Mutagenetix > Incidental Mutation

Incidental Mutation 'R5093:Rai1'

387941

Institutional Source

Beutler Lab

Gene Symbol

Rai1

Ensembl Gene

ENSMUSG00000062115

Gene Name

retinoic acid induced 1

Synonyms

Gt1

MMRRC Submission

042682-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5093 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

59995839-60090023 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 60079482 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 1182 (M1182K)

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: M1182K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: M1182K

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: M1182K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: M1182K

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: M1182K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: M1182K

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: M1182K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: M1182K

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

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.1%

Validation Efficiency

99% (90/91)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4833420G17Rik	C	T	13: 119,610,573 (GRCm39)		probably benign	Het
Abca9	A	T	11: 110,032,358 (GRCm39)	L753Q	probably damaging	Het
Acvrl1	A	G	15: 101,032,628 (GRCm39)		probably null	Het
Adgrv1	A	T	13: 81,740,704 (GRCm39)	N141K	probably damaging	Het
Aftph	C	T	11: 20,659,619 (GRCm39)		probably null	Het
Aifm1	C	T	X: 47,571,637 (GRCm39)	G371S	probably benign	Het
Aldh3b2	A	G	19: 4,029,433 (GRCm39)	M269V	probably benign	Het
Ankrd44	T	C	1: 54,802,877 (GRCm39)	Y207C	probably damaging	Het
Arhgap15	G	T	2: 44,212,767 (GRCm39)	M412I	probably damaging	Het
Auts2	A	C	5: 131,468,296 (GRCm39)	L783R	probably damaging	Het
Baiap2l1	A	T	5: 144,215,363 (GRCm39)	Y381N	probably damaging	Het
Baiap3	T	C	17: 25,469,243 (GRCm39)	D180G	probably damaging	Het
Cant1	T	C	11: 118,302,038 (GRCm39)	Y93C	probably damaging	Het
Catsperg2	T	C	7: 29,416,423 (GRCm39)	S330G	probably benign	Het
Ccdc73	A	T	2: 104,848,111 (GRCm39)		probably benign	Het
Cdc5l	A	T	17: 45,703,967 (GRCm39)	F752L	possibly damaging	Het
Celsr2	G	T	3: 108,320,689 (GRCm39)	H708N	possibly damaging	Het
Cep170	T	A	1: 176,596,896 (GRCm39)	K487M	possibly damaging	Het
Cerkl	A	T	2: 79,163,867 (GRCm39)	N66K	probably damaging	Het
Cilk1	G	A	9: 78,047,303 (GRCm39)	V68I	probably benign	Het
Clec11a	C	T	7: 43,954,150 (GRCm39)	A268T	probably damaging	Het
Ctnna2	C	A	6: 77,091,912 (GRCm39)		probably null	Het
Diaph3	C	A	14: 87,222,236 (GRCm39)	R416L	probably damaging	Het
Dnmbp	T	A	19: 43,838,315 (GRCm39)	N1170I	probably damaging	Het
Erbb2	G	T	11: 98,318,279 (GRCm39)	C505F	probably damaging	Het
Ercc6	T	A	14: 32,289,479 (GRCm39)	F904L	probably damaging	Het
Exo5	C	T	4: 120,779,514 (GRCm39)	G117D	probably damaging	Het
F2	CAGAAAG	CAG	2: 91,465,302 (GRCm39)		probably benign	Het
Fbxl5	A	G	5: 43,930,896 (GRCm39)	Y64H	probably damaging	Het
Gabra4	T	A	5: 71,798,207 (GRCm39)	M207L	probably damaging	Het
Galnt15	T	C	14: 31,771,786 (GRCm39)	L277P	probably damaging	Het
Gclm	T	C	3: 122,049,261 (GRCm39)		probably null	Het
Gm5493	T	A	17: 22,966,201 (GRCm39)	C29S	possibly damaging	Het
Grik3	A	G	4: 125,564,382 (GRCm39)	T455A	probably benign	Het
Grm3	A	G	5: 9,639,766 (GRCm39)	V93A	probably benign	Het
Hdgfl2	C	T	17: 56,406,217 (GRCm39)	A535V	possibly damaging	Het
Hfm1	A	T	5: 107,049,597 (GRCm39)	S455T	probably damaging	Het
Hmcn1	T	A	1: 150,613,007 (GRCm39)	D1424V	probably benign	Het
Hsd3b6	C	T	3: 98,715,120 (GRCm39)	V91I	probably benign	Het
Igdcc4	G	A	9: 65,030,039 (GRCm39)	S363N	possibly damaging	Het
Intu	T	C	3: 40,647,347 (GRCm39)	V740A	probably benign	Het
Itga2	C	T	13: 114,992,717 (GRCm39)	V838I	probably benign	Het
Kif9	A	G	9: 110,318,965 (GRCm39)	E143G	probably damaging	Het
Kmt2c	T	A	5: 25,614,205 (GRCm39)	I172F	probably benign	Het
Kmt2d	G	A	15: 98,754,043 (GRCm39)	R21W	probably damaging	Het
Mdh1b	A	T	1: 63,750,620 (GRCm39)	D449E	probably benign	Het
Meis1	T	C	11: 18,831,785 (GRCm39)	I418V	probably benign	Het
Nags	T	A	11: 102,037,395 (GRCm39)	M162K	probably damaging	Het
Nufip1	A	G	14: 76,348,413 (GRCm39)	D14G	probably benign	Het
Or2l13	T	A	16: 19,306,227 (GRCm39)	I213N	probably damaging	Het
Or2n1c	A	C	17: 38,519,208 (GRCm39)	E24A	possibly damaging	Het
Or7g28	T	G	9: 19,272,274 (GRCm39)	I126L	probably damaging	Het
Osmr	A	C	15: 6,850,560 (GRCm39)	V681G	probably damaging	Het
Paxip1	G	T	5: 27,971,282 (GRCm39)	Q356K	unknown	Het
Pcdhac1	T	A	18: 37,223,595 (GRCm39)	F136Y	probably damaging	Het
Pla2g6	A	G	15: 79,171,328 (GRCm39)	V699A	probably benign	Het
Plcb3	A	T	19: 6,943,578 (GRCm39)	V107E	probably damaging	Het
Plch1	T	A	3: 63,681,136 (GRCm39)	I164F	probably damaging	Het
Plpp3	A	T	4: 105,052,077 (GRCm39)	I73F	probably damaging	Het
Plscr5	G	A	9: 92,080,574 (GRCm39)	R20Q	probably benign	Het
Prdm10	G	A	9: 31,252,779 (GRCm39)	R504Q	probably damaging	Het
Prss58	T	C	6: 40,874,751 (GRCm39)	Y30C	probably damaging	Het
Psg19	T	A	7: 18,530,894 (GRCm39)	T87S	probably benign	Het
Ptpn22	T	G	3: 103,789,418 (GRCm39)	M294R	probably benign	Het
Sez6	T	A	11: 77,867,388 (GRCm39)	V795D	possibly damaging	Het
Shcbp1	A	G	8: 4,789,214 (GRCm39)	V535A	possibly damaging	Het
Skint9	A	G	4: 112,246,447 (GRCm39)	Y222H	probably benign	Het
Slc13a3	T	A	2: 165,253,816 (GRCm39)	I446F	probably damaging	Het
Slc2a3	C	T	6: 122,714,196 (GRCm39)	R57H	probably damaging	Het
Slc44a4	A	G	17: 35,140,219 (GRCm39)	D208G	probably benign	Het
Spata31d1b	A	T	13: 59,863,838 (GRCm39)	N329Y	possibly damaging	Het
Strbp	C	T	2: 37,517,499 (GRCm39)	R192K	probably damaging	Het
Tctn3	A	T	19: 40,600,548 (GRCm39)	L14Q	probably damaging	Het
Tenm2	T	A	11: 36,834,989 (GRCm39)	D2V	probably damaging	Het
Tln2	T	G	9: 67,241,596 (GRCm39)	K1003T	probably benign	Het
Tmem63b	T	C	17: 45,971,800 (GRCm39)	E805G	probably damaging	Het
Trhr	A	T	15: 44,060,980 (GRCm39)	N167Y	probably damaging	Het
Trpc2	A	G	7: 101,744,390 (GRCm39)	R721G	probably benign	Het
Ttn	C	A	2: 76,701,267 (GRCm39)		probably benign	Het
Wdr91	A	G	6: 34,869,288 (GRCm39)	I412T	probably damaging	Het
Zcchc4	T	A	5: 52,953,952 (GRCm39)	S211T	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
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'- AAGCGGGTCGGAAAACCATC -3'
(R):5'- TGTAGACAACCCCATGCATG -3'

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

Posted On

2016-06-06