Mutagenetix > Incidental Mutation

Incidental Mutation 'R9718:Rai1'

730617

Institutional Source

Beutler Lab

Gene Symbol

Rai1

Ensembl Gene

ENSMUSG00000062115

Gene Name

retinoic acid induced 1

Synonyms

Gt1

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9718 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

60105013-60199197 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 60189339 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 1410 (A1410T)

Ref Sequence

ENSEMBL: ENSMUSP00000070896 (fasta)

Gene Model

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

AlphaFold

Q61818

Predicted Effect

probably benign
Transcript: ENSMUST00000064190
AA Change: A1410T

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000070896
Gene: ENSMUSG00000062115
AA Change: A1410T

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: A1410T

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

SMART Domains

Protein: ENSMUSP00000088315
Gene: ENSMUSG00000062115
AA Change: A1410T

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: A1410T

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000099749
Gene: ENSMUSG00000062115
AA Change: A1410T

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

probably benign
Transcript: ENSMUST00000171108
AA Change: A1410T

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000126183
Gene: ENSMUSG00000062115
AA Change: A1410T

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

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
9430097D07Rik	A	C	2: 32,575,235		probably benign	Het
Acvr1c	A	T	2: 58,315,995	D34E	probably benign	Het
Arhgef19	T	C	4: 141,249,292	V455A	probably damaging	Het
Cbfa2t3	T	A	8: 122,638,197	D282V	probably benign	Het
Ccl9	T	A	11: 83,575,412	N114I	probably benign	Het
Cdan1	G	T	2: 120,724,169	A875E	probably damaging	Het
Celf2	A	T	2: 6,721,538	F61L	probably damaging	Het
Chd9	T	C	8: 90,986,173	Y875H	unknown	Het
Ckap5	A	T	2: 91,548,832	K39M	probably benign	Het
Clcn3	T	C	8: 60,937,400	H169R	possibly damaging	Het
Csmd3	C	A	15: 47,696,687	V1416F		Het
Cyp4v3	A	T	8: 45,320,666	H155Q	probably damaging	Het
Dhx36	A	G	3: 62,472,045	F874S	possibly damaging	Het
Dnah14	A	T	1: 181,622,979	Q719L	probably benign	Het
Evi2	C	T	11: 79,515,757	V331M	probably damaging	Het
Fcgrt	T	G	7: 45,095,429	E205A	possibly damaging	Het
Fkrp	G	T	7: 16,811,187	T250N	probably benign	Het
Galc	G	A	12: 98,259,314	P6S		Het
Gm13420	A	T	2: 29,747,536	L42Q	probably damaging	Het
Gm5134	A	T	10: 75,992,497	M304L	possibly damaging	Het
Gm813	A	G	16: 58,614,611	L117S	probably benign	Het
Haao	T	C	17: 83,834,786	E208G	probably damaging	Het
Hook1	T	A	4: 96,016,441	H553Q	probably benign	Het
Igdcc3	A	G	9: 65,182,998		probably null	Het
Ighv10-3	C	T	12: 114,523,634	V56I	probably benign	Het
Ighv1-62-1	G	T	12: 115,387,085	A15E	probably benign	Het
Krtap24-1	T	C	16: 88,611,490	*249W	probably null	Het
Ktn1	T	G	14: 47,673,051	I318R	probably damaging	Het
L3mbtl2	A	G	15: 81,687,922	T710A	unknown	Het
Ldha	A	T	7: 46,855,032	Q326L	possibly damaging	Het
Map4	G	A	9: 110,072,706		probably null	Het
Mdfic	T	A	6: 15,770,515	H173Q	probably damaging	Het
Noxred1	T	A	12: 87,224,918	Q159L	possibly damaging	Het
Olfr114	C	T	17: 37,590,023	G110D	probably benign	Het
Olfr584	T	C	7: 103,085,989	V152A	probably benign	Het
Omd	T	C	13: 49,589,860	S129P	probably damaging	Het
Parp16	A	G	9: 65,233,727	Y193C	probably damaging	Het
Pdzk1	A	G	3: 96,855,858	T201A		Het
Phldb2	T	A	16: 45,781,393	H728L	possibly damaging	Het
Ptchd4	C	T	17: 42,502,750	T514I	probably damaging	Het
Pusl1	T	C	4: 155,891,637	D24G	probably benign	Het
Rint1	T	A	5: 23,800,723	H134Q	possibly damaging	Het
Rnf170	A	G	8: 26,129,215	S156G	unknown	Het
Rtf1	A	G	2: 119,705,505	D180G	possibly damaging	Het
Sectm1a	G	T	11: 121,069,664	D108E	probably damaging	Het
Senp7	T	A	16: 56,123,914	D200E	probably damaging	Het
Sfswap	A	G	5: 129,539,784	S431G	probably benign	Het
Sh3bp4	T	A	1: 89,145,750	D773E	probably damaging	Het
Shprh	T	C	10: 11,213,504	L1662P	probably damaging	Het
Slx4	G	T	16: 3,986,464	P829T	possibly damaging	Het
Snapc4	A	T	2: 26,378,521	S43T	probably damaging	Het
Ssh3	C	T	19: 4,262,409	R636Q	probably benign	Het
Strn4	G	A	7: 16,838,571	V679M	probably damaging	Het
Tas2r121	T	G	6: 132,700,802	Y69S	probably benign	Het
Tcerg1	C	T	18: 42,530,771	T341M	unknown	Het
Tjp2	A	C	19: 24,100,843	S895R	probably damaging	Het
Tmem220	G	T	11: 67,025,260	A28S	probably damaging	Het
Trdv1	G	A	14: 53,882,206	C109Y	probably damaging	Het
Trpc6	A	G	9: 8,634,189	Y423C	probably damaging	Het
Ttn	T	C	2: 76,794,683	M15184V	possibly damaging	Het
Ugt2b37	T	A	5: 87,242,943	Y355F	probably benign	Het
Vnn3	C	T	10: 23,869,556	R468*	probably null	Het
Washc5	T	A	15: 59,345,343	T792S	probably benign	Het
Wdfy4	T	C	14: 33,125,936	M820V		Het
Zfp961	T	A	8: 71,968,089	C149S	possibly damaging	Het
Zmat4	G	A	8: 23,748,491	V30M	probably damaging	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
R4894:Rai1	UTSW	11	60186746	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
R8196:Rai1	UTSW	11	60185970	missense	probably damaging	1.00
R8857:Rai1	UTSW	11	60186567	missense	probably benign	0.39
R9161:Rai1	UTSW	11	60185856	missense	probably benign	0.08
R9210:Rai1	UTSW	11	60189391	missense	probably benign
R9570:Rai1	UTSW	11	60185742	missense	probably benign
R9653:Rai1	UTSW	11	60189316	missense	probably benign	0.00
R9788:Rai1	UTSW	11	60187254	missense	possibly damaging	0.77
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
Z1186:Rai1	UTSW	11	60187563	missense	probably benign
Z1187:Rai1	UTSW	11	60187563	missense	probably benign
Z1188:Rai1	UTSW	11	60187563	missense	probably benign
Z1189:Rai1	UTSW	11	60187563	missense	probably benign
Z1190:Rai1	UTSW	11	60187563	missense	probably benign
Z1191:Rai1	UTSW	11	60187563	missense	probably benign
Z1192:Rai1	UTSW	11	60187563	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AATGGGGCAAATGCTACCAG -3'
(R):5'- CGCTTGGAATAGCTGCTGTAG -3'

Sequencing Primer
(F):5'- TACCAGCAGCTTCCGGAG -3'
(R):5'- CTGCTGTAGCTGGCTTGGC -3'

Posted On

2022-10-06