Incidental Mutation 'R1712:Rai1'
ID 190689
Institutional Source Beutler Lab
Gene Symbol Rai1
Ensembl Gene ENSMUSG00000062115
Gene Name retinoic acid induced 1
Synonyms Gt1
MMRRC Submission 039745-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1712 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 59995839-60090023 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 60078428 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 831 (T831A)
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: T831A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: T831A

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: T831A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: T831A

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: T831A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: T831A

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 benign
Transcript: ENSMUST00000171108
AA Change: T831A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: T831A

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: 98.4%
  • 10x: 96.5%
  • 20x: 93.2%
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: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Accs T A 2: 93,678,448 (GRCm39) E12D probably damaging Het
Ahnak2 C A 12: 112,748,998 (GRCm39) R283L probably benign Het
BC005624 T C 2: 30,864,020 (GRCm39) E191G probably damaging Het
C1galt1 A G 6: 7,871,217 (GRCm39) N351S probably benign Het
Ccdc162 T C 10: 41,415,427 (GRCm39) R2179G probably benign Het
Ccdc88c G A 12: 100,905,284 (GRCm39) T1108M probably benign Het
Cd47 T C 16: 49,714,543 (GRCm39) L184P probably damaging Het
Cdc40 T C 10: 40,717,372 (GRCm39) K440E probably damaging Het
Cenpe G A 3: 134,971,694 (GRCm39) V2262I probably damaging Het
Cep290 A G 10: 100,390,361 (GRCm39) K2035E probably benign Het
Cks1brt G T 8: 85,898,172 (GRCm39) L8F probably benign Het
Col17a1 T C 19: 47,637,442 (GRCm39) probably benign Het
Coro6 A T 11: 77,360,293 (GRCm39) N421I probably benign Het
Cps1 T C 1: 67,269,440 (GRCm39) S1480P probably damaging Het
Csrnp3 G T 2: 65,832,826 (GRCm39) A110S probably damaging Het
Cyp2d10 G T 15: 82,287,240 (GRCm39) T461K probably damaging Het
Dmxl2 A G 9: 54,308,769 (GRCm39) V1994A probably benign Het
Dnah11 T A 12: 118,160,379 (GRCm39) N117I probably benign Het
Dnajc3 A G 14: 119,195,307 (GRCm39) Y74C probably damaging Het
Fam13c T A 10: 70,390,403 (GRCm39) F555I possibly damaging Het
Fbn1 T A 2: 125,188,354 (GRCm39) D1495V probably damaging Het
Fbrsl1 T C 5: 110,595,862 (GRCm39) T58A probably benign Het
Gjd3 A G 11: 102,691,706 (GRCm39) I99T possibly damaging Het
Glce T C 9: 61,977,857 (GRCm39) N9S probably damaging Het
Gosr1 T C 11: 76,641,704 (GRCm39) T125A possibly damaging Het
Ifi27l2a T A 12: 103,406,202 (GRCm39) probably null Het
Jph1 C T 1: 17,167,456 (GRCm39) D125N possibly damaging Het
Kbtbd12 A T 6: 88,595,676 (GRCm39) S51R probably damaging Het
Klra9 A T 6: 130,166,659 (GRCm39) probably null Het
Kmo A T 1: 175,484,289 (GRCm39) M340L probably benign Het
Lama1 T C 17: 68,024,181 (GRCm39) I93T possibly damaging Het
Limk2 A T 11: 3,308,104 (GRCm39) probably null Het
Mgat5 C A 1: 127,248,375 (GRCm39) N92K probably benign Het
Mib2 T A 4: 155,739,256 (GRCm39) I908F probably damaging Het
Mical1 T G 10: 41,356,359 (GRCm39) L304R probably damaging Het
Mtbp G T 15: 55,434,690 (GRCm39) probably null Het
Myo3a T C 2: 22,455,004 (GRCm39) Y70H probably damaging Het
Neb T C 2: 52,133,401 (GRCm39) Y3379C probably damaging Het
Neurod2 G T 11: 98,218,029 (GRCm39) N378K probably damaging Het
Oog4 G A 4: 143,166,484 (GRCm39) L107F probably damaging Het
Or2g25 A G 17: 37,970,799 (GRCm39) S142P probably benign Het
Or4k40 T A 2: 111,251,003 (GRCm39) M98L probably benign Het
Or6x1 A G 9: 40,099,161 (GRCm39) Y250C probably damaging Het
Or8k20 T A 2: 86,106,337 (GRCm39) T165S probably damaging Het
Pfdn6 T C 17: 34,158,528 (GRCm39) Y82C probably damaging Het
Pla2g4d C A 2: 120,107,971 (GRCm39) A313S possibly damaging Het
Ptcd3 C A 6: 71,885,637 (GRCm39) E30* probably null Het
Rims1 G A 1: 22,367,172 (GRCm39) T1176M probably damaging Het
Rin1 A C 19: 5,105,171 (GRCm39) I744L probably benign Het
Rora T A 9: 69,282,771 (GRCm39) S430T probably benign Het
Rsph10b T A 5: 143,873,967 (GRCm39) S23T probably damaging Het
Ryr1 T C 7: 28,746,928 (GRCm39) N3773S probably benign Het
Scn4a A G 11: 106,230,180 (GRCm39) Y543H probably damaging Het
Scn4a C A 11: 106,236,373 (GRCm39) G296C probably benign Het
Scn7a T C 2: 66,535,447 (GRCm39) T435A probably benign Het
Shank2 G T 7: 143,964,890 (GRCm39) D833Y probably damaging Het
Slc9a2 T C 1: 40,802,770 (GRCm39) S607P possibly damaging Het
Slx4 G A 16: 3,809,458 (GRCm39) R346W probably damaging Het
Spata20 A T 11: 94,371,340 (GRCm39) C675S probably benign Het
Suclg2 A T 6: 95,563,997 (GRCm39) I196N probably damaging Het
Sv2b G A 7: 74,798,807 (GRCm39) H272Y possibly damaging Het
Svep1 T C 4: 58,070,629 (GRCm39) I2386V probably benign Het
Taf13 A T 3: 108,488,445 (GRCm39) E109D possibly damaging Het
Tanc2 A G 11: 105,790,606 (GRCm39) T976A probably benign Het
Tax1bp1 A G 6: 52,706,311 (GRCm39) Y104C probably damaging Het
Tfeb T C 17: 48,099,911 (GRCm39) probably null Het
Tlr9 T C 9: 106,101,248 (GRCm39) Y180H probably damaging Het
Trappc9 G A 15: 72,897,816 (GRCm39) R377W probably damaging Het
Ttc12 T A 9: 49,356,499 (GRCm39) T510S probably benign Het
Ubqln1 T C 13: 58,339,895 (GRCm39) E280G probably damaging Het
Urm1 T C 2: 29,731,437 (GRCm39) W44R probably damaging Het
Usp32 A T 11: 84,933,406 (GRCm39) I34N probably benign Het
Vars1 T C 17: 35,233,728 (GRCm39) L1018P probably damaging Het
Vcan A T 13: 89,869,894 (GRCm39) V206D probably damaging Het
Vim T C 2: 13,583,270 (GRCm39) V224A probably damaging Het
Vmn2r106 G T 17: 20,498,997 (GRCm39) H305N probably benign Het
Vmn2r78 A G 7: 86,604,132 (GRCm39) N770S probably damaging Het
Wdr33 T A 18: 32,029,684 (GRCm39) L961Q unknown Het
Xylt2 A G 11: 94,559,575 (GRCm39) S356P possibly damaging Het
Zbtb14 A G 17: 69,694,575 (GRCm39) N91S probably damaging Het
Zc3h6 T C 2: 128,858,654 (GRCm39) L895S probably damaging Het
Zc3h7b C T 15: 81,661,289 (GRCm39) P376L probably benign Het
Zfp131 T C 13: 120,228,079 (GRCm39) T523A probably benign 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
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
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'- GACTGCTTTCCAGATACACCCACTG -3'
(R):5'- AGCTCTGAACCTTTGATTGGGCAC -3'

Sequencing Primer
(F):5'- GCTTACCAAGGGCTTGGAAC -3'
(R):5'- TTTGATTGGGCACCCACAGAG -3'
Posted On 2014-05-14