Incidental Mutation 'R2024:Rai1'
ID 220316
Institutional Source Beutler Lab
Gene Symbol Rai1
Ensembl Gene ENSMUSG00000062115
Gene Name retinoic acid induced 1
Synonyms Gt1
MMRRC Submission 040033-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2024 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 59995839-60090023 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 60076415 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 160 (F160L)
Ref Sequence ENSEMBL: ENSMUSP00000126183 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000064190] [ENSMUST00000090806] [ENSMUST00000102688] [ENSMUST00000132012] [ENSMUST00000171108]
AlphaFold Q61818
Predicted Effect probably damaging
Transcript: ENSMUST00000064190
AA Change: F160L

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: F160L

DomainStartEndE-ValueType
low complexity region 55 69 N/A INTRINSIC
low complexity region 115 129 N/A INTRINSIC
low complexity region 168 175 N/A INTRINSIC
low complexity region 294 304 N/A INTRINSIC
low complexity region 322 336 N/A INTRINSIC
low complexity region 409 424 N/A INTRINSIC
low complexity region 699 708 N/A INTRINSIC
low complexity region 836 842 N/A INTRINSIC
low complexity region 1015 1030 N/A INTRINSIC
low complexity region 1049 1064 N/A INTRINSIC
low complexity region 1084 1102 N/A INTRINSIC
low complexity region 1262 1272 N/A INTRINSIC
low complexity region 1375 1388 N/A INTRINSIC
low complexity region 1455 1465 N/A INTRINSIC
low complexity region 1499 1515 N/A INTRINSIC
low complexity region 1597 1609 N/A INTRINSIC
low complexity region 1680 1690 N/A INTRINSIC
low complexity region 1714 1732 N/A INTRINSIC
PHD 1838 1885 3.59e-6 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000090806
AA Change: F160L

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: F160L

DomainStartEndE-ValueType
low complexity region 55 69 N/A INTRINSIC
low complexity region 115 129 N/A INTRINSIC
low complexity region 168 175 N/A INTRINSIC
low complexity region 294 304 N/A INTRINSIC
low complexity region 322 336 N/A INTRINSIC
low complexity region 409 424 N/A INTRINSIC
low complexity region 699 708 N/A INTRINSIC
low complexity region 836 842 N/A INTRINSIC
low complexity region 1015 1030 N/A INTRINSIC
low complexity region 1049 1064 N/A INTRINSIC
low complexity region 1084 1102 N/A INTRINSIC
low complexity region 1262 1272 N/A INTRINSIC
low complexity region 1375 1388 N/A INTRINSIC
low complexity region 1455 1465 N/A INTRINSIC
low complexity region 1499 1515 N/A INTRINSIC
low complexity region 1597 1609 N/A INTRINSIC
low complexity region 1680 1690 N/A INTRINSIC
low complexity region 1714 1732 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000102688
AA Change: F160L

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: F160L

DomainStartEndE-ValueType
low complexity region 55 69 N/A INTRINSIC
low complexity region 115 129 N/A INTRINSIC
low complexity region 168 175 N/A INTRINSIC
low complexity region 294 304 N/A INTRINSIC
low complexity region 322 336 N/A INTRINSIC
low complexity region 409 424 N/A INTRINSIC
low complexity region 699 708 N/A INTRINSIC
low complexity region 836 842 N/A INTRINSIC
low complexity region 1015 1030 N/A INTRINSIC
low complexity region 1049 1064 N/A INTRINSIC
low complexity region 1084 1102 N/A INTRINSIC
low complexity region 1262 1272 N/A INTRINSIC
low complexity region 1375 1388 N/A INTRINSIC
low complexity region 1455 1465 N/A INTRINSIC
low complexity region 1499 1515 N/A INTRINSIC
low complexity region 1597 1609 N/A INTRINSIC
low complexity region 1680 1690 N/A INTRINSIC
low complexity region 1714 1732 N/A INTRINSIC
PHD 1838 1885 3.59e-6 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000132012
SMART Domains Protein: ENSMUSP00000118543
Gene: ENSMUSG00000062115

DomainStartEndE-ValueType
low complexity region 55 69 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149770
Predicted Effect probably damaging
Transcript: ENSMUST00000171108
AA Change: F160L

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: F160L

DomainStartEndE-ValueType
low complexity region 55 69 N/A INTRINSIC
low complexity region 115 129 N/A INTRINSIC
low complexity region 168 175 N/A INTRINSIC
low complexity region 294 304 N/A INTRINSIC
low complexity region 322 336 N/A INTRINSIC
low complexity region 409 424 N/A INTRINSIC
low complexity region 699 708 N/A INTRINSIC
low complexity region 836 842 N/A INTRINSIC
low complexity region 1015 1030 N/A INTRINSIC
low complexity region 1049 1064 N/A INTRINSIC
low complexity region 1084 1102 N/A INTRINSIC
low complexity region 1262 1272 N/A INTRINSIC
low complexity region 1375 1388 N/A INTRINSIC
low complexity region 1455 1465 N/A INTRINSIC
low complexity region 1499 1515 N/A INTRINSIC
low complexity region 1597 1609 N/A INTRINSIC
low complexity region 1680 1690 N/A INTRINSIC
low complexity region 1714 1732 N/A INTRINSIC
PHD 1838 1885 3.59e-6 SMART
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.1%
  • 20x: 90.8%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is located within the Smith-Magenis syndrome region on chromosome 17. It is highly similar to its mouse counterpart and is expressed at high levels mainly in neuronal tissues. The protein encoded by this gene includes a polymorphic polyglutamine tract in the N-terminal domain. Expression of the mouse counterpart in neurons is induced by retinoic acid. This gene is associated with both the severity of the phenotype and the response to medication in schizophrenic patients. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for disruptions of this gene usually die as embryos. Survivors have shortened life spans and show severe craniofacial and axial skeleton defects. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Arid2 A G 15: 96,259,680 (GRCm39) D280G probably damaging Het
Atosa A G 9: 74,917,672 (GRCm39) D757G probably damaging Het
Azi2 C T 9: 117,878,390 (GRCm39) R77* probably null Het
Chd8 T C 14: 52,468,950 (GRCm39) D556G probably benign Het
Cit T C 5: 116,085,983 (GRCm39) M849T probably damaging Het
Cit T C 5: 116,143,899 (GRCm39) S1923P probably damaging Het
Col17a1 T A 19: 47,639,185 (GRCm39) H1120L probably benign Het
Col6a5 G T 9: 105,814,193 (GRCm39) H606Q unknown Het
Dnajc2 A C 5: 21,981,788 (GRCm39) H45Q probably damaging Het
Dpp6 A G 5: 27,914,457 (GRCm39) D514G possibly damaging Het
Dync2h1 A G 9: 7,129,062 (GRCm39) S1818P probably damaging Het
Efemp1 A T 11: 28,864,696 (GRCm39) Y250F possibly damaging Het
Emc1 G A 4: 139,088,257 (GRCm39) E342K possibly damaging Het
Fam3c T C 6: 22,329,592 (GRCm39) D45G probably benign Het
Fchsd2 A C 7: 100,847,740 (GRCm39) D210A possibly damaging Het
Flg T A 3: 93,186,722 (GRCm39) M58K probably damaging Het
Gabra5 G A 7: 57,138,698 (GRCm39) R117C probably damaging Het
Gm6741 G A 17: 91,544,309 (GRCm39) S24N probably benign Het
Grin2a T C 16: 9,462,107 (GRCm39) D675G possibly damaging Het
Hectd4 T G 5: 121,419,981 (GRCm39) V642G possibly damaging Het
Herc6 C T 6: 57,560,317 (GRCm39) T119M probably benign Het
Hjurp GT GTT 1: 88,194,246 (GRCm39) probably null Het
Hmgcs2 T C 3: 98,206,530 (GRCm39) S371P probably damaging Het
Idua C T 5: 108,828,600 (GRCm39) A271V probably damaging Het
Inpp5d T A 1: 87,623,072 (GRCm39) C125* probably null Het
Krt14 C T 11: 100,098,044 (GRCm39) G80R unknown Het
Lama5 T C 2: 179,820,923 (GRCm39) Y3176C probably benign Het
Lce1k C T 3: 92,713,809 (GRCm39) C125Y unknown Het
Lig4 A T 8: 10,022,436 (GRCm39) L448Q probably damaging Het
Macf1 C T 4: 123,265,711 (GRCm39) A4821T probably damaging Het
Meioc C T 11: 102,566,184 (GRCm39) A600V probably benign Het
Mepe T C 5: 104,474,957 (GRCm39) S13P possibly damaging Het
Mms22l A G 4: 24,588,365 (GRCm39) Y999C probably damaging Het
Ncbp3 T A 11: 72,944,346 (GRCm39) M116K possibly damaging Het
Ndufa10 A G 1: 92,367,614 (GRCm39) Y339H probably damaging Het
Nkx3-1 T C 14: 69,428,266 (GRCm39) I38T probably damaging Het
Nup155 A T 15: 8,187,244 (GRCm39) H1391L probably damaging Het
Or4k49 T A 2: 111,495,168 (GRCm39) M199K possibly damaging Het
Padi6 T G 4: 140,456,279 (GRCm39) I572L possibly damaging Het
Pdss2 A T 10: 43,269,871 (GRCm39) N238I possibly damaging Het
Pkd1l2 A G 8: 117,746,272 (GRCm39) V1906A probably benign Het
Pom121 T C 5: 135,410,404 (GRCm39) probably benign Het
Psmd9 T C 5: 123,379,925 (GRCm39) F115L probably damaging Het
Ptch1 T G 13: 63,672,773 (GRCm39) E944A probably benign Het
Rhbdl2 A T 4: 123,720,665 (GRCm39) R234S probably damaging Het
Rnase2a T A 14: 51,493,245 (GRCm39) Y40F probably damaging Het
Setd2 T C 9: 110,378,201 (GRCm39) V672A possibly damaging Het
Sgpp2 A G 1: 78,393,857 (GRCm39) I287V probably benign Het
Sh3pxd2a T C 19: 47,255,703 (GRCm39) E1033G probably benign Het
Slc5a9 G A 4: 111,747,728 (GRCm39) T284I probably damaging Het
Slfn9 A G 11: 82,872,507 (GRCm39) L743P probably damaging Het
Smchd1 T A 17: 71,677,923 (GRCm39) N1473I probably benign Het
Stx1b A T 7: 127,414,575 (GRCm39) D16E probably benign Het
Tectb T C 19: 55,170,361 (GRCm39) F71L probably damaging Het
Tmem220 T C 11: 66,924,979 (GRCm39) I138T possibly damaging Het
Tmtc4 T C 14: 123,158,677 (GRCm39) N682S probably benign Het
Tnc A G 4: 63,882,858 (GRCm39) V1921A probably damaging Het
Ubn1 T G 16: 4,882,487 (GRCm39) L316W probably damaging Het
Vwa5a T C 9: 38,647,357 (GRCm39) S579P probably damaging Het
Xdh A G 17: 74,228,300 (GRCm39) L367P possibly damaging Het
Zfp280b T C 10: 75,874,328 (GRCm39) L69S probably damaging Het
Zfp990 A C 4: 145,263,974 (GRCm39) Y324S possibly damaging Het
Other mutations in Rai1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00232:Rai1 APN 11 60,076,217 (GRCm39) missense probably damaging 1.00
IGL00952:Rai1 APN 11 60,078,818 (GRCm39) nonsense probably null
IGL01118:Rai1 APN 11 60,078,264 (GRCm39) missense probably damaging 0.98
IGL02540:Rai1 APN 11 60,077,750 (GRCm39) missense probably benign 0.09
IGL02624:Rai1 APN 11 60,079,569 (GRCm39) missense probably damaging 1.00
IGL02696:Rai1 APN 11 60,084,782 (GRCm39) missense probably benign
IGL02940:Rai1 APN 11 60,077,844 (GRCm39) missense probably benign 0.03
IGL02970:Rai1 APN 11 60,076,559 (GRCm39) missense probably damaging 1.00
IGL03006:Rai1 APN 11 60,079,031 (GRCm39) missense possibly damaging 0.95
R0557:Rai1 UTSW 11 60,081,321 (GRCm39) missense probably benign 0.00
R1438:Rai1 UTSW 11 60,076,221 (GRCm39) missense probably benign 0.00
R1712:Rai1 UTSW 11 60,078,428 (GRCm39) missense probably benign
R1837:Rai1 UTSW 11 60,080,224 (GRCm39) missense probably damaging 1.00
R1899:Rai1 UTSW 11 60,076,746 (GRCm39) missense probably benign 0.16
R2141:Rai1 UTSW 11 60,080,293 (GRCm39) missense possibly damaging 0.94
R2168:Rai1 UTSW 11 60,078,422 (GRCm39) missense probably benign 0.01
R2404:Rai1 UTSW 11 60,080,750 (GRCm39) missense probably benign
R4869:Rai1 UTSW 11 60,077,588 (GRCm39) missense probably damaging 1.00
R4894:Rai1 UTSW 11 60,077,572 (GRCm39) missense probably damaging 1.00
R5082:Rai1 UTSW 11 60,076,745 (GRCm39) missense possibly damaging 0.48
R5093:Rai1 UTSW 11 60,079,482 (GRCm39) missense probably benign 0.00
R5221:Rai1 UTSW 11 60,081,423 (GRCm39) missense probably damaging 1.00
R5503:Rai1 UTSW 11 60,077,279 (GRCm39) missense probably benign 0.00
R5587:Rai1 UTSW 11 60,080,685 (GRCm39) missense probably damaging 1.00
R5849:Rai1 UTSW 11 60,081,347 (GRCm39) missense possibly damaging 0.90
R5914:Rai1 UTSW 11 60,078,630 (GRCm39) missense probably benign
R5950:Rai1 UTSW 11 60,078,419 (GRCm39) missense probably damaging 1.00
R6111:Rai1 UTSW 11 60,078,732 (GRCm39) missense probably damaging 0.99
R6450:Rai1 UTSW 11 60,077,429 (GRCm39) missense probably benign 0.30
R6785:Rai1 UTSW 11 60,079,620 (GRCm39) missense probably benign
R6889:Rai1 UTSW 11 60,076,541 (GRCm39) missense probably damaging 1.00
R7296:Rai1 UTSW 11 60,079,499 (GRCm39) missense probably benign 0.39
R7388:Rai1 UTSW 11 60,080,201 (GRCm39) missense possibly damaging 0.46
R8196:Rai1 UTSW 11 60,076,796 (GRCm39) missense probably damaging 1.00
R8857:Rai1 UTSW 11 60,077,393 (GRCm39) missense probably benign 0.39
R9161:Rai1 UTSW 11 60,076,682 (GRCm39) missense probably benign 0.08
R9210:Rai1 UTSW 11 60,080,217 (GRCm39) missense probably benign
R9570:Rai1 UTSW 11 60,076,568 (GRCm39) missense probably benign
R9653:Rai1 UTSW 11 60,080,142 (GRCm39) missense probably benign 0.00
R9718:Rai1 UTSW 11 60,080,165 (GRCm39) missense probably benign 0.00
R9788:Rai1 UTSW 11 60,078,080 (GRCm39) missense possibly damaging 0.77
X0018:Rai1 UTSW 11 60,077,262 (GRCm39) missense probably benign 0.03
X0019:Rai1 UTSW 11 60,080,766 (GRCm39) missense probably benign 0.14
X0024:Rai1 UTSW 11 60,078,221 (GRCm39) missense possibly damaging 0.65
Z1186:Rai1 UTSW 11 60,078,389 (GRCm39) missense probably benign
Z1187:Rai1 UTSW 11 60,078,389 (GRCm39) missense probably benign
Z1188:Rai1 UTSW 11 60,078,389 (GRCm39) missense probably benign
Z1189:Rai1 UTSW 11 60,078,389 (GRCm39) missense probably benign
Z1190:Rai1 UTSW 11 60,078,389 (GRCm39) missense probably benign
Z1191:Rai1 UTSW 11 60,078,389 (GRCm39) missense probably benign
Z1192:Rai1 UTSW 11 60,078,389 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- ATGTTCAAGACAGCAGCCCC -3'
(R):5'- CTGTGCAGCTCTTGTAGGAG -3'

Sequencing Primer
(F):5'- CTACCCAGGGCGCTACTCTG -3'
(R):5'- CCTGCACTGTTGGGGCATAAG -3'
Posted On 2014-08-25