Mutagenetix > Incidental Mutation

Incidental Mutation 'R7296:Rai1'

571643

Institutional Source

Beutler Lab

Gene Symbol

Rai1

Ensembl Gene

ENSMUSG00000062115

Gene Name

retinoic acid induced 1

Synonyms

Gt1

MMRRC Submission

045400-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7296 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

59995839-60090023 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 60079499 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 1188 (V1188I)

Ref Sequence

ENSEMBL: ENSMUSP00000070896 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000064190] [ENSMUST00000090806] [ENSMUST00000102688] [ENSMUST00000132012] [ENSMUST00000171108]

AlphaFold

Q61818

Predicted Effect

probably benign
Transcript: ENSMUST00000064190
AA Change: V1188I

PolyPhen 2 Score 0.387 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: V1188I

Domain	Start	End	E-Value	Type
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

possibly damaging
Transcript: ENSMUST00000090806
AA Change: V1188I

PolyPhen 2 Score 0.529 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: V1188I

Domain	Start	End	E-Value	Type
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: V1188I

PolyPhen 2 Score 0.387 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: V1188I

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
low complexity region	55	69	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000171108
AA Change: V1188I

PolyPhen 2 Score 0.387 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: V1188I

Domain	Start	End	E-Value	Type
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: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.8%

Validation Efficiency

98% (85/87)

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700066M21Rik	T	A	1: 57,422,302 (GRCm39)	M226K	probably benign	Het
4921524L21Rik	T	G	18: 6,626,385 (GRCm39)	S132R	probably damaging	Het
A4gnt	T	G	9: 99,502,335 (GRCm39)	I165S	probably damaging	Het
Abca14	G	A	7: 119,877,534 (GRCm39)	D1061N	probably benign	Het
Abcc9	G	A	6: 142,617,319 (GRCm39)	P582S	probably damaging	Het
Abhd5	G	A	9: 122,208,638 (GRCm39)	V343I	probably benign	Het
Adam6a	C	T	12: 113,509,192 (GRCm39)	R522C	probably damaging	Het
Ankle2	G	A	5: 110,385,590 (GRCm39)	R313H	probably damaging	Het
Aplf	G	A	6: 87,623,197 (GRCm39)	T315I	probably damaging	Het
Asic5	C	T	3: 81,928,383 (GRCm39)	P491S	probably benign	Het
Atp5f1b	T	C	10: 127,921,391 (GRCm39)	Y230H	probably benign	Het
B4galt6	A	T	18: 20,861,099 (GRCm39)	I51N	probably damaging	Het
Bmal2	G	A	6: 146,723,632 (GRCm39)	V321I	not run	Het
C4b	A	G	17: 34,962,633 (GRCm39)	L23S	probably damaging	Het
Cables2	A	G	2: 179,902,129 (GRCm39)	V410A		Het
Ccdc168	T	A	1: 44,100,076 (GRCm39)	K341*	probably null	Het
Cdyl	A	G	13: 36,047,378 (GRCm39)	M489V	probably damaging	Het
Clip4	T	C	17: 72,096,996 (GRCm39)	M40T	probably damaging	Het
Col12a1	T	C	9: 79,589,348 (GRCm39)	Y1069C	probably damaging	Het
Col6a3	T	C	1: 90,755,708 (GRCm39)	M194V	probably benign	Het
Colec11	T	A	12: 28,644,714 (GRCm39)	D260V	probably damaging	Het
Cracdl	T	C	1: 37,653,699 (GRCm39)	T1036A	possibly damaging	Het
Cux2	T	C	5: 121,999,319 (GRCm39)	D1207G	probably benign	Het
Cyp2d34	G	T	15: 82,501,436 (GRCm39)	N297K	possibly damaging	Het
Dmbt1	A	G	7: 130,713,861 (GRCm39)	Y1643C	unknown	Het
Dnmt3c	A	G	2: 153,556,946 (GRCm39)	T288A	probably benign	Het
Dock8	T	A	19: 25,162,245 (GRCm39)	F1842I	probably benign	Het
Dysf	A	G	6: 84,083,880 (GRCm39)	I740V	probably benign	Het
Epha6	T	A	16: 59,736,201 (GRCm39)	M778L	probably benign	Het
Eri2	A	T	7: 119,385,739 (GRCm39)	L254*	probably null	Het
Fam43b	A	G	4: 138,123,152 (GRCm39)	F56S	probably damaging	Het
Fat4	C	A	3: 38,943,294 (GRCm39)	S729*	probably null	Het
Fbxw22	C	A	9: 109,211,143 (GRCm39)	W386L	probably benign	Het
Fgd6	T	A	10: 93,879,909 (GRCm39)	C254*	probably null	Het
Fgd6	C	A	10: 93,975,743 (GRCm39)	T1386K	probably benign	Het
Fkbp7	G	T	2: 76,502,108 (GRCm39)	D98E	possibly damaging	Het
Hectd1	C	T	12: 51,832,635 (GRCm39)	C913Y	possibly damaging	Het
Hgf	T	A	5: 16,769,841 (GRCm39)	M105K	probably benign	Het
Icam1	A	C	9: 20,930,311 (GRCm39)	D55A	probably benign	Het
Itga2	A	C	13: 114,993,930 (GRCm39)		probably null	Het
Kcnj5	A	C	9: 32,234,045 (GRCm39)	L90R	probably damaging	Het
Klra17	T	A	6: 129,808,555 (GRCm39)	N226I	possibly damaging	Het
Krt1	T	A	15: 101,759,064 (GRCm39)	R33S	unknown	Het
L3mbtl3	T	A	10: 26,158,728 (GRCm39)	D615V	unknown	Het
Lrp2	T	A	2: 69,312,725 (GRCm39)	Y2521F	probably benign	Het
Megf10	A	T	18: 57,408,825 (GRCm39)	N589I	probably damaging	Het
Metap1d	G	C	2: 71,337,129 (GRCm39)	G14A	probably benign	Het
Mfap5	T	A	6: 122,505,381 (GRCm39)	D162E	probably benign	Het
Mixl1	T	C	1: 180,524,523 (GRCm39)	I19V	probably benign	Het
Mtrr	G	T	13: 68,716,979 (GRCm39)	Y411*	probably null	Het
Myh7	T	C	14: 55,227,482 (GRCm39)	T318A	probably benign	Het
Nbeal1	T	A	1: 60,349,383 (GRCm39)	Y2348*	probably null	Het
Nhsl3	A	G	4: 129,119,211 (GRCm39)	Y170H	probably damaging	Het
Niban2	T	C	2: 32,812,654 (GRCm39)	S468P	possibly damaging	Het
Nlrc3	T	C	16: 3,781,454 (GRCm39)	S668G	probably damaging	Het
Nutm1	G	A	2: 112,080,401 (GRCm39)	R505C	probably damaging	Het
Or10ag59	T	A	2: 87,406,052 (GRCm39)	V208E	probably damaging	Het
Or12j2	A	T	7: 139,916,654 (GRCm39)	D293V	possibly damaging	Het
Or4c117	C	A	2: 88,955,180 (GRCm39)	R298S	probably benign	Het
Pcna	A	G	2: 132,094,797 (GRCm39)	S54P	probably benign	Het
Pde6a	A	G	18: 61,391,364 (GRCm39)	T570A	probably damaging	Het
Phf21b	A	T	15: 84,739,918 (GRCm39)	M1K	probably null	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 110,350,827 (GRCm39)		probably benign	Het
Prob1	A	G	18: 35,786,352 (GRCm39)	F634S	possibly damaging	Het
Prss50	A	G	9: 110,690,357 (GRCm39)	T167A	probably damaging	Het
Ptpn1	T	C	2: 167,816,692 (GRCm39)	V249A	probably damaging	Het
Ric1	G	A	19: 29,561,978 (GRCm39)		probably null	Het
Robo1	C	T	16: 72,786,519 (GRCm39)	Q844*	probably null	Het
Rpn1	A	G	6: 88,061,619 (GRCm39)	D36G	possibly damaging	Het
Serpinb1b	A	T	13: 33,277,810 (GRCm39)	M348L	probably benign	Het
Setd4	T	C	16: 93,380,830 (GRCm39)		probably null	Het
Setd5	T	G	6: 113,124,518 (GRCm39)	S1124A	probably benign	Het
Slc35c1	C	A	2: 92,289,084 (GRCm39)	V154F	probably damaging	Het
Slc7a6os	G	T	8: 106,937,121 (GRCm39)	S113*	probably null	Het
Syne2	T	A	12: 76,149,810 (GRCm39)	D1787E	probably benign	Het
Tas2r144	A	C	6: 42,192,373 (GRCm39)	I38L	probably damaging	Het
Tepsin	G	T	11: 119,982,534 (GRCm39)	T512K	possibly damaging	Het
Utp20	A	G	10: 88,606,586 (GRCm39)	V1662A	probably benign	Het
Vmn1r201	C	T	13: 22,659,509 (GRCm39)	A241V	possibly damaging	Het
Vmn2r60	T	A	7: 41,785,826 (GRCm39)	S210T	probably benign	Het
Wdr6	G	T	9: 108,451,784 (GRCm39)	H700N	probably damaging	Het
Zdhhc8	T	C	16: 18,052,790 (GRCm39)	T29A	probably benign	Het
Zfp335	A	G	2: 164,742,052 (GRCm39)	I614T	probably damaging	Het
Zfp54	T	A	17: 21,653,844 (GRCm39)	S113T	probably benign	Het
Zfp873	T	A	10: 81,897,071 (GRCm39)	C601S	probably damaging	Het
Zfyve26	T	C	12: 79,325,146 (GRCm39)		probably null	Het
Zmynd8	T	C	2: 165,681,929 (GRCm39)	T201A	probably damaging	Het

Other mutations in Rai1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
R6785:Rai1	UTSW	11	60,079,620 (GRCm39)	missense	probably benign
R6889:Rai1	UTSW	11	60,076,541 (GRCm39)	missense	probably damaging	1.00
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'- AAGCGGGTCGGAAAACCATC -3'
(R):5'- TGTAGACAACCCCATGCATG -3'

Sequencing Primer
(F):5'- TGTTGCCTCAGACAGCAG -3'
(R):5'- AGGCCATCCTCCGTAAGAG -3'

Posted On

2019-09-13