Incidental Mutation 'R5718:Rarg'
ID 451314
Institutional Source Beutler Lab
Gene Symbol Rarg
Ensembl Gene ENSMUSG00000001288
Gene Name retinoic acid receptor, gamma
Synonyms RAR gamma 2, RARgamma2
MMRRC Submission 043338-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.741) question?
Stock # R5718 (G1)
Quality Score 225
Status Not validated
Chromosome 15
Chromosomal Location 102143373-102165891 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 102149502 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Alanine at position 156 (S156A)
Ref Sequence ENSEMBL: ENSMUSP00000118615 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000043172] [ENSMUST00000063339] [ENSMUST00000130204] [ENSMUST00000135466] [ENSMUST00000155563]
AlphaFold P18911
Predicted Effect possibly damaging
Transcript: ENSMUST00000043172
AA Change: S156A

PolyPhen 2 Score 0.942 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000048838
Gene: ENSMUSG00000001288
AA Change: S156A

DomainStartEndE-ValueType
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: S145A

PolyPhen 2 Score 0.973 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000067266
Gene: ENSMUSG00000001288
AA Change: S145A

DomainStartEndE-ValueType
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 damaging
Transcript: ENSMUST00000135466
AA Change: S156A

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000118615
Gene: ENSMUSG00000001288
AA Change: S156A

DomainStartEndE-ValueType
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: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.8%
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: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgra2 T C 8: 27,603,514 (GRCm39) probably null Het
Ahctf1 G T 1: 179,596,904 (GRCm39) H81N possibly damaging Het
Alyref2 T C 1: 171,331,678 (GRCm39) S152P possibly damaging Het
Arhgef7 C T 8: 11,835,774 (GRCm39) T20I probably damaging Het
Armc3 T G 2: 19,308,610 (GRCm39) Y759* probably null Het
Atg5 A G 10: 44,238,983 (GRCm39) S255G probably benign Het
Atp11b A G 3: 35,891,665 (GRCm39) I1026V probably benign Het
Atp1a2 C A 1: 172,107,009 (GRCm39) K770N probably damaging Het
Bptf G T 11: 107,002,260 (GRCm39) A284E probably damaging Het
Celsr2 A G 3: 108,300,674 (GRCm39) S815P probably benign Het
Chrna5 A G 9: 54,905,389 (GRCm39) H67R probably benign Het
Cic A G 7: 24,972,203 (GRCm39) I645V probably benign Het
Clpx A T 9: 65,207,246 (GRCm39) Q48L probably benign Het
Crhr2 G A 6: 55,069,085 (GRCm39) Q397* probably null Het
Cyp11a1 G A 9: 57,925,508 (GRCm39) V48I probably benign Het
Dchs1 C T 7: 105,404,955 (GRCm39) R2529H probably benign Het
Dnah7c A T 1: 46,787,826 (GRCm39) H3293L possibly damaging Het
Dock6 G T 9: 21,735,789 (GRCm39) D986E probably benign Het
Efcab6 T A 15: 83,788,439 (GRCm39) N952Y probably damaging Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Epg5 G A 18: 78,029,618 (GRCm39) C1327Y probably damaging Het
Fbxw18 T C 9: 109,520,636 (GRCm39) E241G probably benign Het
Fsd1 T G 17: 56,297,542 (GRCm39) probably benign Het
Gcnt3 A G 9: 69,941,552 (GRCm39) S339P probably benign Het
Gldc T A 19: 30,088,172 (GRCm39) K829* probably null Het
Gli3 G A 13: 15,652,750 (GRCm39) probably null Het
Gm11595 G A 11: 99,663,381 (GRCm39) R100C unknown Het
Greb1l G A 18: 10,542,427 (GRCm39) E1341K probably damaging Het
Hmcn1 A T 1: 150,566,351 (GRCm39) C2217* probably null Het
Hmcn1 A T 1: 150,485,417 (GRCm39) I4395N probably damaging Het
Hmgxb3 A G 18: 61,273,909 (GRCm39) M861T probably benign Het
Ift172 A G 5: 31,412,621 (GRCm39) S1545P possibly damaging Het
Jak3 C A 8: 72,136,998 (GRCm39) L725M probably damaging Het
Lrig2 A T 3: 104,375,931 (GRCm39) C90* probably null Het
Mcm7 C T 5: 138,163,081 (GRCm39) R357H possibly damaging Het
Mcoln2 T C 3: 145,887,581 (GRCm39) S333P probably damaging Het
Mrpl22 A T 11: 58,068,109 (GRCm39) I136L probably benign Het
Ncam2 A T 16: 81,386,702 (GRCm39) probably null Het
Ncdn G A 4: 126,643,743 (GRCm39) Q360* probably null Het
Nsun2 A G 13: 69,771,403 (GRCm39) K338E probably benign Het
Obscn T C 11: 58,927,634 (GRCm39) T6105A probably damaging Het
Or2aj6 G A 16: 19,443,139 (GRCm39) S237F probably benign Het
Or8g36 A T 9: 39,422,338 (GRCm39) L226H probably damaging Het
Pcnx4 T A 12: 72,613,968 (GRCm39) F638I possibly damaging Het
Pfn3 T C 13: 55,562,853 (GRCm39) I43V probably benign Het
Pigm C A 1: 172,205,012 (GRCm39) probably null Het
Pkhd1l1 T A 15: 44,408,813 (GRCm39) S2433R probably damaging Het
Pomt1 C A 2: 32,138,704 (GRCm39) A440D possibly damaging Het
Ptprj T C 2: 90,288,613 (GRCm39) D691G probably benign Het
Qrich1 T A 9: 108,406,022 (GRCm39) S72T probably damaging Het
Ralgapa2 T A 2: 146,295,326 (GRCm39) probably null Het
Rasl11a A G 5: 146,783,954 (GRCm39) K133R probably benign Het
Rcor1 A G 12: 111,068,069 (GRCm39) D158G probably benign Het
Rpn2 C T 2: 157,163,747 (GRCm39) T613M probably damaging Het
Sipa1l2 T A 8: 126,217,987 (GRCm39) H450L probably damaging Het
Slc25a21 T C 12: 56,764,941 (GRCm39) I263V probably benign Het
Slc25a32 A T 15: 38,960,957 (GRCm39) V242E probably benign Het
Slc5a5 T A 8: 71,340,399 (GRCm39) T484S probably benign Het
Tdrd3 T C 14: 87,743,876 (GRCm39) V608A probably benign Het
Thnsl1 C A 2: 21,216,811 (GRCm39) H188Q possibly damaging Het
Tshz1 A T 18: 84,032,649 (GRCm39) H586Q probably damaging Het
Vmn2r27 C T 6: 124,169,103 (GRCm39) A676T possibly damaging Het
Wasf1 G A 10: 40,802,570 (GRCm39) R75Q probably damaging Het
Xbp1 T A 11: 5,471,903 (GRCm39) F10I probably benign Het
Zbtb1 G A 12: 76,433,698 (GRCm39) M561I probably benign Het
Zfp708 T C 13: 67,218,522 (GRCm39) K446E probably benign Het
Other mutations in Rarg
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- AGCCATCTCAGGATCTGTCC -3'
(R):5'- CAGCACCCTGTTTAGTGACAC -3'

Sequencing Primer
(F):5'- GGATCTGTCCTGTGAAAGAACAG -3'
(R):5'- GACACTCCTGCTTCCAAATTCAGG -3'
Posted On 2017-01-03