Mutagenetix > Incidental Mutation

Incidental Mutation 'R4869:Rai1'

376433

Institutional Source

Beutler Lab

Gene Symbol

Rai1

Ensembl Gene

ENSMUSG00000062115

Gene Name

retinoic acid induced 1

Synonyms

Gt1

MMRRC Submission

042479-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4869 (G1)

Quality Score

200

Status

Validated

Chromosome

Chromosomal Location

59995839-60090023 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 60077588 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 551 (S551P)

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: S551P

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

SMART Domains

Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: S551P

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: S551P

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

SMART Domains

Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: S551P

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: S551P

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

SMART Domains

Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: S551P

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: S551P

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

SMART Domains

Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: S551P

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

0.1338

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.0%
20x: 94.3%

Validation Efficiency

99% (102/103)

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700017B05Rik	C	A	9: 57,161,488 (GRCm39)	K943N	probably damaging	Het
Abca13	G	A	11: 9,265,434 (GRCm39)		probably null	Het
Ankub1	A	G	3: 57,597,751 (GRCm39)	L73P	probably damaging	Het
Birc6	A	G	17: 74,893,007 (GRCm39)	I982V	probably benign	Het
Cabyr	G	T	18: 12,884,875 (GRCm39)	*454L	probably null	Het
Ccdc57	C	T	11: 120,794,344 (GRCm39)		probably null	Het
Cd209c	A	G	8: 3,994,077 (GRCm39)	F128L	probably benign	Het
Cdh23	A	T	10: 60,212,713 (GRCm39)	I1566N	probably damaging	Het
Cdon	T	C	9: 35,364,200 (GRCm39)	V106A	possibly damaging	Het
Cebpa	G	T	7: 34,819,246 (GRCm39)	G135C	probably damaging	Het
Cfap65	A	G	1: 74,958,420 (GRCm39)	S896P	probably benign	Het
Ciz1	T	C	2: 32,254,247 (GRCm39)	S63P	probably damaging	Het
Clybl	G	A	14: 122,621,618 (GRCm39)	V269M	probably damaging	Het
Ctnnb1	G	T	9: 120,782,060 (GRCm39)	V358L	possibly damaging	Het
Cwh43	G	T	5: 73,586,016 (GRCm39)		probably null	Het
Cyp2d10	G	A	15: 82,287,967 (GRCm39)	R379C	probably benign	Het
Dab2ip	C	A	2: 35,610,049 (GRCm39)	R727S	probably damaging	Het
Dmrt1	T	A	19: 25,483,219 (GRCm39)	M1K	probably null	Het
Dock1	A	T	7: 134,335,800 (GRCm39)	I65F	probably damaging	Het
Ercc2	T	C	7: 19,120,732 (GRCm39)	V155A	probably damaging	Het
Exph5	A	C	9: 53,287,539 (GRCm39)	D1540A	possibly damaging	Het
Fat3	T	A	9: 16,288,773 (GRCm39)	H250L	probably damaging	Het
Fbxw10	C	A	11: 62,753,557 (GRCm39)	A517E	probably damaging	Het
Furin	A	T	7: 80,046,727 (GRCm39)	N176K	probably damaging	Het
Gabrb3	A	G	7: 57,442,207 (GRCm39)		probably benign	Het
Gabrg2	A	T	11: 41,811,231 (GRCm39)	S305T	probably damaging	Het
Gas6	G	T	8: 13,525,086 (GRCm39)	S299R	possibly damaging	Het
Gga3	G	T	11: 115,477,111 (GRCm39)		probably benign	Het
Gle1	A	G	2: 29,826,032 (GRCm39)	E37G	possibly damaging	Het
Gm7964	A	G	7: 83,405,350 (GRCm39)	D80G	possibly damaging	Het
Gne	C	T	4: 44,055,204 (GRCm39)		probably null	Het
Grid2	G	T	6: 64,406,724 (GRCm39)	G695W	probably damaging	Het
H2-M10.6	A	T	17: 37,123,425 (GRCm39)	M40L	probably benign	Het
Hectd4	G	T	5: 121,460,735 (GRCm39)	V905L	possibly damaging	Het
Isyna1	C	A	8: 71,049,412 (GRCm39)	S441R	possibly damaging	Het
Kcnh3	C	T	15: 99,139,913 (GRCm39)	S933L	probably benign	Het
Knl1	T	C	2: 118,902,832 (GRCm39)	I1511T	possibly damaging	Het
Krt73	T	C	15: 101,704,833 (GRCm39)	E351G	probably damaging	Het
Lipo4	C	T	19: 33,478,953 (GRCm39)		probably null	Het
Llgl1	T	A	11: 60,598,036 (GRCm39)	L360*	probably null	Het
Map2k5	G	A	9: 63,229,525 (GRCm39)	R169*	probably null	Het
Muc19	A	T	15: 91,781,910 (GRCm39)		noncoding transcript	Het
Muc4	G	A	16: 32,754,836 (GRCm38)		probably benign	Het
Myh4	A	G	11: 67,143,490 (GRCm39)	E1074G	probably damaging	Het
Naip5	C	T	13: 100,381,639 (GRCm39)	G210E	probably damaging	Het
Nalcn	A	G	14: 123,837,296 (GRCm39)	S23P	probably benign	Het
Nepro	T	A	16: 44,550,536 (GRCm39)	M176K	probably damaging	Het
Nlrp6	G	A	7: 140,504,006 (GRCm39)	C704Y	probably damaging	Het
Notch1	A	G	2: 26,361,191 (GRCm39)	S1100P	probably benign	Het
Nrxn3	A	G	12: 88,762,352 (GRCm39)	E133G	possibly damaging	Het
Obi1	A	G	14: 104,716,252 (GRCm39)	I707T	probably damaging	Het
Parp9	T	C	16: 35,777,274 (GRCm39)	L406S	probably damaging	Het
Peak1	G	T	9: 56,134,876 (GRCm39)	A155D	probably benign	Het
Piezo1	G	A	8: 123,214,284 (GRCm39)	H1628Y	probably benign	Het
Piwil2	A	G	14: 70,632,811 (GRCm39)	V587A	probably benign	Het
Pkn2	A	G	3: 142,509,379 (GRCm39)	Y722H	probably damaging	Het
Plch2	A	T	4: 155,073,885 (GRCm39)	I834K	probably benign	Het
Pld1	A	G	3: 28,163,951 (GRCm39)	T795A	possibly damaging	Het
Plekhh1	A	G	12: 79,097,160 (GRCm39)	S103G	probably benign	Het
Ppl	T	C	16: 4,922,753 (GRCm39)	Y246C	probably damaging	Het
Prpf40b	G	A	15: 99,207,726 (GRCm39)		probably benign	Het
Prr14l	A	G	5: 32,986,177 (GRCm39)	L1106P	probably damaging	Het
Ptbp3	T	A	4: 59,524,443 (GRCm39)	I28F	possibly damaging	Het
Ptrh2	A	T	11: 86,580,631 (GRCm39)	K83*	probably null	Het
Rapgefl1	A	T	11: 98,741,935 (GRCm39)	Q633L	probably damaging	Het
Rb1cc1	T	C	1: 6,285,245 (GRCm39)		probably benign	Het
Rif1	T	A	2: 51,983,623 (GRCm39)		probably benign	Het
Rnf141	A	G	7: 110,424,557 (GRCm39)	Y101H	probably damaging	Het
Rttn	T	A	18: 89,061,138 (GRCm39)	L1102*	probably null	Het
Sall4	G	A	2: 168,597,637 (GRCm39)	S401F	probably damaging	Het
Saxo5	G	A	8: 3,537,148 (GRCm39)	S498N	probably damaging	Het
Sec11c	T	C	18: 65,934,541 (GRCm39)	I36T	probably benign	Het
Sel1l	A	G	12: 91,780,828 (GRCm39)		probably benign	Het
Setd1a	T	C	7: 127,396,776 (GRCm39)		probably benign	Het
Sez6l2	C	T	7: 126,561,014 (GRCm39)	P433L	probably benign	Het
Sgf29	T	C	7: 126,248,547 (GRCm39)		probably benign	Het
Slc47a1	A	G	11: 61,253,520 (GRCm39)	V305A	probably benign	Het
Slco1a8	T	C	6: 141,933,492 (GRCm39)	D431G	probably damaging	Het
Sun2	T	C	15: 79,612,587 (GRCm39)		probably benign	Het
Tecta	T	C	9: 42,286,830 (GRCm39)	S609G	probably benign	Het
Tmprss6	T	A	15: 78,327,880 (GRCm39)		probably null	Het
Tns1	T	C	1: 73,991,774 (GRCm39)	H968R	probably benign	Het
Tomm34	G	A	2: 163,896,637 (GRCm39)	A270V	probably damaging	Het
Tpo	T	C	12: 30,153,364 (GRCm39)	K330R	probably benign	Het
Ttn	T	A	2: 76,542,837 (GRCm39)	Y33383F	probably damaging	Het
Unc13c	G	T	9: 73,587,716 (GRCm39)	A1439D	probably benign	Het
Vcp	C	T	4: 42,993,691 (GRCm39)	R147H	probably benign	Het
Vps13d	A	G	4: 144,854,612 (GRCm39)	L2272P	probably damaging	Het
Wdfy3	A	G	5: 102,042,787 (GRCm39)	L1988P	probably damaging	Het
Wwc2	A	G	8: 48,373,713 (GRCm39)	F51S	probably damaging	Het
Zfp454	C	T	11: 50,763,980 (GRCm39)	C373Y	probably damaging	Het
Zfp853	A	T	5: 143,274,048 (GRCm39)	V473E	probably damaging	Het
Zfp959	A	T	17: 56,204,228 (GRCm39)	R85S	possibly 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
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'- AAGAACCTCGTGTCCAGGAC -3'
(R):5'- TCAGCCTTCTCAACAATGGC -3'

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

Posted On

2016-03-17