Mutagenetix > Incidental Mutation

Incidental Mutation 'R5503:Rai1'

430752

Institutional Source

Beutler Lab

Gene Symbol

Rai1

Ensembl Gene

ENSMUSG00000062115

Gene Name

retinoic acid induced 1

Synonyms

Gt1

MMRRC Submission

043064-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5503 (G1)

Quality Score

220

Status

Validated

Chromosome

Chromosomal Location

59995839-60090023 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 60077279 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 448 (V448I)

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: V448I

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: V448I

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: ENSMUST00000090806
AA Change: V448I

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: V448I

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: V448I

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: V448I

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

noncoding transcript
Transcript: ENSMUST00000149770

Predicted Effect

probably benign
Transcript: ENSMUST00000171108
AA Change: V448I

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: V448I

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

Meta Mutation Damage Score

0.0585

Coding Region Coverage

1x: 98.3%
3x: 97.4%
10x: 95.4%
20x: 91.5%

Validation Efficiency

96% (103/107)

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	A	T	12: 71,211,321 (GRCm39)	E685V	possibly damaging	Het
2700049A03Rik	G	T	12: 71,211,320 (GRCm39)	E685*	probably null	Het
Abca6	A	G	11: 110,109,083 (GRCm39)	S696P	probably damaging	Het
Abca9	G	A	11: 110,032,436 (GRCm39)	T727M	probably damaging	Het
Alpk2	T	C	18: 65,439,312 (GRCm39)	R1161G	probably benign	Het
Amy1	T	C	3: 113,349,709 (GRCm39)	D487G	probably benign	Het
Arap2	G	A	5: 62,787,529 (GRCm39)	A1409V	probably damaging	Het
B4galt6	C	A	18: 20,878,409 (GRCm39)		probably null	Het
Cacna1s	G	A	1: 136,014,480 (GRCm39)	G382D	probably damaging	Het
Camk2a	A	G	18: 61,111,072 (GRCm39)	D87G	probably damaging	Het
Cdh18	A	G	15: 23,436,620 (GRCm39)	Y492C	probably damaging	Het
Cert1	C	T	13: 96,679,747 (GRCm39)	R26C	possibly damaging	Het
Col18a1	C	T	10: 76,907,454 (GRCm39)	G861D	probably damaging	Het
Crybg1	C	A	10: 43,874,762 (GRCm39)	S782I	probably benign	Het
Csgalnact1	G	A	8: 68,914,125 (GRCm39)	L27F	probably damaging	Het
Dab1	T	A	4: 104,369,461 (GRCm39)	C3S	probably benign	Het
Dapk1	T	C	13: 60,873,126 (GRCm39)	F343L	probably benign	Het
Dgat1	A	T	15: 76,386,394 (GRCm39)		probably benign	Het
Dnah11	C	A	12: 117,844,186 (GRCm39)		probably null	Het
Dsg2	T	A	18: 20,713,708 (GRCm39)	Y226*	probably null	Het
Epg5	T	A	18: 77,994,422 (GRCm39)	M351K	possibly damaging	Het
F13b	A	G	1: 139,450,281 (GRCm39)	T648A	probably benign	Het
Fgf17	T	C	14: 70,874,408 (GRCm39)	Y127C	probably damaging	Het
Fkbp15	G	A	4: 62,246,124 (GRCm39)	P435S	probably benign	Het
Gfm1	G	A	3: 67,361,060 (GRCm39)		probably null	Het
Gigyf1	T	C	5: 137,521,729 (GRCm39)		probably benign	Het
Gm12830	A	T	4: 114,678,936 (GRCm39)	T6S	unknown	Het
Gm6465	A	T	5: 11,898,150 (GRCm39)	N88I	probably damaging	Het
Gpr18	C	T	14: 122,149,159 (GRCm39)	V289I	probably damaging	Het
Ipp	G	T	4: 116,395,135 (GRCm39)	E557*	probably null	Het
Klhl12	T	A	1: 134,413,653 (GRCm39)		probably null	Het
Klhl38	A	G	15: 58,185,745 (GRCm39)	V328A	possibly damaging	Het
Kndc1	A	G	7: 139,511,802 (GRCm39)	T1470A	probably damaging	Het
Kntc1	T	A	5: 123,957,939 (GRCm39)	D2173E	possibly damaging	Het
Lipi	T	C	16: 75,370,864 (GRCm39)	K118E	probably benign	Het
Marf1	A	C	16: 13,970,095 (GRCm39)	L208R	probably damaging	Het
Misp	G	A	10: 79,662,552 (GRCm39)	R323K	probably damaging	Het
Mlxip	T	A	5: 123,533,390 (GRCm39)	M133K	probably damaging	Het
Mon2	A	T	10: 122,868,550 (GRCm39)	M501K	possibly damaging	Het
Myh2	A	G	11: 67,064,275 (GRCm39)	I77V	probably benign	Het
Napa	C	A	7: 15,849,549 (GRCm39)	Q254K	probably benign	Het
Nckap5l	C	A	15: 99,323,503 (GRCm39)	G1000V	probably damaging	Het
Neo1	A	T	9: 58,892,933 (GRCm39)	S236R	possibly damaging	Het
Neurl4	T	A	11: 69,797,194 (GRCm39)	Y594N	probably damaging	Het
Nmral1	G	A	16: 4,533,493 (GRCm39)	P94L	probably benign	Het
Notch3	A	T	17: 32,366,029 (GRCm39)	I1024N	probably benign	Het
Nsd1	T	A	13: 55,393,752 (GRCm39)	I451K	probably damaging	Het
Nt5c3b	T	C	11: 100,323,883 (GRCm39)	D143G	probably benign	Het
Oplah	A	G	15: 76,189,646 (GRCm39)		probably null	Het
Or13a17	A	C	7: 140,271,309 (GRCm39)	M164L	probably benign	Het
Or2ak4	T	A	11: 58,649,154 (GRCm39)	V221E	probably damaging	Het
Or6b2b	C	A	1: 92,418,918 (GRCm39)	K186N	probably benign	Het
Or7d10	A	G	9: 19,831,675 (GRCm39)	T57A	probably benign	Het
Or8b48	T	C	9: 38,493,368 (GRCm39)	V265A	probably benign	Het
Or8g19	A	G	9: 39,055,780 (GRCm39)	N128S	probably benign	Het
Phb2	T	A	6: 124,689,985 (GRCm39)		probably benign	Het
Plcl2	A	G	17: 50,816,957 (GRCm39)	I108V	probably benign	Het
Plpp6	T	A	19: 28,942,146 (GRCm39)	M249K	probably damaging	Het
Pnpt1	G	A	11: 29,088,156 (GRCm39)	G189E	probably damaging	Het
Pramel17	A	T	4: 101,692,999 (GRCm39)	Y334N	probably benign	Het
Ptprn	C	T	1: 75,228,519 (GRCm39)	V853M	probably damaging	Het
Ptprq	T	C	10: 107,524,189 (GRCm39)		probably null	Het
Rbm20	T	A	19: 53,839,785 (GRCm39)	C925S	possibly damaging	Het
Rin3	C	A	12: 102,279,314 (GRCm39)	P41Q	probably benign	Het
Rpl31-ps21	T	C	5: 21,324,505 (GRCm39)		noncoding transcript	Het
Rpl39-ps	A	T	15: 102,543,561 (GRCm39)		noncoding transcript	Het
Rtn4ip1	T	A	10: 43,783,879 (GRCm39)	D133E	probably benign	Het
Ryr1	T	C	7: 28,768,453 (GRCm39)	K2839E	possibly damaging	Het
Septin5	T	C	16: 18,442,118 (GRCm39)	K268R	probably benign	Het
Serpinb6b	T	A	13: 33,161,642 (GRCm39)	D238E	possibly damaging	Het
Slc15a2	C	T	16: 36,582,747 (GRCm39)	V214M	probably damaging	Het
Smarca2	T	C	19: 26,601,336 (GRCm39)	M18T	probably damaging	Het
Smarca2	C	A	19: 26,659,446 (GRCm39)	T912K	possibly damaging	Het
Smdt1	A	T	15: 82,232,101 (GRCm39)	R46S	possibly damaging	Het
Spa17	A	C	9: 37,523,273 (GRCm39)	F5V	probably damaging	Het
Spag17	A	G	3: 99,934,560 (GRCm39)	E614G	possibly damaging	Het
Sstr4	CGAGGAGGAGGAGGA	CGAGGAGGAGGAGGAGGA	2: 148,237,471 (GRCm39)		probably benign	Het
Tlr1	A	T	5: 65,083,635 (GRCm39)	V314D	probably damaging	Het
Trappc8	A	T	18: 20,969,957 (GRCm39)	L1011Q	probably benign	Het
Tsga10	A	G	1: 37,800,028 (GRCm39)	*691Q	probably null	Het
Vav1	A	T	17: 57,610,079 (GRCm39)	K420*	probably null	Het
Vmn1r174	C	G	7: 23,453,562 (GRCm39)	T76R	probably benign	Het
Vmn2r116	A	G	17: 23,605,778 (GRCm39)	E230G	probably benign	Het
Vps13b	A	G	15: 35,452,312 (GRCm39)	T637A	probably damaging	Het
Zbtb7a	A	G	10: 80,980,631 (GRCm39)	E275G	probably damaging	Het
Zfp280b	A	G	10: 75,875,296 (GRCm39)		probably null	Het
Zfp763	A	G	17: 33,238,507 (GRCm39)	Y213H	possibly damaging	Het
Zfp78	T	A	7: 6,381,528 (GRCm39)	W161R	probably benign	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
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'- GACCACAGCCACTTTATGCC -3'
(R):5'- AGCCACTCAGGTAGTCAGTG -3'

Sequencing Primer
(F):5'- AACAGATGCTGCCAGCTCTG -3'
(R):5'- CACTCAGGTAGTCAGTGTCCTG -3'

Posted On

2016-10-05