Mutagenetix > Incidental Mutation

Incidental Mutation 'R2057:Rarg'

228304

Institutional Source

Beutler Lab

Gene Symbol

Rarg

Ensembl Gene

ENSMUSG00000001288

Gene Name

retinoic acid receptor, gamma

Synonyms

RAR gamma 2, RARgamma2

MMRRC Submission

040062-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.741) question?

Stock #

R2057 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

102143373-102165891 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 102147939 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Serine at position 291 (A291S)

Ref Sequence

ENSEMBL: ENSMUSP00000067266 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000043172] [ENSMUST00000063339] [ENSMUST00000130204] [ENSMUST00000135466] [ENSMUST00000155563]

AlphaFold

P18911

Predicted Effect

possibly damaging
Transcript: ENSMUST00000043172
AA Change: A302S

PolyPhen 2 Score 0.954 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000048838
Gene: ENSMUSG00000001288
AA Change: A302S

Domain	Start	End	E-Value	Type
low complexity region	10	32	N/A	INTRINSIC
low complexity region	75	84	N/A	INTRINSIC
ZnF_C4	87	158	1.53e-40	SMART
HOLI	232	390	9.07e-34	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000063339
AA Change: A291S

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000067266
Gene: ENSMUSG00000001288
AA Change: A291S

Domain	Start	End	E-Value	Type
low complexity region	10	29	N/A	INTRINSIC
low complexity region	48	61	N/A	INTRINSIC
low complexity region	64	73	N/A	INTRINSIC
ZnF_C4	76	147	1.53e-40	SMART
HOLI	221	379	9.07e-34	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124224

Predicted Effect

probably benign
Transcript: ENSMUST00000130204

Predicted Effect

probably benign
Transcript: ENSMUST00000135466

SMART Domains

Protein: ENSMUSP00000118615
Gene: ENSMUSG00000001288

Domain	Start	End	E-Value	Type
low complexity region	10	32	N/A	INTRINSIC
low complexity region	75	84	N/A	INTRINSIC
ZnF_C4	87	158	1.53e-40	SMART
PDB:1EXX\|A	178	227	5e-28	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000155563

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.5%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a retinoic acid receptor that belongs to the nuclear hormone receptor family. Retinoic acid receptors (RARs) act as ligand-dependent transcriptional regulators. When bound to ligands, RARs activate transcription by binding as heterodimers to the retinoic acid response elements (RARE) found in the promoter regions of the target genes. In their unbound form, RARs repress transcription of their target genes. RARs are involved in various biological processes, including limb bud development, skeletal growth, and matrix homeostasis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
PHENOTYPE: Homozygotes for targeted null mutations exhibit stunted growth, homeotic transformations of the rostral axial skeleton and tracheal cartilage, Harderian gland agenesis, high postnatal mortality, and male sterility. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 78 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc2	A	G	19: 43,806,477 (GRCm39)	K764E	probably damaging	Het
Abcg2	T	C	6: 58,667,525 (GRCm39)	V129A	probably benign	Het
Adgrf5	A	G	17: 43,739,477 (GRCm39)	Y72C	possibly damaging	Het
Ago1	C	T	4: 126,337,021 (GRCm39)	R228H	probably damaging	Het
Ano1	A	G	7: 144,201,789 (GRCm39)	V334A	probably damaging	Het
Apob	A	T	12: 8,052,164 (GRCm39)	R1202*	probably null	Het
Arfgap3	G	T	15: 83,194,501 (GRCm39)	D389E	probably benign	Het
Atf6b	A	T	17: 34,867,549 (GRCm39)		probably null	Het
Atoh8	T	C	6: 72,212,112 (GRCm39)	K13E	probably damaging	Het
Bicral	G	T	17: 47,135,814 (GRCm39)	N465K	possibly damaging	Het
Bves	T	A	10: 45,219,231 (GRCm39)	Y110N	probably damaging	Het
C4b	A	G	17: 34,947,594 (GRCm39)	Y1695H	probably damaging	Het
Cage1	A	G	13: 38,207,356 (GRCm39)	V163A	probably benign	Het
Canx	T	C	11: 50,195,252 (GRCm39)	N272S	probably damaging	Het
Caskin1	G	T	17: 24,715,433 (GRCm39)	G93V	probably damaging	Het
Cd34	T	C	1: 194,641,450 (GRCm39)	V292A	probably damaging	Het
Cd84	A	G	1: 171,700,317 (GRCm39)	T145A	possibly damaging	Het
Cdh16	C	A	8: 105,348,597 (GRCm39)	G144*	probably null	Het
Chaf1b	T	A	16: 93,691,795 (GRCm39)	H280Q	probably damaging	Het
Chpf2	G	A	5: 24,796,220 (GRCm39)	G389R	probably damaging	Het
Crb1	T	C	1: 139,242,488 (GRCm39)	Y330C	probably damaging	Het
Cux2	A	T	5: 122,007,567 (GRCm39)	V698E	probably benign	Het
Dhtkd1	A	G	2: 5,947,430 (GRCm39)	V18A	unknown	Het
Dmbt1	G	A	7: 130,707,900 (GRCm39)	A1381T	possibly damaging	Het
Enpp1	C	G	10: 24,536,090 (GRCm39)	A437P	probably damaging	Het
Fat2	C	T	11: 55,172,686 (GRCm39)	V2676I	possibly damaging	Het
Fzd2	A	G	11: 102,496,759 (GRCm39)	D401G	probably damaging	Het
Gcm2	T	C	13: 41,263,430 (GRCm39)	M1V	probably null	Het
Gnai3	C	T	3: 108,019,812 (GRCm39)	V233I	probably benign	Het
Golim4	T	A	3: 75,802,194 (GRCm39)	D366V	possibly damaging	Het
Grin1	T	A	2: 25,206,832 (GRCm39)	T110S	probably damaging	Het
Grin2a	A	G	16: 9,487,608 (GRCm39)	V430A	probably benign	Het
Gstp3	G	A	19: 4,109,282 (GRCm39)	T5I	probably damaging	Het
Il17rb	T	A	14: 29,719,111 (GRCm39)	M324L	probably benign	Het
Jmy	A	G	13: 93,596,211 (GRCm39)	Y473H	probably damaging	Het
Khdc1b	A	G	1: 21,454,534 (GRCm39)	D79G	probably benign	Het
Kremen2	T	C	17: 23,961,691 (GRCm39)	E272G	possibly damaging	Het
Lmo7	G	C	14: 102,124,614 (GRCm39)	A358P	probably damaging	Het
Mdh1b	T	C	1: 63,760,741 (GRCm39)	I107V	probably benign	Het
Mlkl	T	C	8: 112,060,242 (GRCm39)	Q48R	probably benign	Het
Myh2	G	A	11: 67,079,665 (GRCm39)		probably null	Het
Naip1	T	A	13: 100,562,081 (GRCm39)	Q1028L	probably damaging	Het
Ncald	T	A	15: 37,397,423 (GRCm39)	I86F	possibly damaging	Het
Nid1	A	C	13: 13,675,058 (GRCm39)	H926P	probably benign	Het
Nlrp9a	T	A	7: 26,256,787 (GRCm39)	I46K	possibly damaging	Het
Or1p1	A	G	11: 74,179,652 (GRCm39)	Y60C	probably damaging	Het
Or9r3	A	T	10: 129,947,859 (GRCm39)	S267T	probably benign	Het
Pak1	T	A	7: 97,557,004 (GRCm39)		probably null	Het
Parpbp	T	A	10: 87,960,824 (GRCm39)	M221L	probably benign	Het
Pde12	T	C	14: 26,390,035 (GRCm39)	I225V	probably benign	Het
Phf19	G	T	2: 34,789,620 (GRCm39)	R367S	probably benign	Het
Plcl2	A	G	17: 50,975,139 (GRCm39)		probably null	Het
Plxnb1	A	T	9: 108,938,294 (GRCm39)	I1283F	possibly damaging	Het
Pramel6	T	A	2: 87,339,059 (GRCm39)	N86K	possibly damaging	Het
Prkdc	A	G	16: 15,545,469 (GRCm39)	T1862A	probably benign	Het
Prpf40a	A	T	2: 53,034,851 (GRCm39)	I779K	probably damaging	Het
Prss3b	G	A	6: 41,009,315 (GRCm39)	T173I	probably benign	Het
Ptpn20	A	T	14: 33,352,942 (GRCm39)	E227V	probably damaging	Het
Rad54b	C	T	4: 11,606,088 (GRCm39)	R499C	probably benign	Het
Rnf169	A	T	7: 99,574,615 (GRCm39)	L660Q	probably damaging	Het
Scn4a	A	G	11: 106,226,550 (GRCm39)	V670A	probably damaging	Het
Serpinb9c	A	T	13: 33,340,854 (GRCm39)	C81*	probably null	Het
Sik1	A	G	17: 32,067,771 (GRCm39)	S435P	probably benign	Het
Slc35g2	G	A	9: 100,435,329 (GRCm39)	A114V	probably damaging	Het
Slc7a14	A	T	3: 31,291,645 (GRCm39)	V211E	probably damaging	Het
Snrpn	A	T	7: 59,637,204 (GRCm39)	H37Q	possibly damaging	Het
Spock3	T	A	8: 63,698,204 (GRCm39)	C185*	probably null	Het
Tbc1d4	A	G	14: 101,714,591 (GRCm39)	S627P	probably damaging	Het
Tgoln1	T	C	6: 72,592,653 (GRCm39)	T276A	probably benign	Het
Tmem176b	G	A	6: 48,813,267 (GRCm39)	T64I	probably damaging	Het
Tnpo2	T	C	8: 85,776,742 (GRCm39)	L483P	probably damaging	Het
Tpte	T	A	8: 22,808,355 (GRCm39)	D163E	probably benign	Het
Trim36	A	T	18: 46,329,229 (GRCm39)	D70E	probably benign	Het
Umodl1	G	A	17: 31,227,740 (GRCm39)		probably null	Het
Wdr90	T	C	17: 26,074,173 (GRCm39)	T691A	probably benign	Het
Zdhhc8	A	G	16: 18,046,210 (GRCm39)	S118P	probably damaging	Het
Zfp438	T	C	18: 5,214,085 (GRCm39)	E291G	probably benign	Het
Zfp879	C	T	11: 50,723,428 (GRCm39)	E543K	probably benign	Het

Other mutations in Rarg

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02877:Rarg	APN	15	102,150,374 (GRCm39)	splice site	probably null
R0033:Rarg	UTSW	15	102,147,270 (GRCm39)	missense	probably damaging	0.99
R0539:Rarg	UTSW	15	102,147,312 (GRCm39)	missense	probably damaging	1.00
R1137:Rarg	UTSW	15	102,149,595 (GRCm39)	missense	probably damaging	1.00
R1593:Rarg	UTSW	15	102,148,376 (GRCm39)	missense	probably damaging	1.00
R1916:Rarg	UTSW	15	102,160,880 (GRCm39)	missense	probably benign	0.00
R1926:Rarg	UTSW	15	102,147,980 (GRCm39)	missense	probably damaging	1.00
R2211:Rarg	UTSW	15	102,147,959 (GRCm39)	missense	probably benign	0.20
R4581:Rarg	UTSW	15	102,160,986 (GRCm39)	missense	possibly damaging	0.70
R5718:Rarg	UTSW	15	102,149,502 (GRCm39)	missense	probably damaging	1.00
R6197:Rarg	UTSW	15	102,150,327 (GRCm39)	missense	possibly damaging	0.94
R6991:Rarg	UTSW	15	102,150,350 (GRCm39)	missense	probably damaging	1.00
R7300:Rarg	UTSW	15	102,160,852 (GRCm39)	critical splice donor site	probably null
R8104:Rarg	UTSW	15	102,148,334 (GRCm39)	missense	probably damaging	1.00
R8121:Rarg	UTSW	15	102,148,393 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TATCCAGGGCTTCTGCGTTC -3'
(R):5'- AGGCTTTCCTTACTGGGAACC -3'

Sequencing Primer
(F):5'- CTGAGAAGTCTGTAGGAACAATTC -3'
(R):5'- GGAACCAAACTCACTTAGGAATC -3'

Posted On

2014-09-17