Mutagenetix > Incidental Mutation

Incidental Mutation 'R9476:Rara'

715797

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 #

R9476 (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: 99.7%
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 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: 83 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
Abcb4	A	T	5: 8,977,790 (GRCm39)	D456V	probably damaging	Het
Abcc8	T	C	7: 45,819,270 (GRCm39)	E186G	possibly damaging	Het
Adam18	T	C	8: 25,115,807 (GRCm39)	N629S	probably benign	Het
Angpt2	T	G	8: 18,764,143 (GRCm39)	N133T	probably benign	Het
Ankrd13c	T	A	3: 157,697,396 (GRCm39)	S334T	probably benign	Het
Ankrd13d	A	T	19: 4,320,289 (GRCm39)	S151T	unknown	Het
Ap3d1	G	A	10: 80,545,655 (GRCm39)	P1025S	probably benign	Het
Bhlhe41	G	A	6: 145,808,948 (GRCm39)	A288V	possibly damaging	Het
Cacna1b	T	C	2: 24,540,058 (GRCm39)	E1467G	probably damaging	Het
Cacna1h	T	A	17: 25,611,524 (GRCm39)	T425S	probably damaging	Het
Cdk13	A	C	13: 17,902,747 (GRCm39)	C934W	probably damaging	Het
Ces1b	T	A	8: 93,799,890 (GRCm39)	N162I	probably damaging	Het
Clec9a	T	A	6: 129,398,023 (GRCm39)	I187K	possibly damaging	Het
Cpsf3	A	G	12: 21,350,080 (GRCm39)	I266M	probably 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
Csmd1	T	A	8: 15,981,215 (GRCm39)		probably null	Het
Cul9	G	A	17: 46,821,833 (GRCm39)	R1881W	probably damaging	Het
Cyth1	C	T	11: 118,076,206 (GRCm39)		probably null	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
Dnmt3a	A	G	12: 3,957,707 (GRCm39)	H896R	probably damaging	Het
Dock1	T	G	7: 134,592,279 (GRCm39)	I938S	probably benign	Het
Dock6	G	A	9: 21,724,821 (GRCm39)	L1515F	probably damaging	Het
Dusp16	T	C	6: 134,695,226 (GRCm39)	H535R	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
Frmd4a	A	G	2: 4,608,324 (GRCm39)	T731A	probably benign	Het
Gm44501	T	A	17: 40,889,820 (GRCm39)	H111Q	possibly damaging	Het
Gsdmc	T	C	15: 63,650,551 (GRCm39)	M277V	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
Itpr3	G	A	17: 27,337,651 (GRCm39)		probably benign	Het
Kcnk12	C	A	17: 88,054,122 (GRCm39)	R180L	probably benign	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
Mrpl21	T	G	19: 3,337,704 (GRCm39)	V137G	probably damaging	Het
Nrbp2	T	C	15: 75,961,626 (GRCm39)	N218S	probably damaging	Het
Nrip1	T	C	16: 76,089,820 (GRCm39)	N579S	probably benign	Het
Nsf	T	C	11: 103,763,988 (GRCm39)	N365S	probably damaging	Het
Or6c5	A	G	10: 129,074,656 (GRCm39)	I213V	probably damaging	Het
Or7g28	A	T	9: 19,272,383 (GRCm39)	D89E	probably benign	Het
Osbpl3	C	T	6: 50,313,194 (GRCm39)		probably null	Het
Oscar	T	A	7: 3,614,843 (GRCm39)	H43L	probably benign	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
Plce1	G	A	19: 38,766,337 (GRCm39)	E2121K	possibly damaging	Het
Prune2	T	A	19: 17,096,706 (GRCm39)	Y737N	possibly damaging	Het
Ptch1	G	A	13: 63,681,448 (GRCm39)	P613L	probably benign	Het
Ptprt	A	C	2: 161,397,381 (GRCm39)	C1129G	probably damaging	Het
Rest	T	A	5: 77,416,098 (GRCm39)	M104K	probably damaging	Het
Rfc1	A	G	5: 65,437,142 (GRCm39)	S513P	probably damaging	Het
Rnf40	T	A	7: 127,201,808 (GRCm39)	I1000N	probably damaging	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
Shank1	G	A	7: 43,962,342 (GRCm39)	S71N	unknown	Het
Smc4	T	G	3: 68,914,662 (GRCm39)	S92A	probably damaging	Het
Spata31d1b	A	G	13: 59,863,467 (GRCm39)	D205G	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
Tet3	T	C	6: 83,380,935 (GRCm39)	E411G	possibly damaging	Het
Tet3	T	A	6: 83,381,808 (GRCm39)		probably null	Het
Tns3	A	G	11: 8,395,702 (GRCm39)	I1234T	probably damaging	Het
Trim34b	A	G	7: 103,980,503 (GRCm39)	E197G	probably damaging	Het
Vcan	G	T	13: 89,851,531 (GRCm39)	T1143K	possibly damaging	Het
Vmn2r61	T	A	7: 41,949,593 (GRCm39)	V671E	probably damaging	Het
Wdtc1	A	G	4: 133,049,529 (GRCm39)	V29A	probably damaging	Het
Zfp462	G	A	4: 55,080,735 (GRCm39)	M2450I	probably benign	Het
Zfp869	A	T	8: 70,159,849 (GRCm39)	C241*	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
R9510:Rara	UTSW	11	98,860,983 (GRCm39)	missense	probably benign	0.02

Predicted Primers

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

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

Posted On

2022-06-15