Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL03194:Rara'

412736

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Rara

Ensembl Gene

ENSMUSG00000037992

Gene Name

retinoic acid receptor, alpha

Synonyms

RAR alpha 1, RARalpha1

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL03194

Quality Score

Status

Chromosome

Chromosomal Location

98927818-98974942 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 98971664 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 297 (M297T)

Ref Sequence

ENSEMBL: ENSMUSP00000129791 (fasta)

Gene Model

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

AlphaFold

P11416

Predicted Effect

possibly damaging
Transcript: ENSMUST00000068133
AA Change: M297T

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
AA Change: M297T

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

possibly damaging
Transcript: ENSMUST00000107473
AA Change: M294T

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: M294T

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

possibly damaging
Transcript: ENSMUST00000107474
AA Change: M297T

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
AA Change: M297T

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

possibly damaging
Transcript: ENSMUST00000107475
AA Change: M297T

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
AA Change: M297T

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

possibly damaging
Transcript: ENSMUST00000164748
AA Change: M297T

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
AA Change: M297T

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

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: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgre5	T	C	8: 83,734,018	S64G	possibly damaging	Het
Clcn7	T	C	17: 25,150,548	V306A	probably damaging	Het
Clec4b2	G	A	6: 123,200,987	G87D	probably benign	Het
Disp2	A	T	2: 118,787,629	R219W	probably damaging	Het
Dstyk	A	T	1: 132,456,316		probably benign	Het
F830045P16Rik	T	C	2: 129,460,320	S451G	possibly damaging	Het
Fam155a	T	C	8: 9,232,975	D358G	probably damaging	Het
Fat2	T	A	11: 55,310,995	T418S	probably benign	Het
Fto	G	A	8: 91,409,787	D228N	probably damaging	Het
Gins4	A	T	8: 23,234,746		probably benign	Het
Gm10220	T	A	5: 26,121,233	R40W	probably damaging	Het
Gm11149	G	A	9: 49,546,346		probably benign	Het
Gm5431	T	G	11: 48,895,537		probably benign	Het
Hebp1	A	G	6: 135,155,192	M59T	probably benign	Het
Lrp1	A	T	10: 127,568,685	V1989D	probably damaging	Het
Lrrc6	A	T	15: 66,442,199	D317E	probably benign	Het
Ltc4s	T	C	11: 50,236,571	*151W	probably null	Het
Map3k21	A	G	8: 125,924,062	T268A	possibly damaging	Het
Mdp1	A	G	14: 55,658,987	L164P	probably damaging	Het
Mroh4	T	C	15: 74,611,539	T650A	probably damaging	Het
Mss51	T	C	14: 20,485,097	N202D	probably benign	Het
Mtus2	G	A	5: 148,107,103	A834T	probably damaging	Het
Ncoa6	A	G	2: 155,415,868	M585T	possibly damaging	Het
Nelfcd	G	A	2: 174,426,832	A559T	possibly damaging	Het
Npvf	A	C	6: 50,650,898	D180E	possibly damaging	Het
Nup188	A	T	2: 30,304,334	Y173F	possibly damaging	Het
Oas3	C	A	5: 120,758,953	A868S	probably damaging	Het
Pkhd1l1	A	G	15: 44,518,135	T1086A	probably damaging	Het
Pla2g6	G	A	15: 79,317,785	P62L	probably damaging	Het
Tmc1	T	C	19: 20,804,653	E567G	probably damaging	Het
Tnxb	C	T	17: 34,695,947	Q1970*	probably null	Het
Usp11	T	C	X: 20,712,417	I162T	probably benign	Het
Utrn	A	G	10: 12,406,429		probably benign	Het
Zfhx3	A	G	8: 108,794,727	E827G	probably damaging	Het

Other mutations in Rara

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00951:Rara	APN	11	98968166	missense	probably benign	0.00
IGL01155:Rara	APN	11	98968184	missense	possibly damaging	0.92
IGL02141:Rara	APN	11	98968081	missense	probably damaging	1.00
annie	UTSW	11	98973626	missense	unknown
kane	UTSW	11	98971769	missense	probably damaging	1.00
Orphan	UTSW	11	98970163	missense	probably damaging	1.00
warbucks	UTSW	11	98970569	missense	probably damaging	1.00
PIT4486001:Rara	UTSW	11	98973495	missense	possibly damaging	0.88
R0626:Rara	UTSW	11	98971580	critical splice acceptor site	probably null
R1973:Rara	UTSW	11	98971670	missense	possibly damaging	0.91
R3975:Rara	UTSW	11	98970569	missense	probably damaging	1.00
R4357:Rara	UTSW	11	98968111	missense	probably damaging	0.98
R5102:Rara	UTSW	11	98966359	missense	possibly damaging	0.80
R5147:Rara	UTSW	11	98950724	missense	probably benign	0.35
R5381:Rara	UTSW	11	98971584	missense	possibly damaging	0.93
R5570:Rara	UTSW	11	98972652	missense	probably damaging	1.00
R5861:Rara	UTSW	11	98968161	nonsense	probably null
R6273:Rara	UTSW	11	98970222	missense	probably benign	0.00
R6404:Rara	UTSW	11	98961013	missense	probably benign	0.16
R8906:Rara	UTSW	11	98970163	missense	probably damaging	1.00
R8921:Rara	UTSW	11	98973626	missense	unknown
R8978:Rara	UTSW	11	98971769	missense	probably damaging	1.00
R9224:Rara	UTSW	11	98966410	frame shift	probably null
R9476:Rara	UTSW	11	98970157	missense	probably benign	0.02
R9510:Rara	UTSW	11	98970157	missense	probably benign	0.02

Posted On

2016-08-02