Mutagenetix > Incidental Mutation

Incidental Mutation 'R9510:Rara'

718112

Institutional Source

Beutler Lab

Gene Symbol

Rara

Ensembl Gene

ENSMUSG00000037992

Gene Name

retinoic acid receptor, alpha

Synonyms

RARalpha1, RAR alpha 1

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9510 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

98818644-98865768 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 98860983 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Leucine at position 157 (S157L)

Ref Sequence

ENSEMBL: ENSMUSP00000069744 (fasta)

Gene Model

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

AlphaFold

P11416

Predicted Effect

probably benign
Transcript: ENSMUST00000068133
AA Change: S157L

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000069744
Gene: ENSMUSG00000037992
AA Change: S157L

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 benign
Transcript: ENSMUST00000107473
AA Change: S154L

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000103097
Gene: ENSMUSG00000037992
AA Change: S154L

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 benign
Transcript: ENSMUST00000107474
AA Change: S157L

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000103098
Gene: ENSMUSG00000037992
AA Change: S157L

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 benign
Transcript: ENSMUST00000107475
AA Change: S157L

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000103099
Gene: ENSMUSG00000037992
AA Change: S157L

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 benign
Transcript: ENSMUST00000164748
AA Change: S157L

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000129791
Gene: ENSMUSG00000037992
AA Change: S157L

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930578G10Rik	T	G	4: 42,760,998 (GRCm39)	W6G	unknown	Het
Aatk	A	T	11: 119,901,094 (GRCm39)	C1101S	probably benign	Het
Ankrd61	T	C	5: 143,828,322 (GRCm39)	T218A	possibly damaging	Het
Cacna1b	T	C	2: 24,540,058 (GRCm39)	E1467G	probably damaging	Het
Ccdc186	T	C	19: 56,802,016 (GRCm39)	T34A	probably benign	Het
Cdc42bpb	G	A	12: 111,261,372 (GRCm39)	P1656S	probably benign	Het
Cdk13	A	C	13: 17,902,747 (GRCm39)	C934W	probably damaging	Het
Cebpg	T	C	7: 34,750,080 (GRCm39)	N61S	probably benign	Het
Cldn13	T	A	5: 134,943,843 (GRCm39)	E114V	probably benign	Het
Clec9a	T	A	6: 129,398,023 (GRCm39)	I187K	possibly damaging	Het
Cr2	G	T	1: 194,840,416 (GRCm39)	L509M	probably damaging	Het
Creb3l2	C	A	6: 37,311,446 (GRCm39)	G448W	probably damaging	Het
Csf2rb	T	A	15: 78,229,760 (GRCm39)		probably null	Het
Cyth1	C	T	11: 118,076,206 (GRCm39)		probably null	Het
Dapk1	A	T	13: 60,910,203 (GRCm39)	D1441V	unknown	Het
Dnhd1	A	T	7: 105,352,889 (GRCm39)	N2681Y	possibly damaging	Het
Dnm1	T	C	2: 32,213,739 (GRCm39)	M476V	probably benign	Het
Dock1	T	G	7: 134,592,279 (GRCm39)	I938S	probably benign	Het
Duox1	G	A	2: 122,160,023 (GRCm39)	V713I	possibly damaging	Het
Dusp16	T	C	6: 134,695,226 (GRCm39)	H535R	probably benign	Het
Eif3j2	TGCCGCCGCCGCCGCCGCCGCCGCCGCC	TGCCGCCGCCGCCGCCGCCGCCGCC	18: 43,610,782 (GRCm39)		probably benign	Het
Fancd2os	T	A	6: 113,574,994 (GRCm39)	Y4F	probably damaging	Het
Fat4	A	T	3: 39,037,886 (GRCm39)	Q3846L	probably benign	Het
Fbxw10	A	C	11: 62,743,814 (GRCm39)	H240P	probably benign	Het
Fer1l5	T	C	1: 36,442,662 (GRCm39)	L727P	probably damaging	Het
Fezf1	A	C	6: 23,247,845 (GRCm39)	F77V	probably benign	Het
Fli1	T	C	9: 32,335,493 (GRCm39)	D313G	probably damaging	Het
Frmd4a	A	G	2: 4,608,324 (GRCm39)	T731A	probably benign	Het
Gfy	T	C	7: 44,828,090 (GRCm39)	Q2R	possibly damaging	Het
Ggt5	T	C	10: 75,445,139 (GRCm39)	V382A	probably benign	Het
Hira	A	G	16: 18,772,789 (GRCm39)	D867G	probably damaging	Het
Hmcn1	A	G	1: 150,462,127 (GRCm39)	S5184P	probably benign	Het
Ighv1-26	A	C	12: 114,752,407 (GRCm39)	F7V	probably benign	Het
Igkv4-81	C	T	6: 68,967,796 (GRCm39)	E102K	possibly damaging	Het
Inmt	G	T	6: 55,147,990 (GRCm39)	S213Y	possibly damaging	Het
Ints2	T	A	11: 86,135,335 (GRCm39)	M360L	probably benign	Het
Itih3	A	G	14: 30,631,416 (GRCm39)	S827P	probably benign	Het
Kcnk12	C	A	17: 88,054,122 (GRCm39)	R180L	probably benign	Het
Klhl2	T	C	8: 65,202,113 (GRCm39)	N521S	probably benign	Het
Kmt2a	A	T	9: 44,734,531 (GRCm39)	F2104I	unknown	Het
Kndc1	G	A	7: 139,510,031 (GRCm39)	S1291N	probably benign	Het
Mettl21a	T	C	1: 64,647,285 (GRCm39)	T91A	probably damaging	Het
Mmrn2	A	G	14: 34,120,407 (GRCm39)	I426V	possibly damaging	Het
Mrpl2	T	C	17: 46,958,440 (GRCm39)	V74A	probably benign	Het
Msantd4	A	G	9: 4,385,007 (GRCm39)	D244G	probably benign	Het
Mtfmt	C	T	9: 65,343,147 (GRCm39)	R18C	probably benign	Het
Ncam2	A	G	16: 81,420,341 (GRCm39)	*838W	probably null	Het
Ncor1	CTG	CTGATG	11: 62,324,442 (GRCm39)		probably benign	Het
Nsf	T	C	11: 103,763,988 (GRCm39)	N365S	probably damaging	Het
Osbpl3	C	T	6: 50,313,194 (GRCm39)		probably null	Het
Pam	C	T	1: 97,826,065 (GRCm39)		probably null	Het
Parn	A	T	16: 13,358,942 (GRCm39)	M600K	probably benign	Het
Pcdha11	C	A	18: 37,139,532 (GRCm39)	T387N	probably benign	Het
Ptprt	A	C	2: 161,397,381 (GRCm39)	C1129G	probably damaging	Het
Ralgapb	T	A	2: 158,285,856 (GRCm39)	S645T	probably damaging	Het
Rnf40	T	A	7: 127,201,808 (GRCm39)	I1000N	probably damaging	Het
Sap25	C	T	5: 137,640,494 (GRCm39)	T141I	probably null	Het
Scube2	C	T	7: 109,430,969 (GRCm39)	G410E	probably damaging	Het
Sh3gl2	A	G	4: 85,304,089 (GRCm39)	E264G	probably benign	Het
Smc4	T	G	3: 68,914,662 (GRCm39)	S92A	probably damaging	Het
Sorcs1	C	T	19: 50,666,521 (GRCm39)	R129Q	probably benign	Het
Spata31e4	A	G	13: 50,856,149 (GRCm39)	T596A	possibly damaging	Het
Spef2	T	C	15: 9,713,203 (GRCm39)	R390G	probably damaging	Het
Speg	T	C	1: 75,377,768 (GRCm39)	F842S	probably damaging	Het
Stk17b	G	T	1: 53,796,898 (GRCm39)	H290N	probably damaging	Het
Stpg3	A	T	2: 25,103,516 (GRCm39)	V191D	probably benign	Het
Supt6	C	T	11: 78,120,290 (GRCm39)	R350H	probably damaging	Het
Taf1b	G	A	12: 24,566,947 (GRCm39)	A214T	possibly damaging	Het
Tet3	T	C	6: 83,380,935 (GRCm39)	E411G	possibly damaging	Het
Tet3	T	A	6: 83,381,808 (GRCm39)		probably null	Het
Tg	T	C	15: 66,545,913 (GRCm39)	Y212H	probably damaging	Het
Tns3	A	G	11: 8,395,702 (GRCm39)	I1234T	probably damaging	Het
Traf6	C	T	2: 101,521,825 (GRCm39)	T220I	possibly damaging	Het
Tram2	C	G	1: 21,074,150 (GRCm39)	A263P	possibly damaging	Het
Treml1	T	G	17: 48,673,771 (GRCm39)	S261A	probably damaging	Het
Trim34b	A	G	7: 103,980,503 (GRCm39)	E197G	probably damaging	Het
Tspan18	C	T	2: 93,050,462 (GRCm39)	G54S	probably damaging	Het
Wdtc1	A	G	4: 133,049,529 (GRCm39)	V29A	probably damaging	Het
Zdhhc16	T	C	19: 41,929,155 (GRCm39)	Y253H	probably damaging	Het
Zfp366	A	G	13: 99,365,874 (GRCm39)	Y345C	probably damaging	Het
Zfp423	T	A	8: 88,510,041 (GRCm39)	D101V	possibly damaging	Het
Zfp462	G	A	4: 55,080,735 (GRCm39)	M2450I	probably benign	Het
Zfp52	C	T	17: 21,782,218 (GRCm39)	L689F	possibly damaging	Het
Zim1	G	A	7: 6,690,739 (GRCm39)	Q29*	probably null	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
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

Predicted Primers

PCR Primer
(F):5'- GTCCCAGGCCCTAAAATAGG -3'
(R):5'- TCCTGACAGTGTAGGAGGAG -3'

Sequencing Primer
(F):5'- TAGGATTTAGGATATGAGTCAGACAG -3'
(R):5'- TGTGCAGTACCCCTCGC -3'

Posted On

2022-07-18