low complexity region 893 911 N/A INTRINSIC
low complexity region 919 935 N/A INTRINSIC
Pfam:Collagen 973 1041 2.9e-8 PFAM
low complexity region 1052 1086 N/A INTRINSIC
low complexity region 1103 1151 N/A INTRINSIC
low complexity region 1160 1238 N/A INTRINSIC
low complexity region 1255 1271 N/A INTRINSIC
low complexity region 1328 1359 N/A INTRINSIC
Pfam:Collagen 1394 1456 1.5e-8 PFAM
COLFI 1493 1688 4.42e-117 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000116612
AA Change: V246A

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000112311
Gene: ENSMUSG00000039656
AA Change: V246A

DomainStartEndE-ValueType
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: ENSMUST00000174033
Predicted Effect probably damaging
Transcript: ENSMUST00000173354
AA Change: V246A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000133661
Gene: ENSMUSG00000039656
AA Change: V246A

DomainStartEndE-ValueType
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 unknown
Transcript: ENSMUST00000174299
AA Change: V294A
SMART Domains Protein: ENSMUSP00000133775
Gene: ENSMUSG00000039656
AA Change: V294A

DomainStartEndE-ValueType
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: ENSMUST00000168978
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174578
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174130
Predicted Effect noncoding transcript
Transcript: ENSMUST00000170491
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173810
Predicted Effect probably benign
Transcript: ENSMUST00000173554
SMART Domains Protein: ENSMUSP00000134299
Gene: ENSMUSG00000039656

DomainStartEndE-ValueType
Pfam:Nuc_recep-AF1 2 76 4.9e-11 PFAM
ZnF_C4 79 150 3.98e-39 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000169397
SMART Domains Protein: ENSMUSP00000130102
Gene: ENSMUSG00000024327

DomainStartEndE-ValueType
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 probably benign
Transcript: ENSMUST00000131134
SMART Domains Protein: ENSMUSP00000122082
Gene: ENSMUSG00000024330

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
TSPN 31 214 4.25e-72 SMART
LamG 82 213 1.08e-9 SMART
low complexity region 303 314 N/A INTRINSIC
low complexity region 342 354 N/A INTRINSIC
Pfam:Collagen 392 450 7.8e-10 PFAM
Pfam:Collagen 484 543 1.4e-10 PFAM
Pfam:Collagen 514 581 9.5e-11 PFAM
Pfam:Collagen 565 624 2.1e-11 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000171872
SMART Domains Protein: ENSMUSP00000133146
Gene: ENSMUSG00000024327

DomainStartEndE-ValueType
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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174645
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174740
Coding Region Coverage
  • 1x: 98.3%
  • 3x: 97.3%
  • 10x: 95.4%
  • 20x: 91.4%
Validation Efficiency
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: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acadm G A 3: 153,644,273 (GRCm39) T70M probably benign Het
Adamtsl3 G A 7: 82,223,650 (GRCm39) A218T possibly damaging Het
Ahnak2 T C 12: 112,741,642 (GRCm39) D810G probably damaging Het
Ak7 T A 12: 105,707,341 (GRCm39) L315* probably null Het
Apoa5 T C 9: 46,181,887 (GRCm39) F321S possibly damaging Het
Baiap2l1 G C 5: 144,212,768 (GRCm39) P416A probably damaging Het
Bco1 A G 8: 117,835,432 (GRCm39) I128V possibly damaging Het
Bpifb2 T C 2: 153,717,905 (GRCm39) probably benign Het
Cdt1 G A 8: 123,294,832 (GRCm39) R13H possibly damaging Het
Cenpj A G 14: 56,789,880 (GRCm39) V723A probably benign Het
Chl1 T A 6: 103,685,675 (GRCm39) W849R probably damaging Het
Cpne9 A G 6: 113,267,192 (GRCm39) D169G probably damaging Het
Cyp2d22 A G 15: 82,256,772 (GRCm39) V334A probably damaging Het
Cyp4f39 C A 17: 32,689,807 (GRCm39) N84K probably benign Het
Cyp4f40 T A 17: 32,888,796 (GRCm39) F192I probably damaging Het
Disp3 T C 4: 148,342,554 (GRCm39) D632G probably benign Het
Dnhd1 G A 7: 105,352,416 (GRCm39) R2523Q probably damaging Het
Echs1 G T 7: 139,692,426 (GRCm39) T107K probably benign Het
Ehmt2 C T 17: 35,118,067 (GRCm39) R40* probably null Het
Ergic1 G A 17: 26,843,580 (GRCm39) V17I probably damaging Het
Fank1 G T 7: 133,478,569 (GRCm39) C210F probably damaging Het
Fbxo15 T G 18: 84,978,194 (GRCm39) M136R probably damaging Het
Ggcx C A 6: 72,401,017 (GRCm39) P240H probably damaging Het
Gpr179 T C 11: 97,227,608 (GRCm39) R1516G probably benign Het
Gprin3 G A 6: 59,330,931 (GRCm39) Q459* probably null Het
Hadha C A 5: 30,350,252 (GRCm39) V99F possibly damaging Het
Hirip3 A G 7: 126,463,034 (GRCm39) D330G possibly damaging Het
Irx2 T C 13: 72,779,714 (GRCm39) W333R probably damaging Het
Kansl1l T C 1: 66,841,271 (GRCm39) T10A probably benign Het
Kcnd2 T C 6: 21,723,211 (GRCm39) I467T probably benign Het
Klc3 A T 7: 19,130,932 (GRCm39) I215N probably damaging Het
Kmt2c A G 5: 25,504,337 (GRCm39) V3657A probably benign Het
Lin28b A T 10: 45,345,164 (GRCm39) L54* probably null Het
Mgll T C 6: 88,702,743 (GRCm39) V14A probably benign Het
Mrc2 A G 11: 105,234,408 (GRCm39) N976S probably benign Het
Myh8 C A 11: 67,196,788 (GRCm39) A1807E possibly damaging Het
Nalcn G A 14: 123,647,155 (GRCm39) P573S probably damaging Het
Ncam2 C T 16: 81,231,766 (GRCm39) R77* probably null Het
Neb T C 2: 52,168,827 (GRCm39) S1903G probably benign Het
Nfe2 T A 15: 103,157,556 (GRCm39) D145V probably damaging Het
Or52a20 T A 7: 103,366,687 (GRCm39) Y295* probably null Het
Padi1 A T 4: 140,542,164 (GRCm39) V586D probably damaging Het
Pcdh12 T C 18: 38,416,192 (GRCm39) D311G probably damaging Het
Pcdha11 A T 18: 37,145,439 (GRCm39) H510L probably damaging Het
Plcb1 C A 2: 135,102,486 (GRCm39) P221H probably benign Het
Plekhg2 A T 7: 28,069,856 (GRCm39) V58E probably damaging Het
Pparg A C 6: 115,467,032 (GRCm39) Q435P probably damaging Het
Ppp1r36 A G 12: 76,484,892 (GRCm39) T282A possibly damaging Het
Prcd T C 11: 116,559,110 (GRCm39) probably benign Het
Pygo1 A T 9: 72,852,266 (GRCm39) H151L possibly damaging Het
Rnmt A G 18: 68,446,773 (GRCm39) Y266C probably benign Het
Sart1 A G 19: 5,433,704 (GRCm39) S378P probably damaging Het
Sema4d T C 13: 51,865,390 (GRCm39) N318S possibly damaging Het
Sis C T 3: 72,798,754 (GRCm39) V1765I probably benign Het
Slc17a6 A T 7: 51,276,598 (GRCm39) K116* probably null Het
Smc6 T A 12: 11,341,540 (GRCm39) H519Q probably benign Het
Sowahc T A 10: 59,058,785 (GRCm39) M307K probably benign Het
Sptbn1 A G 11: 30,087,560 (GRCm39) Y960H probably damaging Het
Tmem270 A C 5: 134,931,636 (GRCm39) V102G probably benign Het
Tmprss11d A G 5: 86,486,729 (GRCm39) F54L probably benign Het
Top1 T A 2: 160,544,695 (GRCm39) Y270* probably null Het
Trpm2 A G 10: 77,771,795 (GRCm39) F615L probably benign Het
Ttf2 A G 3: 100,866,558 (GRCm39) S525P probably damaging Het
Ttn A T 2: 76,777,241 (GRCm39) M1387K possibly damaging Het
Upk3bl A T 5: 136,088,954 (GRCm39) R156W probably damaging Het
Usp34 G T 11: 23,299,198 (GRCm39) R290L probably benign Het
Vwf T C 6: 125,620,005 (GRCm39) V1561A Het
Zan A G 5: 137,420,155 (GRCm39) I2834T unknown Het
Zfp105 A G 9: 122,755,454 (GRCm39) Y90C probably benign Het
Zfp804a T C 2: 82,089,339 (GRCm39) V1056A probably damaging Het
Zfp956 A T 6: 47,930,455 (GRCm39) probably benign Het
Other mutations in Rxrb
AlleleSourceChrCoordTypePredicted EffectPPH 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
R5119:Rxrb UTSW 17 34,252,562 (GRCm39) missense probably benign 0.10
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'- CCTCTCACAAGGAAGGTGTC -3'
(R):5'- GGACATCAATGGACCGATGG -3'

Sequencing Primer
(F):5'- CTGTTCACACTCGTTGAG -3'
(R):5'- AATGAGGAGCTCGTTCCAGC -3'
Posted On 2016-10-05