Mutagenetix > Incidental Mutation

Incidental Mutation 'R5861:Rara'

453929

Institutional Source

Beutler Lab

Gene Symbol

Rara

Ensembl Gene

ENSMUSG00000037992

Gene Name

retinoic acid receptor, alpha

Synonyms

RARalpha1, RAR alpha 1

MMRRC Submission

044073-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5861 (G1)

Quality Score

168

Status

Validated

Chromosome

Chromosomal Location

98818644-98865768 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 98858987 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Stop codon at position 148 (C148*)

Ref Sequence

ENSEMBL: ENSMUSP00000129791 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000068133] [ENSMUST00000107473] [ENSMUST00000107474] [ENSMUST00000107475] [ENSMUST00000164748]

AlphaFold

P11416

Predicted Effect

probably null
Transcript: ENSMUST00000068133
AA Change: C148*

SMART Domains

Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
AA Change: C148*

Domain	Start	End	E-Value	Type
low complexity region	19	30	N/A	INTRINSIC
low complexity region	65	80	N/A	INTRINSIC
ZnF_C4	85	156	7.53e-40	SMART
HOLI	230	388	1.22e-34	SMART
low complexity region	425	436	N/A	INTRINSIC
low complexity region	439	462	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000107473
AA Change: C145*

SMART Domains

Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: C145*

Domain	Start	End	E-Value	Type
low complexity region	54	77	N/A	INTRINSIC
ZnF_C4	82	153	7.53e-40	SMART
HOLI	227	385	1.22e-34	SMART
low complexity region	422	433	N/A	INTRINSIC
low complexity region	436	459	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000107474
AA Change: C148*

SMART Domains

Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
AA Change: C148*

Domain	Start	End	E-Value	Type
low complexity region	19	30	N/A	INTRINSIC
low complexity region	65	80	N/A	INTRINSIC
ZnF_C4	85	156	7.53e-40	SMART
HOLI	230	388	1.22e-34	SMART
low complexity region	425	436	N/A	INTRINSIC
low complexity region	439	462	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000107475
AA Change: C148*

SMART Domains

Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
AA Change: C148*

Domain	Start	End	E-Value	Type
low complexity region	19	30	N/A	INTRINSIC
low complexity region	65	80	N/A	INTRINSIC
ZnF_C4	85	156	7.53e-40	SMART
HOLI	230	388	1.22e-34	SMART
low complexity region	425	436	N/A	INTRINSIC
low complexity region	439	462	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000164748
AA Change: C148*

SMART Domains

Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
AA Change: C148*

Domain	Start	End	E-Value	Type
low complexity region	19	30	N/A	INTRINSIC
low complexity region	65	80	N/A	INTRINSIC
ZnF_C4	85	156	7.53e-40	SMART
HOLI	230	388	1.22e-34	SMART
low complexity region	425	436	N/A	INTRINSIC
low complexity region	439	462	N/A	INTRINSIC

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.9%
3x: 99.4%
10x: 97.3%
20x: 91.3%

Validation Efficiency

98% (81/83)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]
PHENOTYPE: Homozygotes for targeted null mutations show high neonatal mortality due to maternal cannibalization, failure to thrive, and excess mortality during the postnatal period. Male survivors exhibit testicular degeneration. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	G	T	16: 20,218,644 (GRCm39)	T246N	probably damaging	Het
Aopep	A	G	13: 63,446,626 (GRCm39)	D143G	probably damaging	Het
Arhgap10	C	T	8: 78,037,393 (GRCm39)	A612T	probably damaging	Het
Arsg	T	A	11: 109,454,014 (GRCm39)	F407I	probably damaging	Het
Asxl1	C	A	2: 153,241,310 (GRCm39)	A620D	probably damaging	Het
C2cd3	A	G	7: 100,093,682 (GRCm39)		probably benign	Het
Chn2	G	A	6: 54,267,359 (GRCm39)	V92I	probably damaging	Het
Cog2	T	C	8: 125,264,617 (GRCm39)	F332S	probably damaging	Het
Crhbp	G	A	13: 95,580,333 (GRCm39)	A82V	probably damaging	Het
Cyp2j6	A	G	4: 96,434,040 (GRCm39)	V90A	possibly damaging	Het
Dennd4c	A	T	4: 86,709,589 (GRCm39)	M397L	probably benign	Het
Dnajb8	A	G	6: 88,200,088 (GRCm39)	D208G	possibly damaging	Het
Ecm1	G	C	3: 95,643,909 (GRCm39)	L230V	probably damaging	Het
Ercc2	G	C	7: 19,128,066 (GRCm39)	A696P	possibly damaging	Het
Fkbpl	G	A	17: 34,864,303 (GRCm39)	A24T	probably benign	Het
Gm13035	A	G	4: 146,009,859 (GRCm39)		noncoding transcript	Het
Gm28042	T	C	2: 119,865,116 (GRCm39)	V247A	probably damaging	Het
Gm28455	T	A	7: 39,148,003 (GRCm39)		noncoding transcript	Het
Gpr150	A	T	13: 76,204,192 (GRCm39)	V251D	possibly damaging	Het
Grip1	C	T	10: 119,765,875 (GRCm39)	S69L	probably damaging	Het
Hs6st3	A	G	14: 119,376,265 (GRCm39)	I147V	possibly damaging	Het
Il5	G	A	11: 53,614,743 (GRCm39)	E102K	probably benign	Het
Kif1c	T	C	11: 70,594,621 (GRCm39)	F94L	probably damaging	Het
Lrrc63	T	C	14: 75,344,806 (GRCm39)	E427G	possibly damaging	Het
Man1b1	A	G	2: 25,238,066 (GRCm39)	T384A	probably benign	Het
Mapk15	C	A	15: 75,868,208 (GRCm39)		probably benign	Het
Mfsd10	T	C	5: 34,791,588 (GRCm39)		probably benign	Het
Mgat5	C	A	1: 127,315,129 (GRCm39)	A285E	probably damaging	Het
Mroh4	T	A	15: 74,478,456 (GRCm39)		probably benign	Het
Myf5	A	T	10: 107,320,069 (GRCm39)	C194S	probably benign	Het
Myh7	A	G	14: 55,226,347 (GRCm39)	V431A	possibly damaging	Het
Nadsyn1	A	C	7: 143,364,964 (GRCm39)	M247R	possibly damaging	Het
Nipsnap3b	A	G	4: 53,021,177 (GRCm39)	D166G	probably damaging	Het
Nqo2	A	T	13: 34,156,413 (GRCm39)	L42F	probably damaging	Het
Nt5dc3	A	T	10: 86,651,738 (GRCm39)	D180V	probably damaging	Het
Numa1	C	A	7: 101,658,494 (GRCm39)		probably null	Het
Olfm3	T	A	3: 114,916,052 (GRCm39)	L328Q	probably damaging	Het
Or4e1	T	C	14: 52,700,953 (GRCm39)	Y171C	probably damaging	Het
Or5w17	A	T	2: 87,583,922 (GRCm39)	N138K	probably benign	Het
Or7a37	A	T	10: 78,805,765 (GRCm39)	Y94F	probably damaging	Het
Papolb	T	C	5: 142,514,992 (GRCm39)	N217S	possibly damaging	Het
Pcmtd2	C	A	2: 181,484,268 (GRCm39)	T26K	probably damaging	Het
Pld5	T	G	1: 175,917,571 (GRCm39)	N59H	probably damaging	Het
Ppm1d	T	C	11: 85,202,674 (GRCm39)	S126P	possibly damaging	Het
Ppp1r21	T	C	17: 88,889,937 (GRCm39)	L727P	probably damaging	Het
Pramel20	G	T	4: 143,297,810 (GRCm39)	V77L	probably benign	Het
Prpsap2	C	T	11: 61,627,870 (GRCm39)	R202H	probably damaging	Het
Rexo2	A	T	9: 48,386,481 (GRCm39)	I83N	probably damaging	Het
Rnf213	A	G	11: 119,364,203 (GRCm39)	R4501G	probably damaging	Het
Rps5	T	A	7: 12,659,501 (GRCm39)	F97L	probably damaging	Het
Sigirr	G	A	7: 140,671,292 (GRCm39)	R397W	probably damaging	Het
Slc6a6	T	C	6: 91,718,014 (GRCm39)	Y318H	probably damaging	Het
Spam1	A	G	6: 24,796,570 (GRCm39)	T174A	probably benign	Het
Stam2	G	T	2: 52,632,116 (GRCm39)		probably benign	Het
Taar7a	T	C	10: 23,868,337 (GRCm39)	E348G	probably benign	Het
Taf11	T	C	17: 28,120,644 (GRCm39)	T209A	probably benign	Het
Tenm4	A	G	7: 96,492,424 (GRCm39)		probably benign	Het
Tmed6	G	T	8: 107,790,786 (GRCm39)	T87K	probably damaging	Het
Trim5	G	T	7: 103,928,726 (GRCm39)	H72N	probably benign	Het
Trim5	A	C	7: 103,928,728 (GRCm39)	L71R	probably benign	Het
Uevld	A	T	7: 46,576,104 (GRCm39)	S461T	probably benign	Het
Vmn2r6	T	A	3: 64,463,454 (GRCm39)	N460I	probably benign	Het
Ylpm1	C	T	12: 85,087,660 (GRCm39)	P1148L	probably damaging	Het
Zfp316	T	C	5: 143,249,095 (GRCm39)	Y180C	unknown	Het
Zfp941	A	G	7: 140,392,052 (GRCm39)	S436P	probably damaging	Het
Zfp979	G	A	4: 147,697,966 (GRCm39)	Q248*	probably null	Het
Zscan29	G	T	2: 120,994,518 (GRCm39)	T489N	probably damaging	Het

Other mutations in Rara

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00951:Rara	APN	11	98,858,992 (GRCm39)	missense	probably benign	0.00
IGL01155:Rara	APN	11	98,859,010 (GRCm39)	missense	possibly damaging	0.92
IGL02141:Rara	APN	11	98,858,907 (GRCm39)	missense	probably damaging	1.00
IGL03194:Rara	APN	11	98,862,490 (GRCm39)	missense	possibly damaging	0.96
annie	UTSW	11	98,864,452 (GRCm39)	missense	unknown
kane	UTSW	11	98,862,595 (GRCm39)	missense	probably damaging	1.00
Orphan	UTSW	11	98,860,989 (GRCm39)	missense	probably damaging	1.00
warbucks	UTSW	11	98,861,395 (GRCm39)	missense	probably damaging	1.00
PIT4486001:Rara	UTSW	11	98,864,321 (GRCm39)	missense	possibly damaging	0.88
R0626:Rara	UTSW	11	98,862,406 (GRCm39)	critical splice acceptor site	probably null
R1973:Rara	UTSW	11	98,862,496 (GRCm39)	missense	possibly damaging	0.91
R3975:Rara	UTSW	11	98,861,395 (GRCm39)	missense	probably damaging	1.00
R4357:Rara	UTSW	11	98,858,937 (GRCm39)	missense	probably damaging	0.98
R5102:Rara	UTSW	11	98,857,185 (GRCm39)	missense	possibly damaging	0.80
R5147:Rara	UTSW	11	98,841,550 (GRCm39)	missense	probably benign	0.35
R5381:Rara	UTSW	11	98,862,410 (GRCm39)	missense	possibly damaging	0.93
R5570:Rara	UTSW	11	98,863,478 (GRCm39)	missense	probably damaging	1.00
R6273:Rara	UTSW	11	98,861,048 (GRCm39)	missense	probably benign	0.00
R6404:Rara	UTSW	11	98,851,839 (GRCm39)	missense	probably benign	0.16
R8906:Rara	UTSW	11	98,860,989 (GRCm39)	missense	probably damaging	1.00
R8921:Rara	UTSW	11	98,864,452 (GRCm39)	missense	unknown
R8978:Rara	UTSW	11	98,862,595 (GRCm39)	missense	probably damaging	1.00
R9224:Rara	UTSW	11	98,857,236 (GRCm39)	frame shift	probably null
R9476:Rara	UTSW	11	98,860,983 (GRCm39)	missense	probably benign	0.02
R9510:Rara	UTSW	11	98,860,983 (GRCm39)	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- TTTCAAAAGAGTCATCCTCCCC -3'
(R):5'- CTTAACTAGAAGCTTGCCCGC -3'

Sequencing Primer
(F):5'- TACATAGGCCATAGCAAAAGCTTAG -3'
(R):5'- TGTATACACAGGCACACAC -3'

Posted On

2017-02-10