Incidental Mutation 'R6785:Rai1'
ID 531635
Institutional Source Beutler Lab
Gene Symbol Rai1
Ensembl Gene ENSMUSG00000062115
Gene Name retinoic acid induced 1
Synonyms Gt1
MMRRC Submission 044899-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6785 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 59995839-60090023 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 60079620 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Serine at position 1228 (N1228S)
Ref Sequence ENSEMBL: ENSMUSP00000126183 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000064190] [ENSMUST00000090806] [ENSMUST00000102688] [ENSMUST00000132012] [ENSMUST00000171108]
AlphaFold Q61818
Predicted Effect probably benign
Transcript: ENSMUST00000064190
AA Change: N1228S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: N1228S

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: ENSMUST00000090806
AA Change: N1228S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: N1228S

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 benign
Transcript: ENSMUST00000102688
AA Change: N1228S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: N1228S

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 probably benign
Transcript: ENSMUST00000171108
AA Change: N1228S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: N1228S

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 0.0898 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.6%
  • 20x: 96.3%
Validation Efficiency 98% (59/60)
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: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abi1 A G 2: 22,843,479 (GRCm39) V316A probably benign Het
Acad12 T C 5: 121,747,908 (GRCm39) Y170C probably damaging Het
Acss2 T C 2: 155,402,605 (GRCm39) V587A probably damaging Het
Adamtsl3 A G 7: 82,171,212 (GRCm39) I422V probably damaging Het
Aldh18a1 A G 19: 40,556,788 (GRCm39) L375P probably damaging Het
B020011L13Rik A G 1: 117,728,799 (GRCm39) D102G possibly damaging Het
Cfap74 T A 4: 155,538,481 (GRCm39) probably benign Het
Coa4 G A 7: 100,188,460 (GRCm39) V58M probably damaging Het
Crybg1 T C 10: 43,875,167 (GRCm39) N647S probably benign Het
Dync1h1 G A 12: 110,596,113 (GRCm39) G1547S probably damaging Het
Espnl A G 1: 91,249,943 (GRCm39) D30G probably benign Het
Fasl T A 1: 161,609,404 (GRCm39) Y194F probably benign Het
Fbxw8 T C 5: 118,230,754 (GRCm39) E349G probably damaging Het
Gen1 A G 12: 11,312,531 (GRCm39) V13A possibly damaging Het
Gm4559 A G 7: 141,827,845 (GRCm39) C86R unknown Het
H2-M9 T C 17: 36,953,125 (GRCm39) N61D probably damaging Het
H6pd C T 4: 150,067,247 (GRCm39) E380K possibly damaging Het
Herc1 TCCC TCC 9: 66,408,470 (GRCm39) probably null Het
Hnrnpd C A 5: 100,126,283 (GRCm39) K67N probably benign Het
Hspg2 T C 4: 137,235,709 (GRCm39) S170P probably damaging Het
Igsf10 G T 3: 59,226,665 (GRCm39) P2336Q probably damaging Het
Itih3 C T 14: 30,634,572 (GRCm39) probably null Het
Katnb1 T C 8: 95,822,270 (GRCm39) Y298H probably benign Het
Kif21a A T 15: 90,819,933 (GRCm39) N1610K probably damaging Het
Lce1l A T 3: 92,757,500 (GRCm39) C119* probably null Het
Lcn2 C T 2: 32,277,039 (GRCm39) probably null Het
Lmf2 A T 15: 89,236,236 (GRCm39) S588T probably benign Het
Mboat7 A G 7: 3,688,835 (GRCm39) L231P probably benign Het
Mier2 T C 10: 79,380,547 (GRCm39) R288G probably damaging Het
Mybbp1a T C 11: 72,338,392 (GRCm39) V694A probably benign Het
Ndnf C A 6: 65,680,047 (GRCm39) L109I probably benign Het
Nfkb1 C A 3: 135,321,064 (GRCm39) E230D probably benign Het
Nostrin A G 2: 69,014,271 (GRCm39) K409R probably benign Het
Or1j10 A G 2: 36,266,854 (GRCm39) Q22R probably benign Het
Or1j10 C A 2: 36,266,963 (GRCm39) Y58* probably null Het
Or8k35 T A 2: 86,424,765 (GRCm39) M136L probably damaging Het
Pdpr C A 8: 111,851,243 (GRCm39) T534N probably benign Het
Plekhf1 G A 7: 37,921,488 (GRCm39) Q27* probably null Het
Ppp6c A T 2: 39,087,593 (GRCm39) H204Q probably benign Het
Prrc2c T C 1: 162,536,670 (GRCm39) probably benign Het
Prrg2 A G 7: 44,709,649 (GRCm39) F83L probably damaging Het
Rab11fip3 T G 17: 26,210,692 (GRCm39) D938A probably damaging Het
Ryr1 G T 7: 28,764,299 (GRCm39) T3060K probably benign Het
Scube2 A G 7: 109,409,824 (GRCm39) I557T probably benign Het
Setdb1 C A 3: 95,233,712 (GRCm39) R1066L probably benign Het
Shoc1 T C 4: 59,049,066 (GRCm39) M1100V probably benign Het
Slc35f3 T C 8: 127,121,198 (GRCm39) V353A probably benign Het
Slfn3 A T 11: 83,105,427 (GRCm39) T475S possibly damaging Het
Snrnp200 T A 2: 127,071,085 (GRCm39) M1122K possibly damaging Het
Tead4 T A 6: 128,219,444 (GRCm39) K223* probably null Het
Tex2 A C 11: 106,424,776 (GRCm39) I334R probably damaging Het
Tfdp1 C T 8: 13,420,485 (GRCm39) R105W probably damaging Het
Tfdp1 G T 8: 13,427,233 (GRCm39) V393F possibly damaging Het
Thsd7b T C 1: 129,358,644 (GRCm39) L26P probably damaging Het
Trim80 T C 11: 115,332,027 (GRCm39) I73T probably damaging Het
Tssk4 T A 14: 55,887,932 (GRCm39) Y43N probably damaging Het
Ttn T C 2: 76,541,839 (GRCm39) T25389A probably damaging Het
Ttn A T 2: 76,578,288 (GRCm39) F24202I probably damaging Het
Vmn1r177 A G 7: 23,565,562 (GRCm39) S105P probably damaging Het
Vmn2r40 T A 7: 8,911,203 (GRCm39) T697S probably benign Het
Zfp267 T A 3: 36,219,601 (GRCm39) C541* probably null 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
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
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'- TGCGTACAAGGTCTCCAGTG -3'
(R):5'- TCTGTACTATGGCCTCCAGC -3'

Sequencing Primer
(F):5'- TCCAGTGGGCCCCAGAAG -3'
(R):5'- GTACTATGGCCTCCAGCTTGAG -3'
Posted On 2018-08-29