Mutagenetix > Incidental Mutation

Incidental Mutation 'R4894:Rai1'

377506

Institutional Source

Beutler Lab

Gene Symbol

Rai1

Ensembl Gene

ENSMUSG00000062115

Gene Name

retinoic acid induced 1

Synonyms

Gt1

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4894 (G1)

Quality Score

217

Status

Not validated

Chromosome

Chromosomal Location

59995839-60090023 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 60077572 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 545 (D545E)

Ref Sequence

ENSEMBL: ENSMUSP00000126183 (fasta)

Gene Model

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

AlphaFold

Q61818

Predicted Effect

probably damaging
Transcript: ENSMUST00000064190
AA Change: D545E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: D545E

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 damaging
Transcript: ENSMUST00000090806
AA Change: D545E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: D545E

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 damaging
Transcript: ENSMUST00000102688
AA Change: D545E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: D545E

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 damaging
Transcript: ENSMUST00000171108
AA Change: D545E

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: D545E

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: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.4%

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrf1	C	A	17: 43,609,975 (GRCm39)	Y176*	probably null	Het
Akap13	T	A	7: 75,375,068 (GRCm39)	M1900K	possibly damaging	Het
Ankrd36	A	G	11: 5,585,332 (GRCm39)	E381G	probably damaging	Het
Ap3s1	T	C	18: 46,891,183 (GRCm39)		probably null	Het
Cacna1e	G	T	1: 154,364,551 (GRCm39)	S341*	probably null	Het
Camk1d	G	A	2: 5,359,539 (GRCm39)	S161L	probably damaging	Het
Cdh23	G	T	10: 60,173,630 (GRCm39)	H1619Q	probably benign	Het
Chd7	T	A	4: 8,838,629 (GRCm39)	I1276N	probably damaging	Het
Clca3a1	A	G	3: 144,719,662 (GRCm39)	V436A	probably damaging	Het
Ctcfl	G	A	2: 172,959,196 (GRCm39)	P177S	probably benign	Het
Dab2ip	A	G	2: 35,620,539 (GRCm39)		probably benign	Het
Dnah8	G	A	17: 30,967,542 (GRCm39)	D2585N	probably benign	Het
Epc1	A	T	18: 6,449,011 (GRCm39)	S495R	probably benign	Het
Espl1	A	G	15: 102,230,758 (GRCm39)		probably null	Het
Eya4	T	C	10: 22,985,753 (GRCm39)	E583G	possibly damaging	Het
Fam111a	C	G	19: 12,565,913 (GRCm39)	T554R	probably benign	Het
Fbh1	A	T	2: 11,767,771 (GRCm39)	I359N	probably damaging	Het
Fer1l6	T	C	15: 58,490,751 (GRCm39)	C1023R	probably damaging	Het
Helz2	G	C	2: 180,877,940 (GRCm39)	P953A	probably benign	Het
Ifi204	G	T	1: 173,587,808 (GRCm39)	S117Y	probably damaging	Het
Ift70a1	T	C	2: 75,810,088 (GRCm39)	*665W	probably null	Het
Igfn1	G	A	1: 135,882,520 (GRCm39)	T2775M	probably damaging	Het
Igsf9	A	G	1: 172,325,634 (GRCm39)	T1101A	probably benign	Het
Ipo13	A	C	4: 117,760,638 (GRCm39)	I614S	probably damaging	Het
Ipo13	A	G	4: 117,761,687 (GRCm39)	I476T	possibly damaging	Het
Kdm2b	C	A	5: 123,079,030 (GRCm39)	E308*	probably null	Het
Klhl20	A	T	1: 160,937,102 (GRCm39)	M91K	possibly damaging	Het
Klrb1f	T	C	6: 129,030,151 (GRCm39)	F64L	probably benign	Het
Ldlrad3	C	T	2: 101,888,293 (GRCm39)	C106Y	probably damaging	Het
Lilra6	T	C	7: 3,915,530 (GRCm39)	T161A	probably benign	Het
Lrriq1	A	T	10: 102,997,613 (GRCm39)	M1334K	possibly damaging	Het
Mepe	C	G	5: 104,473,268 (GRCm39)	P3R	probably damaging	Het
Mgat4e	A	G	1: 134,468,856 (GRCm39)	V396A	probably benign	Het
Nfx1	T	G	4: 40,996,877 (GRCm39)	S651A	probably damaging	Het
Or10ak13	A	T	4: 118,639,483 (GRCm39)	C100S	probably damaging	Het
Or2w6	T	C	13: 21,843,352 (GRCm39)	N47S	probably damaging	Het
Or4c109	T	C	2: 88,817,783 (GRCm39)	I254M	possibly damaging	Het
Rag2	T	C	2: 101,460,022 (GRCm39)	S111P	probably damaging	Het
Ralgps1	A	G	2: 33,033,115 (GRCm39)	V498A	possibly damaging	Het
Rasal2	G	A	1: 157,020,374 (GRCm39)	S205L	probably damaging	Het
Rec8	T	C	14: 55,862,787 (GRCm39)	L582P	probably damaging	Het
Retn	G	A	8: 3,707,358 (GRCm39)	R106H	probably damaging	Het
Rnf112	A	G	11: 61,343,488 (GRCm39)	L116P	probably damaging	Het
Rnf213	T	C	11: 119,372,066 (GRCm39)	Y4885H	probably damaging	Het
Sacm1l	A	G	9: 123,411,409 (GRCm39)	I399M	probably benign	Het
Sez6	G	T	11: 77,866,086 (GRCm39)	G738V	probably damaging	Het
Spata17	A	G	1: 186,872,643 (GRCm39)	V56A	probably benign	Het
Spata31d1a	A	T	13: 59,849,542 (GRCm39)	V862D	probably damaging	Het
Sptb	A	G	12: 76,671,768 (GRCm39)		probably null	Het
Srpk2	C	A	5: 23,750,527 (GRCm39)	G59W	probably damaging	Het
Tyro3	T	C	2: 119,632,779 (GRCm39)	S96P	probably damaging	Het
Ube2v1	A	G	2: 167,452,280 (GRCm39)	S108P	probably damaging	Het
Usp2	C	T	9: 43,987,125 (GRCm39)	S141L	probably benign	Het
Vamp5	T	C	6: 72,347,181 (GRCm39)	D46G	possibly damaging	Het
Vmn1r23	T	A	6: 57,903,310 (GRCm39)	Q156L	probably benign	Het
Vmn2r6	C	T	3: 64,454,829 (GRCm39)	S490N	probably benign	Het
Vps39	A	T	2: 120,183,440 (GRCm39)	I10N	probably damaging	Het
Vwf	C	T	6: 125,622,897 (GRCm39)	Q1755*	probably null	Het
Wdfy4	A	T	14: 32,877,717 (GRCm39)	H82Q	probably benign	Het
Wdr24	T	C	17: 26,045,101 (GRCm39)	Y279H	probably damaging	Het
Wdr72	A	G	9: 74,117,843 (GRCm39)	T852A	probably benign	Het
Zfp1	T	A	8: 112,396,355 (GRCm39)	C92*	probably null	Het
Zfp1004	T	A	2: 150,033,899 (GRCm39)	C104*	probably null	Het
Zfp426	A	T	9: 20,386,369 (GRCm39)		probably benign	Het
Zfp442	C	T	2: 150,253,130 (GRCm39)		probably null	Het
Zfp74	T	C	7: 29,635,470 (GRCm39)		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
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'- AAGAACCTCGTGTCCAGGAC -3'
(R):5'- ACAATGGCTTCCTGCAGTC -3'

Sequencing Primer
(F):5'- AGCACTGTAGCCCTGAAGG -3'
(R):5'- TGCAGTCCCAGGATCTCG -3'

Posted On

2016-03-17