Mutagenetix > Incidental Mutation

Incidental Mutation 'R5935:Rarb'

462212

Institutional Source

Beutler Lab

Gene Symbol

Rarb

Ensembl Gene

ENSMUSG00000017491

Gene Name

retinoic acid receptor, beta

Synonyms

RARbeta2, RAR beta 2, Hap

MMRRC Submission

044129-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5935 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

5650540-6038924 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 16434264 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Serine at position 305 (A305S)

Ref Sequence

ENSEMBL: ENSMUSP00000152980 (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

possibly damaging
Transcript: ENSMUST00000063750
AA Change: A351S

PolyPhen 2 Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000067694
Gene: ENSMUSG00000017491
AA Change: A351S

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 damaging
Transcript: ENSMUST00000225921
AA Change: A305S

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

Meta Mutation Damage Score

0.3736

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.8%

Validation Efficiency

96% (92/96)

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam26b	C	G	8: 43,974,335 (GRCm39)	M222I	probably benign	Het
Ahnak	T	C	19: 8,992,546 (GRCm39)	V4610A	possibly damaging	Het
Ankrd13c	C	T	3: 157,653,220 (GRCm39)		silent	Het
Cables2	A	G	2: 179,903,841 (GRCm39)		probably benign	Het
Cabp2	C	A	19: 4,136,497 (GRCm39)	A181D	probably damaging	Het
Camsap3	A	G	8: 3,651,999 (GRCm39)	D265G	probably damaging	Het
Cbs	G	T	17: 31,851,853 (GRCm39)	T50N	probably damaging	Het
Cenpa	A	T	5: 30,830,381 (GRCm39)	Q83L	possibly damaging	Het
Cit	A	T	5: 116,063,598 (GRCm39)		probably benign	Het
Ckap5	A	G	2: 91,445,445 (GRCm39)	E1694G	possibly damaging	Het
Copz1	A	T	15: 103,203,197 (GRCm39)	M104L	probably benign	Het
Crot	T	A	5: 9,024,192 (GRCm39)	M335L	probably benign	Het
Ctnna2	T	C	6: 77,120,904 (GRCm39)	D373G	probably benign	Het
Ctu2	G	A	8: 123,203,693 (GRCm39)		probably benign	Het
Cyp3a59	T	A	5: 146,027,455 (GRCm39)	Y75*	probably null	Het
Dbi	A	G	1: 120,048,583 (GRCm39)	I21T	probably benign	Het
Dcun1d3	A	G	7: 119,458,799 (GRCm39)	S79P	probably benign	Het
Dock10	T	A	1: 80,483,304 (GRCm39)		probably benign	Het
Dstyk	T	A	1: 132,381,875 (GRCm39)	I543N	probably damaging	Het
Epx	G	T	11: 87,756,318 (GRCm39)	A621E	probably damaging	Het
Farp2	G	A	1: 93,548,367 (GRCm39)		probably null	Het
Gm11992	C	T	11: 9,002,711 (GRCm39)	P25S	probably damaging	Het
Grik5	A	T	7: 24,758,502 (GRCm39)	M307K	possibly damaging	Het
Hnf1b	A	T	11: 83,773,503 (GRCm39)	N234I	probably damaging	Het
Htr2a	A	G	14: 74,882,530 (GRCm39)	D172G	probably damaging	Het
Ifit1bl2	T	C	19: 34,597,128 (GRCm39)	T163A	probably benign	Het
Igsf10	A	T	3: 59,235,578 (GRCm39)	D1534E	probably benign	Het
Il3ra	T	G	14: 14,350,799 (GRCm38)	V178G	probably damaging	Het
Itgb1	A	T	8: 129,439,718 (GRCm39)	K136*	probably null	Het
Itprid1	A	T	6: 55,874,754 (GRCm39)	R235*	probably null	Het
Lama2	T	A	10: 26,891,494 (GRCm39)	I2540F	probably benign	Het
Lrp8	C	A	4: 107,714,493 (GRCm39)	H622Q	probably damaging	Het
Lrrc2	T	A	9: 110,795,629 (GRCm39)	M138K	probably benign	Het
Lrrk2	C	A	15: 91,630,034 (GRCm39)	H1242N	probably benign	Het
Lsm11	G	C	11: 45,835,445 (GRCm39)	R99G	probably benign	Het
Mif4gd	C	T	11: 115,500,439 (GRCm39)	V40M	probably benign	Het
Mpp3	A	T	11: 101,916,241 (GRCm39)	V37D	probably damaging	Het
Mre11a	T	A	9: 14,698,258 (GRCm39)	D35E	probably damaging	Het
Mroh4	C	A	15: 74,493,003 (GRCm39)	V233F	probably damaging	Het
Npy2r	A	T	3: 82,448,068 (GRCm39)	S123T	possibly damaging	Het
Nrip2	A	G	6: 128,385,361 (GRCm39)	Y264C	possibly damaging	Het
Obscn	A	G	11: 58,897,639 (GRCm39)	S6639P	unknown	Het
Or10d4	C	T	9: 39,580,386 (GRCm39)	T11I	probably benign	Het
Or51t4	T	A	7: 102,598,017 (GRCm39)	F105Y	probably benign	Het
Osbpl5	C	T	7: 143,310,695 (GRCm39)		probably benign	Het
Panx1	A	T	9: 14,921,513 (GRCm39)	Y121N	probably damaging	Het
Pcdhb8	A	G	18: 37,489,243 (GRCm39)	D307G	probably damaging	Het
Pde1b	A	G	15: 103,429,866 (GRCm39)	K120E	possibly damaging	Het
Pdzrn4	T	C	15: 92,295,255 (GRCm39)	S154P	probably benign	Het
Ppp1r13b	T	C	12: 111,796,876 (GRCm39)	K889R	probably benign	Het
Ppp4r3a	T	A	12: 101,017,872 (GRCm39)	D439V	probably damaging	Het
Ptk2b	A	G	14: 66,411,328 (GRCm39)	I401T	probably damaging	Het
Rab24	T	C	13: 55,468,343 (GRCm39)	T153A	probably damaging	Het
Rc3h2	GCC	GCCC	2: 37,304,745 (GRCm39)		probably null	Het
Scn10a	G	A	9: 119,456,237 (GRCm39)	T1194I	probably damaging	Het
Scn3a	G	T	2: 65,295,180 (GRCm39)	N1514K	probably damaging	Het
Serpinb3d	T	C	1: 107,011,105 (GRCm39)	T36A	probably benign	Het
Shisa5	T	A	9: 108,885,751 (GRCm39)	M229K	possibly damaging	Het
Sik2	C	T	9: 50,828,431 (GRCm39)	G204R	probably damaging	Het
Sla	C	T	15: 66,665,554 (GRCm39)	G46E	probably damaging	Het
Slc35g3	A	T	11: 69,652,509 (GRCm39)	M1K	probably null	Het
Slc5a7	A	T	17: 54,583,972 (GRCm39)	Y439*	probably null	Het
Slc9a1	T	C	4: 133,147,176 (GRCm39)		probably benign	Het
Slitrk6	T	G	14: 110,987,305 (GRCm39)	T801P	probably benign	Het
Spata31d1c	T	C	13: 65,184,894 (GRCm39)	V812A	possibly damaging	Het
Spata31g1	T	C	4: 42,971,465 (GRCm39)	L230P	probably benign	Het
Spef1l	G	A	7: 139,556,526 (GRCm39)	H154Y	probably benign	Het
Sphkap	A	C	1: 83,317,320 (GRCm39)	L59R	probably damaging	Het
Spmip8	A	T	8: 96,046,620 (GRCm39)	T98S	possibly damaging	Het
Srsf10	C	A	4: 135,583,553 (GRCm39)	R6S	probably damaging	Het
Supt5	T	A	7: 28,028,900 (GRCm39)	R131S	probably benign	Het
Syne1	T	C	10: 5,310,706 (GRCm39)		probably null	Het
Tet2	T	A	3: 133,194,296 (GRCm39)	H46L	possibly damaging	Het
Tnfsf4	T	A	1: 161,244,819 (GRCm39)	N169K	probably damaging	Het
Tprg1	A	T	16: 25,136,011 (GRCm39)	M1L	possibly damaging	Het
Tsen2	A	G	6: 115,536,556 (GRCm39)	Y104C	probably damaging	Het
Ttc6	A	G	12: 57,720,590 (GRCm39)	Y952C	probably damaging	Het
Umod	A	T	7: 119,070,650 (GRCm39)	I414N	probably damaging	Het
Usp10	G	T	8: 120,673,828 (GRCm39)	V398L	possibly damaging	Het
Vmn2r23	A	T	6: 123,718,854 (GRCm39)	I736F	possibly damaging	Het
Vmn2r65	C	A	7: 84,592,869 (GRCm39)	G446V	probably benign	Het
Wbp1l	C	T	19: 46,642,619 (GRCm39)	R191*	probably null	Het
Yars2	A	G	16: 16,127,335 (GRCm39)	I467V	probably benign	Het
Ykt6	A	G	11: 5,909,338 (GRCm39)	E49G	possibly damaging	Het
Zan	T	A	5: 137,442,192 (GRCm39)	M1907L	unknown	Het
Zdhhc2	T	C	8: 40,917,277 (GRCm39)	S225P	probably damaging	Het
Zfc3h1	A	T	10: 115,267,262 (GRCm39)		probably benign	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
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
R9090:Rarb	UTSW	14	16,435,235 (GRCm38)	nonsense	probably null
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'- TGGGACTCCTGATATTAAAATATGGGC -3'
(R):5'- GGGGCATCTTCAAGTGTCAC -3'

Sequencing Primer
(F):5'- CTTTAAAAAGCAAAAGTTGGCCAAGC -3'
(R):5'- CTTCAAGTGTCACTGCTTAAAGC -3'

Posted On

2017-02-28