Mutagenetix > Incidental Mutation

Incidental Mutation 'R5570:Rara'

435625

Institutional Source

Beutler Lab

Gene Symbol

Rara

Ensembl Gene

ENSMUSG00000037992

Gene Name

retinoic acid receptor, alpha

Synonyms

RARalpha1, RAR alpha 1

MMRRC Submission

043127-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5570 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

98818644-98865768 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to G at 98863478 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 382 (R382G)

Ref Sequence

ENSEMBL: ENSMUSP00000103097 (fasta)

Gene Model

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

AlphaFold

P11416

Predicted Effect

probably damaging
Transcript: ENSMUST00000068133
AA Change: R385G

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
AA Change: R385G

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 damaging
Transcript: ENSMUST00000107473
AA Change: R382G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: R382G

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 damaging
Transcript: ENSMUST00000107474
AA Change: R385G

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
AA Change: R385G

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 damaging
Transcript: ENSMUST00000107475
AA Change: R385G

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
AA Change: R385G

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 damaging
Transcript: ENSMUST00000164748
AA Change: R385G

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
AA Change: R385G

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

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 95.5%

Validation Efficiency

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acrv1	C	A	9: 36,605,577 (GRCm39)	S41R	probably damaging	Het
Aqr	G	A	2: 113,979,451 (GRCm39)	T328M	probably damaging	Het
Arhgap26	C	A	18: 39,232,671 (GRCm39)	D99E	probably damaging	Het
Boc	G	A	16: 44,313,187 (GRCm39)	T559I	probably damaging	Het
Cadps	A	T	14: 12,473,497 (GRCm38)	I876N	possibly damaging	Het
Cep72	T	C	13: 74,188,260 (GRCm39)	Q211R	probably benign	Het
Clmp	T	C	9: 40,683,826 (GRCm39)		probably null	Het
Coq6	T	A	12: 84,415,413 (GRCm39)	D145E	probably benign	Het
Crym	T	C	7: 119,801,116 (GRCm39)	E11G	probably benign	Het
Defb36	T	A	2: 152,454,503 (GRCm39)	V54E	probably damaging	Het
Dlg5	C	A	14: 24,242,981 (GRCm39)	E55*	probably null	Het
Dock2	G	T	11: 34,618,233 (GRCm39)	R128S	probably damaging	Het
E330034G19Rik	A	G	14: 24,346,892 (GRCm39)	K60E	possibly damaging	Het
Eps8l2	G	A	7: 140,934,920 (GRCm39)	R76Q	possibly damaging	Het
Espn	T	C	4: 152,208,237 (GRCm39)	E460G	probably damaging	Het
Fbxl18	A	G	5: 142,881,022 (GRCm39)		probably benign	Het
Fgd5	T	C	6: 91,965,668 (GRCm39)	S476P	probably damaging	Het
Gsto1	T	C	19: 47,846,338 (GRCm39)	W62R	probably damaging	Het
Gtf2h3	C	T	5: 124,722,360 (GRCm39)	T121I	probably benign	Het
Gxylt1	A	G	15: 93,152,180 (GRCm39)		probably null	Het
Hs6st1	C	T	1: 36,142,719 (GRCm39)	P218L	probably benign	Het
Kif5c	A	G	2: 49,620,211 (GRCm39)	D226G	possibly damaging	Het
Krt1	A	G	15: 101,755,340 (GRCm39)	F473S	probably benign	Het
Lpxn	T	A	19: 12,810,023 (GRCm39)	M265K	possibly damaging	Het
Map3k9	A	G	12: 81,778,798 (GRCm39)	L505P	possibly damaging	Het
Mcm3ap	C	T	10: 76,316,930 (GRCm39)	R645W	possibly damaging	Het
Msr1	T	C	8: 40,064,760 (GRCm39)	I305V	probably benign	Het
Muc4	A	G	16: 32,598,066 (GRCm39)	E3237G	possibly damaging	Het
Necap1	T	C	6: 122,858,471 (GRCm39)	F105L	probably damaging	Het
Nploc4	C	T	11: 120,275,440 (GRCm39)	V499M	probably benign	Het
Nup93	T	C	8: 95,041,298 (GRCm39)	V812A	probably damaging	Het
Or10ak7	T	A	4: 118,791,263 (GRCm39)	I259F	possibly damaging	Het
Or6e1	A	G	14: 54,519,825 (GRCm39)	F176L	probably damaging	Het
Or9g3	G	A	2: 85,589,994 (GRCm39)	S242F	probably damaging	Het
Parn	G	A	16: 13,483,794 (GRCm39)	P50L	probably damaging	Het
Pcdhb7	T	C	18: 37,477,224 (GRCm39)	C787R	probably benign	Het
Pdk2	A	T	11: 94,920,826 (GRCm39)	I175N	probably damaging	Het
Pelo	T	C	13: 115,226,152 (GRCm39)	I102V	probably benign	Het
Phf12	A	G	11: 77,908,937 (GRCm39)	D339G	possibly damaging	Het
Phlpp1	A	T	1: 106,101,162 (GRCm39)	I477F	probably benign	Het
Pigt	T	A	2: 164,343,482 (GRCm39)	Y319*	probably null	Het
Pmpca	A	G	2: 26,280,553 (GRCm39)	E133G	probably damaging	Het
Ptgs2	A	G	1: 149,979,859 (GRCm39)	I321M		Het
Pus7l	G	A	15: 94,425,746 (GRCm39)	P552S	probably benign	Het
Qsox2	A	G	2: 26,115,230 (GRCm39)	M1T	probably null	Het
Rbbp6	A	G	7: 122,601,057 (GRCm39)		probably benign	Het
Rev3l	T	C	10: 39,728,071 (GRCm39)		probably null	Het
Robo3	T	A	9: 37,336,571 (GRCm39)	Y399F	possibly damaging	Het
Rpl31	C	T	1: 39,409,108 (GRCm39)	R41C	probably benign	Het
Skint3	A	G	4: 112,092,995 (GRCm39)	M20V	probably benign	Het
Slc17a6	A	G	7: 51,308,504 (GRCm39)	D276G	probably benign	Het
Sult3a2	A	T	10: 33,654,268 (GRCm39)	V128D	probably damaging	Het
Syt3	T	A	7: 44,040,043 (GRCm39)	V92E	possibly damaging	Het
Them7	A	G	2: 105,209,153 (GRCm39)	T158A	probably benign	Het
Utp14b	G	A	1: 78,643,118 (GRCm39)	D339N	probably damaging	Het
Vars1	T	C	17: 35,235,214 (GRCm39)	F1259L	probably benign	Het
Vmn1r115	A	C	7: 20,578,555 (GRCm39)	V119G	possibly damaging	Het
Zc3h12a	C	T	4: 125,014,166 (GRCm39)	R293H	probably damaging	Het
Zfp638	A	T	6: 83,956,170 (GRCm39)	E1592D	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
R5861:Rara	UTSW	11	98,858,987 (GRCm39)	nonsense	probably null
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'- CCTGCTCAGGGACAGTTTTG -3'
(R):5'- AAGACACCATGTAGATGCCAAG -3'

Sequencing Primer
(F):5'- GACAGTTTTGTGCTCAGACCGAC -3'
(R):5'- ATGGCGCAACCCTTTAATACAGTTC -3'

Posted On

2016-10-24