Mutagenetix > Incidental Mutation

Incidental Mutation 'R9090:Rarb'

690945

Institutional Source

Beutler Lab

Gene Symbol

Rarb

Ensembl Gene

ENSMUSG00000017491

Gene Name

retinoic acid receptor, beta

Synonyms

RARbeta2, RAR beta 2, Hap

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9090 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

5650540-6038924 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

A to T at 16435235 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Stop codon at position 270 (Y270*)

Ref Sequence

ENSEMBL: ENSMUSP00000067694 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000017629] [ENSMUST00000063750] [ENSMUST00000223576] [ENSMUST00000225921]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000017629

SMART Domains

Protein: ENSMUSP00000017629
Gene: ENSMUSG00000017485

Domain	Start	End	E-Value	Type
Blast:TOP2c	32	70	7e-10	BLAST
HATPase_c	85	234	1.91e-2	SMART
TOP2c	89	679	N/A	SMART
TOP4c	702	1175	2.55e-230	SMART
low complexity region	1201	1215	N/A	INTRINSIC
low complexity region	1287	1299	N/A	INTRINSIC
low complexity region	1324	1336	N/A	INTRINSIC
low complexity region	1360	1382	N/A	INTRINSIC
Pfam:DTHCT	1495	1597	4.6e-31	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000063750
AA Change: Y270*

SMART Domains

Protein: ENSMUSP00000067694
Gene: ENSMUSG00000017491
AA Change: Y270*

Domain	Start	End	E-Value	Type
low complexity region	52	75	N/A	INTRINSIC
ZnF_C4	78	149	3.77e-40	SMART
HOLI	223	381	1.72e-34	SMART
low complexity region	428	445	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000223576

Predicted Effect

probably benign
Transcript: ENSMUST00000225921

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.2%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes retinoic acid receptor beta, a member of the thyroid-steroid hormone receptor superfamily of nuclear transcriptional regulators. This receptor localizes to the cytoplasm and to subnuclear compartments. It binds retinoic acid, the biologically active form of vitamin A which mediates cellular signalling in embryonic morphogenesis, cell growth and differentiation. It is thought that this protein limits growth of many cell types by regulating gene expression. The gene was first identified in a hepatocellular carcinoma where it flanks a hepatitis B virus integration site. Alternate promoter usage and differential splicing result in multiple transcript variants. [provided by RefSeq, Mar 2014]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit reduced growth, but are otherwise normal. Rarb/Rara double knockouts exhibit impaired vitamin A signaling and develop urogenital malformations, including renal hypoplasia and hydronephrosis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 106 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aatk	A	T	11: 119,901,940 (GRCm39)	S819T	probably damaging	Het
Abca13	A	T	11: 9,241,698 (GRCm39)	D1187V	probably damaging	Het
Ak9	C	A	10: 41,300,623 (GRCm39)	T1611K	unknown	Het
Als2	G	T	1: 59,242,189 (GRCm39)	T622K	probably benign	Het
Ankrd40	G	A	11: 94,225,262 (GRCm39)	A98T	probably benign	Het
Ap1b1	T	C	11: 4,973,174 (GRCm39)	L339P	probably damaging	Het
Appl1	A	C	14: 26,669,084 (GRCm39)	H363Q	probably benign	Het
Atf6	T	C	1: 170,622,245 (GRCm39)	N459D	probably damaging	Het
Ccdc6	A	T	10: 70,024,993 (GRCm39)	Q432L	unknown	Het
Ccl21a	T	A	4: 42,773,486 (GRCm39)	Q84L	probably damaging	Het
Cct4	A	G	11: 22,951,389 (GRCm39)	I348V	probably benign	Het
Cd300ld2	A	G	11: 114,904,550 (GRCm39)	Y106H	probably damaging	Het
Cdh19	C	T	1: 110,876,947 (GRCm39)	E131K	probably damaging	Het
Cdon	A	G	9: 35,403,175 (GRCm39)	D1095G	probably damaging	Het
Cep85l	T	A	10: 53,157,670 (GRCm39)	R678*	probably null	Het
Chst3	T	A	10: 60,021,465 (GRCm39)	S461C	probably damaging	Het
Clk1	A	G	1: 58,459,312 (GRCm39)	I149T	possibly damaging	Het
Clvs2	T	A	10: 33,389,301 (GRCm39)	D313V	possibly damaging	Het
Dap3	T	C	3: 88,840,913 (GRCm39)	T75A	probably benign	Het
Dnaaf1	T	A	8: 120,324,392 (GRCm39)	F631L	probably benign	Het
Dnah14	A	T	1: 181,597,325 (GRCm39)	N3549I	probably benign	Het
Dnah17	A	T	11: 117,931,870 (GRCm39)	Y3701N	probably damaging	Het
Dock6	A	G	9: 21,752,796 (GRCm39)	V339A	possibly damaging	Het
Dpp6	T	A	5: 27,803,832 (GRCm39)	C259*	probably null	Het
Dqx1	A	G	6: 83,036,024 (GRCm39)	T119A	probably benign	Het
Dync1h1	G	T	12: 110,583,310 (GRCm39)	R469L	probably benign	Het
Eno4	C	T	19: 58,951,260 (GRCm39)	A424V	probably benign	Het
Entrep1	A	T	19: 23,972,221 (GRCm39)	I161N	possibly damaging	Het
Fads1	T	A	19: 10,163,162 (GRCm39)	D146E	probably damaging	Het
Fam171a1	C	T	2: 3,224,543 (GRCm39)	T303M	probably damaging	Het
Fbxw20	C	T	9: 109,050,423 (GRCm39)	D401N	probably benign	Het
Fcho1	T	A	8: 72,163,068 (GRCm39)	T654S	possibly damaging	Het
Flad1	C	A	3: 89,315,858 (GRCm39)	E235*	probably null	Het
Flrt2	G	T	12: 95,745,907 (GRCm39)	A82S	probably benign	Het
Gabrg3	A	T	7: 56,829,386 (GRCm39)	S124T	probably benign	Het
Galt	C	T	4: 41,756,777 (GRCm39)	T139I	probably benign	Het
Garin4	A	G	1: 190,895,153 (GRCm39)	S497P	probably damaging	Het
Gfod1	T	C	13: 43,456,861 (GRCm39)	E38G	possibly damaging	Het
Gm10330	A	G	12: 23,829,992 (GRCm39)	I63T	possibly damaging	Het
Gm49359	A	G	13: 62,602,867 (GRCm39)	V111A	probably benign	Het
Gpank1	C	T	17: 35,340,734 (GRCm39)		probably benign	Het
Hck	T	C	2: 152,973,185 (GRCm39)	L156P	probably damaging	Het
Hcn3	G	T	3: 89,057,267 (GRCm39)	R444S	probably damaging	Het
Hephl1	T	C	9: 14,988,236 (GRCm39)	N624S	probably damaging	Het
Hmcn1	A	G	1: 150,632,309 (GRCm39)	I876T	probably damaging	Het
Ifi207	CTGTTGATGAAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG	CTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGTTGTTGATAGAGTTGCATGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATACAGTTGCTTGTGGAGCCAGGAGGTTGCTAGATGCTGTTGATAGAGTTGCATATGGAGCCAGGAGGATGCTATATGTTGTTGATGAAGTTGCATGTGGAGCCAGGAG	1: 173,556,762 (GRCm39)		probably benign	Het
Itga9	T	A	9: 118,500,859 (GRCm39)	D377E	possibly damaging	Het
Itpr3	G	A	17: 27,337,651 (GRCm39)		probably benign	Het
Itprid1	G	T	6: 55,944,051 (GRCm39)	R417L	probably benign	Het
Klk1b11	C	T	7: 43,425,954 (GRCm39)	L32F	probably benign	Het
Lta4h	A	G	10: 93,310,412 (GRCm39)	S427G	probably benign	Het
Lxn	T	A	3: 67,368,651 (GRCm39)	I122F	probably damaging	Het
Lyz1	A	G	10: 117,124,492 (GRCm39)	V148A	possibly damaging	Het
Mael	G	T	1: 166,032,424 (GRCm39)	Q326K	probably benign	Het
Magi3	T	C	3: 103,923,264 (GRCm39)	D1151G	possibly damaging	Het
Map3k9	C	A	12: 81,769,261 (GRCm39)	G929V	probably benign	Het
Mcoln1	A	G	8: 3,555,771 (GRCm39)	Y22C	probably damaging	Het
Mier3	G	T	13: 111,827,870 (GRCm39)	M45I	probably benign	Het
Mrpl1	T	C	5: 96,371,746 (GRCm39)	V91A	probably damaging	Het
Myo7a	T	C	7: 97,740,281 (GRCm39)	H571R	probably benign	Het
Myom1	T	A	17: 71,374,325 (GRCm39)	W601R	probably damaging	Het
Myom3	C	T	4: 135,505,479 (GRCm39)	T456I	probably benign	Het
Nags	A	T	11: 102,037,584 (GRCm39)	H225L	probably benign	Het
Ncaph	C	A	2: 126,958,554 (GRCm39)	K488N	probably damaging	Het
Nkain3	C	T	4: 20,484,897 (GRCm39)	R60H	probably damaging	Het
Nlrp9a	A	T	7: 26,261,944 (GRCm39)	M698L	probably benign	Het
Nmur2	A	C	11: 55,931,308 (GRCm39)	I134M	probably benign	Het
Nrp2	A	C	1: 62,784,670 (GRCm39)	E273A	probably benign	Het
Nup85	A	G	11: 115,468,787 (GRCm39)	D210G	possibly damaging	Het
Obscn	A	G	11: 59,006,643 (GRCm39)	F1173S	probably damaging	Het
Or5ac24	A	T	16: 59,165,145 (GRCm39)	C306*	probably null	Het
Otogl	T	A	10: 107,652,974 (GRCm39)	E1126V	probably null	Het
Pfkl	T	C	10: 77,833,426 (GRCm39)	I259V	probably benign	Het
Phkg1	A	T	5: 129,893,863 (GRCm39)	Y291N	probably benign	Het
Piezo2	T	G	18: 63,163,450 (GRCm39)	H2156P	probably damaging	Het
Piezo2	C	A	18: 63,208,790 (GRCm39)	V1408L	probably damaging	Het
Pira13	T	A	7: 3,819,997 (GRCm39)	E640V	unknown	Het
Plekhg3	A	G	12: 76,622,694 (GRCm39)	T646A	probably benign	Het
Plk5	C	G	10: 80,193,830 (GRCm39)	R40G	probably damaging	Het
Ppp1r12a	T	C	10: 108,098,224 (GRCm39)	S838P	probably damaging	Het
Rbm15	T	C	3: 107,239,312 (GRCm39)	E362G	possibly damaging	Het
Rcan1	A	G	16: 92,262,741 (GRCm39)	F76L		Het
Rdh19	T	C	10: 127,696,142 (GRCm39)	L298P	probably damaging	Het
Rims1	T	A	1: 22,498,773 (GRCm39)	H57L		Het
Rlf	T	C	4: 121,004,751 (GRCm39)	T1520A	probably benign	Het
Rnase1	T	A	14: 51,382,964 (GRCm39)	H130L	possibly damaging	Het
Samd8	T	A	14: 21,842,569 (GRCm39)	M360K	probably damaging	Het
Samhd1	A	G	2: 156,956,205 (GRCm39)	L329P	probably damaging	Het
Scube1	C	T	15: 83,494,394 (GRCm39)	E878K	probably damaging	Het
Sema3b	T	C	9: 107,476,154 (GRCm39)	Y689C	probably damaging	Het
Semp2l2a	T	C	8: 13,886,697 (GRCm39)	T465A	possibly damaging	Het
Sh3pxd2b	A	T	11: 32,373,361 (GRCm39)	N843Y	possibly damaging	Het
Slco1a6	C	T	6: 142,035,575 (GRCm39)	C583Y	probably damaging	Het
Smg1	A	C	7: 117,811,786 (GRCm39)	V88G	unknown	Het
Spata24	T	A	18: 35,790,054 (GRCm39)	N146Y	probably damaging	Het
Tcf3	C	A	10: 80,253,191 (GRCm39)	V258L	probably benign	Het
Tiam2	T	C	17: 3,465,011 (GRCm39)	Y247H	probably damaging	Het
Ticrr	T	C	7: 79,310,604 (GRCm39)	F173L	possibly damaging	Het
Tpp2	A	G	1: 43,993,811 (GRCm39)	E232G	probably damaging	Het
Trank1	T	A	9: 111,174,547 (GRCm39)	V138E	probably damaging	Het
Ttll3	T	C	6: 113,369,596 (GRCm39)	S47P	probably benign	Het
Utp4	C	T	8: 107,632,857 (GRCm39)	T280M	probably damaging	Het
Vmn1r123	A	T	7: 20,896,794 (GRCm39)	N229Y	probably benign	Het
Vmn1r85	A	T	7: 12,818,942 (GRCm39)	Y67*	probably null	Het
Zbtb12	T	A	17: 35,114,320 (GRCm39)	V35E	possibly damaging	Het
Zmym6	T	A	4: 127,017,854 (GRCm39)	F1212I	probably damaging	Het

Other mutations in Rarb

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00756:Rarb	APN	14	16,443,791 (GRCm38)	nonsense	probably null
IGL01483:Rarb	APN	14	16,432,273 (GRCm38)	splice site	probably benign
IGL01591:Rarb	APN	14	16,434,207 (GRCm38)	missense	possibly damaging	0.93
IGL01769:Rarb	APN	14	16,443,760 (GRCm38)	missense	probably damaging	0.97
IGL01782:Rarb	APN	14	16,434,180 (GRCm38)	missense	probably damaging	1.00
IGL01866:Rarb	APN	14	16,443,751 (GRCm38)	missense	probably benign	0.17
IGL03299:Rarb	APN	14	16,434,168 (GRCm38)	missense	probably damaging	1.00
IGL03134:Rarb	UTSW	14	16,436,910 (GRCm38)	missense	probably damaging	0.99
R0055:Rarb	UTSW	14	16,509,066 (GRCm38)	missense	probably damaging	1.00
R0055:Rarb	UTSW	14	16,509,066 (GRCm38)	missense	probably damaging	1.00
R0849:Rarb	UTSW	14	16,434,293 (GRCm38)	missense	probably damaging	1.00
R1067:Rarb	UTSW	14	16,436,769 (GRCm38)	missense	probably damaging	0.98
R1314:Rarb	UTSW	14	16,508,932 (GRCm38)	critical splice donor site	probably null
R1416:Rarb	UTSW	14	16,435,177 (GRCm38)	missense	possibly damaging	0.82
R2894:Rarb	UTSW	14	16,435,146 (GRCm38)	missense	probably damaging	1.00
R4637:Rarb	UTSW	14	16,574,875 (GRCm38)	missense	possibly damaging	0.51
R4950:Rarb	UTSW	14	16,432,085 (GRCm38)	unclassified	probably benign
R5420:Rarb	UTSW	14	16,434,249 (GRCm38)	missense	possibly damaging	0.89
R5456:Rarb	UTSW	14	16,436,843 (GRCm38)	missense	probably damaging	1.00
R5635:Rarb	UTSW	14	16,443,788 (GRCm38)	missense	probably damaging	1.00
R5689:Rarb	UTSW	14	16,434,177 (GRCm38)	missense	probably damaging	1.00
R5708:Rarb	UTSW	14	16,548,545 (GRCm38)	missense	probably damaging	0.99
R5819:Rarb	UTSW	14	16,443,820 (GRCm38)	missense	possibly damaging	0.68
R5935:Rarb	UTSW	14	16,434,264 (GRCm38)	missense	probably damaging	1.00
R6264:Rarb	UTSW	14	16,818,819 (GRCm38)	missense	probably benign	0.31
R6823:Rarb	UTSW	14	16,443,824 (GRCm38)	missense	probably damaging	1.00
R6975:Rarb	UTSW	14	16,574,942 (GRCm38)	missense	possibly damaging	0.92
R7295:Rarb	UTSW	14	16,508,932 (GRCm38)	critical splice donor site	probably null
R7402:Rarb	UTSW	14	16,548,419 (GRCm38)	missense	probably damaging	1.00
R7849:Rarb	UTSW	14	16,548,473 (GRCm38)	missense	probably damaging	1.00
R8471:Rarb	UTSW	14	16,548,456 (GRCm38)	unclassified	probably benign
R8833:Rarb	UTSW	14	16,819,015 (GRCm38)	unclassified	probably benign
R8835:Rarb	UTSW	14	16,575,011 (GRCm38)	missense	probably benign	0.23
R8896:Rarb	UTSW	14	16,436,804 (GRCm38)	missense	probably damaging	1.00
R9011:Rarb	UTSW	14	16,435,140 (GRCm38)	missense	probably damaging	0.98
R9184:Rarb	UTSW	14	16,818,882 (GRCm38)	start gained	probably benign
R9184:Rarb	UTSW	14	16,818,881 (GRCm38)	start gained	probably benign
R9271:Rarb	UTSW	14	16,435,235 (GRCm38)	nonsense	probably null
R9574:Rarb	UTSW	14	16,574,858 (GRCm38)	missense	probably damaging	0.96
X0065:Rarb	UTSW	14	16,434,303 (GRCm38)	missense	possibly damaging	0.89
Z1177:Rarb	UTSW	14	16,818,725 (GRCm38)	missense	possibly damaging	0.50

Predicted Primers

PCR Primer
(F):5'- CCACAGATTAAACAGATGGCACTG -3'
(R):5'- GTGCCTGAGAGGTAAGTACTC -3'

Sequencing Primer
(F):5'- GCACTGAGAAGGCCTGTTTC -3'
(R):5'- ATGACCCAGGCTCCTTTT -3'

Posted On

2021-12-30