Mutagenetix > Incidental Mutations

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

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R4894 (G1)

Quality Score

217

Status

Not validated

Chromosome

Chromosomal Location

60105013-60199197 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 60186746 bp

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]

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: 43,299,084	Y176*	probably null	Het
Akap13	T	A	7: 75,725,320	M1900K	possibly damaging	Het
Ankrd36	A	G	11: 5,635,332	E381G	probably damaging	Het
Ap3s1	T	C	18: 46,758,116		probably null	Het
Cacna1e	G	T	1: 154,488,805	S341*	probably null	Het
Camk1d	G	A	2: 5,354,728	S161L	probably damaging	Het
Cdh23	G	T	10: 60,337,851	H1619Q	probably benign	Het
Chd7	T	A	4: 8,838,629	I1276N	probably damaging	Het
Clca1	A	G	3: 145,013,901	V436A	probably damaging	Het
Ctcfl	G	A	2: 173,117,403	P177S	probably benign	Het
Dab2ip	A	G	2: 35,730,527		probably benign	Het
Dnah8	G	A	17: 30,748,568	D2585N	probably benign	Het
Epc1	A	T	18: 6,449,011	S495R	probably benign	Het
Espl1	A	G	15: 102,322,323		probably null	Het
Eya4	T	C	10: 23,109,854	E583G	possibly damaging	Het
Fam111a	C	G	19: 12,588,549	T554R	probably benign	Het
Fbxo18	A	T	2: 11,762,960	I359N	probably damaging	Het
Fer1l6	T	C	15: 58,618,902	C1023R	probably damaging	Het
Gm14139	T	A	2: 150,191,979	C104*	probably null	Het
Helz2	G	C	2: 181,236,147	P953A	probably benign	Het
Ifi204	G	T	1: 173,760,242	S117Y	probably damaging	Het
Igfn1	G	A	1: 135,954,782	T2775M	probably damaging	Het
Igsf9	A	G	1: 172,498,067	T1101A	probably benign	Het
Ipo13	A	C	4: 117,903,441	I614S	probably damaging	Het
Ipo13	A	G	4: 117,904,490	I476T	possibly damaging	Het
Kdm2b	C	A	5: 122,940,967	E308*	probably null	Het
Klhl20	A	T	1: 161,109,532	M91K	possibly damaging	Het
Klrb1f	T	C	6: 129,053,188	F64L	probably benign	Het
Ldlrad3	C	T	2: 102,057,948	C106Y	probably damaging	Het
Lilra6	T	C	7: 3,912,531	T161A	probably benign	Het
Lrriq1	A	T	10: 103,161,752	M1334K	possibly damaging	Het
Mepe	C	G	5: 104,325,402	P3R	probably damaging	Het
Mgat4e	A	G	1: 134,541,118	V396A	probably benign	Het
Nfx1	T	G	4: 40,996,877	S651A	probably damaging	Het
Olfr1214	T	C	2: 88,987,439	I254M	possibly damaging	Het
Olfr1337	A	T	4: 118,782,286	C100S	probably damaging	Het
Olfr1361	T	C	13: 21,659,182	N47S	probably damaging	Het
Rag2	T	C	2: 101,629,677	S111P	probably damaging	Het
Ralgps1	A	G	2: 33,143,103	V498A	possibly damaging	Het
Rasal2	G	A	1: 157,192,804	S205L	probably damaging	Het
Rec8	T	C	14: 55,625,330	L582P	probably damaging	Het
Retn	G	A	8: 3,657,358	R106H	probably damaging	Het
Rnf112	A	G	11: 61,452,662	L116P	probably damaging	Het
Rnf213	T	C	11: 119,481,240	Y4885H	probably damaging	Het
Sacm1l	A	G	9: 123,582,344	I399M	probably benign	Het
Sez6	G	T	11: 77,975,260	G738V	probably damaging	Het
Spata17	A	G	1: 187,140,446	V56A	probably benign	Het
Spata31d1a	A	T	13: 59,701,728	V862D	probably damaging	Het
Sptb	A	G	12: 76,624,994		probably null	Het
Srpk2	C	A	5: 23,545,529	G59W	probably damaging	Het
Ttc30a1	T	C	2: 75,979,744	*665W	probably null	Het
Tyro3	T	C	2: 119,802,298	S96P	probably damaging	Het
Ube2v1	A	G	2: 167,610,360	S108P	probably damaging	Het
Usp2	C	T	9: 44,075,828	S141L	probably benign	Het
Vamp5	T	C	6: 72,370,198	D46G	possibly damaging	Het
Vmn1r23	T	A	6: 57,926,325	Q156L	probably benign	Het
Vmn2r6	C	T	3: 64,547,408	S490N	probably benign	Het
Vps39	A	T	2: 120,352,959	I10N	probably damaging	Het
Vwf	C	T	6: 125,645,934	Q1755*	probably null	Het
Wdfy4	A	T	14: 33,155,760	H82Q	probably benign	Het
Wdr24	T	C	17: 25,826,127	Y279H	probably damaging	Het
Wdr72	A	G	9: 74,210,561	T852A	probably benign	Het
Zfp1	T	A	8: 111,669,723	C92*	probably null	Het
Zfp426	A	T	9: 20,475,073		probably benign	Het
Zfp442	C	T	2: 150,411,210		probably null	Het
Zfp74	T	C	7: 29,936,045		probably benign	Het

Other mutations in Rai1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00232:Rai1	APN	11	60185391	missense	probably damaging	1.00
IGL00952:Rai1	APN	11	60187992	nonsense	probably null
IGL01118:Rai1	APN	11	60187438	missense	probably damaging	0.98
IGL02540:Rai1	APN	11	60186924	missense	probably benign	0.09
IGL02624:Rai1	APN	11	60188743	missense	probably damaging	1.00
IGL02696:Rai1	APN	11	60193956	missense	probably benign
IGL02940:Rai1	APN	11	60187018	missense	probably benign	0.03
IGL02970:Rai1	APN	11	60185733	missense	probably damaging	1.00
IGL03006:Rai1	APN	11	60188205	missense	possibly damaging	0.95
R0557:Rai1	UTSW	11	60190495	missense	probably benign	0.00
R1438:Rai1	UTSW	11	60185395	missense	probably benign	0.00
R1712:Rai1	UTSW	11	60187602	missense	probably benign
R1837:Rai1	UTSW	11	60189398	missense	probably damaging	1.00
R1899:Rai1	UTSW	11	60185920	missense	probably benign	0.16
R2024:Rai1	UTSW	11	60185589	missense	probably damaging	0.99
R2141:Rai1	UTSW	11	60189467	missense	possibly damaging	0.94
R2168:Rai1	UTSW	11	60187596	missense	probably benign	0.01
R2404:Rai1	UTSW	11	60189924	missense	probably benign
R4869:Rai1	UTSW	11	60186762	missense	probably damaging	1.00
R5082:Rai1	UTSW	11	60185919	missense	possibly damaging	0.48
R5093:Rai1	UTSW	11	60188656	missense	probably benign	0.00
R5221:Rai1	UTSW	11	60190597	missense	probably damaging	1.00
R5503:Rai1	UTSW	11	60186453	missense	probably benign	0.00
R5587:Rai1	UTSW	11	60189859	missense	probably damaging	1.00
R5849:Rai1	UTSW	11	60190521	missense	possibly damaging	0.90
R5914:Rai1	UTSW	11	60187804	missense	probably benign
R5950:Rai1	UTSW	11	60187593	missense	probably damaging	1.00
R6111:Rai1	UTSW	11	60187906	missense	probably damaging	0.99
R6450:Rai1	UTSW	11	60186603	missense	probably benign	0.30
R6785:Rai1	UTSW	11	60188794	missense	probably benign
R6889:Rai1	UTSW	11	60185715	missense	probably damaging	1.00
R7296:Rai1	UTSW	11	60188673	missense	probably benign	0.39
R7388:Rai1	UTSW	11	60189375	missense	possibly damaging	0.46
X0018:Rai1	UTSW	11	60186436	missense	probably benign	0.03
X0019:Rai1	UTSW	11	60189940	missense	probably benign	0.14
X0024:Rai1	UTSW	11	60187395	missense	possibly damaging	0.65

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