Incidental Mutation 'R5587:Rai1'
ID 438834
Institutional Source Beutler Lab
Gene Symbol Rai1
Ensembl Gene ENSMUSG00000062115
Gene Name retinoic acid induced 1
Synonyms Gt1
MMRRC Submission 043141-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5587 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 59995839-60090023 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 60080685 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 1583 (V1583A)
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: V1583A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: V1583A

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: V1583A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: V1583A

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: V1583A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: V1583A

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: V1583A

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: V1583A

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
Meta Mutation Damage Score 0.1054 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.5%
  • 20x: 95.9%
Validation Efficiency 96% (78/81)
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik A G 3: 137,771,170 (GRCm39) R120G probably benign Het
Acad11 A G 9: 103,940,966 (GRCm39) T3A probably benign Het
Adamts18 G A 8: 114,501,992 (GRCm39) Q290* probably null Het
Ahnak A G 19: 8,986,840 (GRCm39) D2708G possibly damaging Het
Asxl3 T A 18: 22,658,304 (GRCm39) C2105S probably benign Het
Atp8b1 A T 18: 64,672,281 (GRCm39) F1028I probably damaging Het
Axdnd1 C G 1: 156,178,982 (GRCm39) W615C probably damaging Het
Bcl3 A T 7: 19,543,559 (GRCm39) Y10* probably null Het
Bmp2 T A 2: 133,396,566 (GRCm39) V74E possibly damaging Het
Ccdc121 G T 5: 31,643,428 (GRCm39) G53W probably benign Het
Ccdc78 C A 17: 26,005,651 (GRCm39) P21Q probably benign Het
Cluap1 T A 16: 3,733,348 (GRCm39) V199E probably damaging Het
Cntnap3 T C 13: 64,894,552 (GRCm39) E1120G probably damaging Het
Col1a2 T A 6: 4,540,531 (GRCm39) W1330R unknown Het
Coq4 A G 2: 29,685,526 (GRCm39) probably null Het
Cwf19l1 G A 19: 44,109,316 (GRCm39) T346I possibly damaging Het
Cyct T C 2: 76,184,547 (GRCm39) Y68C probably damaging Het
Dnah10 T C 5: 124,870,977 (GRCm39) L2368P probably benign Het
Dnah2 A T 11: 69,328,068 (GRCm39) F3346I probably damaging Het
Dpp3 A T 19: 4,968,295 (GRCm39) V259E probably damaging Het
Dpyd A C 3: 118,858,600 (GRCm39) S605R probably damaging Het
Emc1 A G 4: 139,089,459 (GRCm39) E209G probably damaging Het
Esrra A G 19: 6,897,575 (GRCm39) S61P probably benign Het
Garin2 C A 12: 78,761,849 (GRCm39) P171H probably damaging Het
Gbx2 T A 1: 89,860,844 (GRCm39) probably benign Het
Hepacam A G 9: 37,295,980 (GRCm39) H377R probably damaging Het
Igkv12-46 T C 6: 69,741,534 (GRCm39) Y107C probably damaging Het
Intu A G 3: 40,629,738 (GRCm39) D356G probably damaging Het
Izumo4 A T 10: 80,539,054 (GRCm39) N113Y probably damaging Het
Krt86 G A 15: 101,371,474 (GRCm39) A15T probably benign Het
Lhx8 A T 3: 154,017,316 (GRCm39) S275R probably damaging Het
Lingo3 A T 10: 80,671,364 (GRCm39) S189T probably damaging Het
Llgl1 T A 11: 60,601,168 (GRCm39) M702K probably benign Het
Lpin1 T C 12: 16,623,715 (GRCm39) Y223C Het
Lrit3 G T 3: 129,582,547 (GRCm39) A359E probably benign Het
Lrp2 T C 2: 69,329,607 (GRCm39) E1720G probably benign Het
Mcub A C 3: 129,710,619 (GRCm39) V271G probably benign Het
Nktr C T 9: 121,577,555 (GRCm39) probably benign Het
Or10g9 A T 9: 39,911,917 (GRCm39) I202N possibly damaging Het
Or13p4 T A 4: 118,547,067 (GRCm39) D194V probably damaging Het
Or1j18 A T 2: 36,624,633 (GRCm39) Q100L probably damaging Het
Or4d5 A T 9: 40,012,540 (GRCm39) L82Q probably damaging Het
Or52z12 T A 7: 103,233,738 (GRCm39) Y170N probably benign Het
Or9i1 G A 19: 13,839,940 (GRCm39) R261H probably damaging Het
Pcdha4 T C 18: 37,087,875 (GRCm39) V686A probably benign Het
Pelo A G 13: 115,226,409 (GRCm39) V16A possibly damaging Het
Plcd1 A G 9: 118,902,900 (GRCm39) S539P probably benign Het
Prss1 A G 6: 41,440,199 (GRCm39) I179V possibly damaging Het
Ptgs2 T C 1: 149,981,306 (GRCm39) Y530H probably damaging Het
Raph1 T G 1: 60,537,632 (GRCm39) D508A probably damaging Het
Rmnd5a A G 6: 71,371,603 (GRCm39) probably benign Het
Rsf1 T C 7: 97,311,328 (GRCm39) L686P probably benign Het
Samd9l T C 6: 3,373,291 (GRCm39) I1323M possibly damaging Het
Scn1a T C 2: 66,103,425 (GRCm39) N1934S probably benign Het
Sec23ip C T 7: 128,352,151 (GRCm39) H176Y probably benign Het
Sh3glb2 A G 2: 30,244,863 (GRCm39) probably null Het
Sis A G 3: 72,821,909 (GRCm39) I1384T possibly damaging Het
Spata31d1a A C 13: 59,850,432 (GRCm39) C565W probably damaging Het
Srbd1 T A 17: 86,435,229 (GRCm39) Q278L probably damaging Het
Sry T C Y: 2,662,625 (GRCm39) H345R unknown Het
Suox A T 10: 128,507,694 (GRCm39) D111E probably damaging Het
Taar7a A T 10: 23,868,726 (GRCm39) F218L probably benign Het
Tfcp2l1 C A 1: 118,592,492 (GRCm39) N288K possibly damaging Het
Tmem128 G T 5: 38,417,765 (GRCm39) R7L possibly damaging Het
Tmem266 A G 9: 55,344,850 (GRCm39) N494S probably damaging Het
Tmprss3 T A 17: 31,412,966 (GRCm39) H80L probably benign Het
Tnrc6c C T 11: 117,640,097 (GRCm39) Q1211* probably null Het
Tns1 T A 1: 73,959,755 (GRCm39) D1671V possibly damaging Het
Trmt1l T A 1: 151,311,455 (GRCm39) probably benign Het
Tshz2 A T 2: 169,726,262 (GRCm39) D286V probably damaging Het
Ttyh2 A G 11: 114,566,485 (GRCm39) E39G probably benign Het
Vmn2r125 G A 4: 156,702,433 (GRCm39) C73Y probably damaging Het
Vmn2r5 T C 3: 64,411,497 (GRCm39) D357G probably damaging Het
Vmn2r61 T C 7: 41,949,911 (GRCm39) F777S probably damaging Het
Vmn2r9 T C 5: 108,995,427 (GRCm39) E407G probably damaging Het
Vwa3a A G 7: 120,379,458 (GRCm39) N521S probably damaging Het
Zan C G 5: 137,390,024 (GRCm39) S4816T unknown Het
Zc3h7b T C 15: 81,656,059 (GRCm39) Y136H possibly damaging Het
Zfp101 T C 17: 33,600,295 (GRCm39) K487R 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
R2024:Rai1 UTSW 11 60,076,415 (GRCm39) missense probably damaging 0.99
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
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'- TCCAAAGGTCCGTTGGAGAAG -3'
(R):5'- AGGTACTTAGGGCCTTGGAC -3'

Sequencing Primer
(F):5'- TTGGAGAAGCGGCCATGTC -3'
(R):5'- TACTTAGGGCCTTGGACACCAC -3'
Posted On 2016-10-26