Mutagenetix > Incidental Mutation

Incidental Mutation 'R1926:Rarg'

213479

Institutional Source

Beutler Lab

Gene Symbol

Rarg

Ensembl Gene

ENSMUSG00000001288

Gene Name

retinoic acid receptor, gamma

Synonyms

RAR gamma 2, RARgamma2

MMRRC Submission

039944-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.749) question?

Stock #

R1926 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

102143373-102165891 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 102147980 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 277 (F277S)

Ref Sequence

ENSEMBL: ENSMUSP00000067266 (fasta)

Gene Model

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

AlphaFold

P18911

Predicted Effect

probably damaging
Transcript: ENSMUST00000043172
AA Change: F288S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000048838
Gene: ENSMUSG00000001288
AA Change: F288S

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: F277S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000067266
Gene: ENSMUSG00000001288
AA Change: F277S

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: 97.3%
3x: 96.7%
10x: 95.0%
20x: 91.6%

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsm3	C	T	7: 119,376,359 (GRCm39)	T362M	probably damaging	Het
Ang6	A	G	14: 44,239,695 (GRCm39)	V11A	possibly damaging	Het
Ankrd17	A	G	5: 90,392,028 (GRCm39)	Y1880H	probably damaging	Het
Bmi1	A	G	2: 18,687,084 (GRCm39)	I55V	probably benign	Het
Bnipl	G	A	3: 95,150,354 (GRCm39)	T297M	probably damaging	Het
Bpifa2	T	C	2: 153,855,669 (GRCm39)	V198A	probably benign	Het
Brms1l	G	T	12: 55,909,946 (GRCm39)	V239F	possibly damaging	Het
Ccdc158	A	G	5: 92,798,647 (GRCm39)	V351A	probably benign	Het
Ces1c	A	G	8: 93,854,232 (GRCm39)	F101S	possibly damaging	Het
Cpb2	T	C	14: 75,479,837 (GRCm39)	Y15H	probably benign	Het
Dglucy	A	T	12: 100,833,414 (GRCm39)	N535I	possibly damaging	Het
Dop1a	C	A	9: 86,405,072 (GRCm39)	H1763Q	probably damaging	Het
Dpy19l1	C	T	9: 24,385,120 (GRCm39)	M236I	probably benign	Het
Efna2	T	C	10: 80,022,710 (GRCm39)	Y85H	probably damaging	Het
Eipr1	A	T	12: 28,914,836 (GRCm39)		probably null	Het
Eln	A	T	5: 134,735,421 (GRCm39)	Y787*	probably null	Het
Erbb2	G	C	11: 98,315,990 (GRCm39)	E364D	probably benign	Het
F5	A	G	1: 164,007,077 (GRCm39)	T294A	probably damaging	Het
Fam47e	A	G	5: 92,733,244 (GRCm39)	T194A	possibly damaging	Het
Galk1	T	C	11: 115,901,073 (GRCm39)	D202G	probably damaging	Het
Glb1l2	T	C	9: 26,682,362 (GRCm39)	D163G	probably damaging	Het
Gmip	A	G	8: 70,268,170 (GRCm39)	E408G	probably benign	Het
Gp1ba	A	T	11: 70,531,715 (GRCm39)		probably benign	Het
Grm3	A	T	5: 9,554,881 (GRCm39)	C804S	probably damaging	Het
Gzmd	A	G	14: 56,367,737 (GRCm39)	C179R	probably damaging	Het
Hadhb	T	A	5: 30,385,935 (GRCm39)	L415Q	possibly damaging	Het
Ift80	T	C	3: 68,823,498 (GRCm39)	Y588C	probably damaging	Het
Jazf1	T	C	6: 53,045,516 (GRCm39)	T13A	probably benign	Het
Kat8	T	A	7: 127,514,467 (GRCm39)	Y67*	probably null	Het
Kcnab1	G	A	3: 65,283,933 (GRCm39)	E384K	possibly damaging	Het
Lhx3	A	T	2: 26,092,200 (GRCm39)	Y230*	probably null	Het
Lmx1b	T	A	2: 33,454,674 (GRCm39)	M365L	probably damaging	Het
Ly6k	G	T	15: 74,669,051 (GRCm39)	P76Q	probably benign	Het
Lypd10	G	A	7: 24,413,541 (GRCm39)	G186R	probably damaging	Het
Map1b	A	T	13: 99,567,200 (GRCm39)	H1840Q	unknown	Het
Map3k2	A	G	18: 32,336,163 (GRCm39)	I117V	probably damaging	Het
Med13	C	A	11: 86,179,899 (GRCm39)	A1350S	possibly damaging	Het
Midn	T	C	10: 79,987,495 (GRCm39)	S109P	probably damaging	Het
Msh6	A	G	17: 88,293,653 (GRCm39)	T803A	probably benign	Het
Nckap1	T	C	2: 80,337,182 (GRCm39)	Y1018C	probably damaging	Het
Ndufc1	A	T	3: 51,314,816 (GRCm39)	N63K	probably benign	Het
Neb	A	T	2: 52,169,647 (GRCm39)	S1811R	probably damaging	Het
Notch1	T	C	2: 26,371,669 (GRCm39)	D260G	probably damaging	Het
Ntn4	C	T	10: 93,543,215 (GRCm39)	R314W	probably damaging	Het
Oas1g	T	C	5: 121,017,205 (GRCm39)	K283R	probably benign	Het
Obscn	T	C	11: 58,954,300 (GRCm39)	T4037A		Het
Or6b1	T	G	6: 42,815,247 (GRCm39)	L144R	probably damaging	Het
Or6b3	A	G	1: 92,439,330 (GRCm39)	L140P	probably damaging	Het
Otop2	A	T	11: 115,217,781 (GRCm39)	T206S	probably benign	Het
Pamr1	A	G	2: 102,471,342 (GRCm39)		probably null	Het
Pkp1	G	A	1: 135,805,411 (GRCm39)	T675I	probably benign	Het
Plxna2	G	A	1: 194,444,758 (GRCm39)	V717I	probably benign	Het
Ptgs2	T	C	1: 149,975,979 (GRCm39)	L2P	possibly damaging	Het
Rassf5	A	T	1: 131,140,076 (GRCm39)	I161N	probably damaging	Het
Resf1	C	T	6: 149,230,902 (GRCm39)	T1316I	probably benign	Het
Rxfp4	A	G	3: 88,559,659 (GRCm39)	V264A	probably benign	Het
Secisbp2l	T	A	2: 125,582,597 (GRCm39)	Q953L	probably damaging	Het
Serpinb9c	T	C	13: 33,334,218 (GRCm39)	I275V	probably benign	Het
Slc2a12	T	C	10: 22,541,141 (GRCm39)	V332A	probably damaging	Het
Slc7a1	T	C	5: 148,285,113 (GRCm39)	S127G	probably damaging	Het
Slc7a4	A	T	16: 17,393,568 (GRCm39)	V77E	probably damaging	Het
Sp8	G	A	12: 118,812,964 (GRCm39)	S273N	possibly damaging	Het
Spag6l	G	T	16: 16,580,921 (GRCm39)	N475K	probably benign	Het
St18	A	G	1: 6,872,913 (GRCm39)	H216R	probably benign	Het
Tcirg1	C	T	19: 3,952,843 (GRCm39)		probably benign	Het
Tmeff1	A	G	4: 48,658,788 (GRCm39)	Y87C	probably damaging	Het
Tmem94	T	C	11: 115,683,726 (GRCm39)	V713A	possibly damaging	Het
Tnrc6b	G	T	15: 80,765,363 (GRCm39)	R955L	probably damaging	Het
Trip12	A	G	1: 84,727,012 (GRCm39)	V1153A	probably damaging	Het
Tshz3	T	C	7: 36,468,800 (GRCm39)	L263S	probably damaging	Het
Tubb6	G	A	18: 67,534,391 (GRCm39)		probably null	Het
Ube3a	T	C	7: 58,926,127 (GRCm39)	W302R	probably damaging	Het
Vcpkmt	A	T	12: 69,629,519 (GRCm39)	V81E	probably damaging	Het
Vmn1r175	T	A	7: 23,508,466 (GRCm39)	I54F	possibly damaging	Het
Vwa8	T	A	14: 79,258,075 (GRCm39)	N741K	probably benign	Het
Yeats2	A	G	16: 20,033,176 (GRCm39)	T1034A	probably benign	Het
Zc3h6	G	A	2: 128,839,715 (GRCm39)	R176Q	probably damaging	Het
Zfp207	T	A	11: 80,286,253 (GRCm39)	Y424*	probably null	Het
Zfp729a	A	G	13: 67,767,676 (GRCm39)	V851A	probably benign	Het
Zkscan1	G	T	5: 138,099,625 (GRCm39)	A450S	probably benign	Het
Zkscan3	A	G	13: 21,580,616 (GRCm39)	V24A	possibly damaging	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
R2057:Rarg	UTSW	15	102,147,939 (GRCm39)	missense	probably damaging	0.99
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'- AGCAGTTCCCTCCTGGTTTG -3'

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

Posted On

2014-07-14