Mutagenetix > Incidental Mutation

Incidental Mutation 'R1915:Rorc'

214750

Institutional Source

Beutler Lab

Gene Symbol

Rorc

Ensembl Gene

ENSMUSG00000028150

Gene Name

RAR-related orphan receptor gamma

Synonyms

Thor, RORgamma, thymus orphan receptor

MMRRC Submission

039933-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.865) question?

Stock #

R1915 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

94280101-94305583 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 94298480 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Arginine at position 322 (C322R)

Ref Sequence

ENSEMBL: ENSMUSP00000143763 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029795] [ENSMUST00000197040] [ENSMUST00000200009]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000029795
AA Change: C343R

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000029795
Gene: ENSMUSG00000028150
AA Change: C343R

Domain	Start	End	E-Value	Type
ZnF_C4	28	99	7.2e-37	SMART
low complexity region	116	133	N/A	INTRINSIC
HOLI	320	474	3.78e-22	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000197040
AA Change: C322R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000143763
Gene: ENSMUSG00000028150
AA Change: C322R

Domain	Start	End	E-Value	Type
ZnF_C4	7	78	7.2e-37	SMART
low complexity region	95	112	N/A	INTRINSIC
HOLI	299	453	3.78e-22	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000198793

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000198829

Predicted Effect

probably benign
Transcript: ENSMUST00000200009

SMART Domains

Protein: ENSMUSP00000143610
Gene: ENSMUSG00000028150

Domain	Start	End	E-Value	Type
ZnF_C4	13	84	7.2e-37	SMART
low complexity region	101	118	N/A	INTRINSIC
PDB:3L0L\|B	243	309	1e-22	PDB

Meta Mutation Damage Score

0.1906

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.6%
20x: 93.4%

Validation Efficiency

100% (85/85)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a DNA-binding transcription factor and is a member of the NR1 subfamily of nuclear hormone receptors. The specific functions of this protein are not known; however, studies of a similar gene in mice have shown that this gene may be essential for lymphoid organogenesis and may play an important regulatory role in thymopoiesis. In addition, studies in mice suggest that the protein encoded by this gene may inhibit the expression of Fas ligand and IL2. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations exhibit lack of peripheral and mesenteric lymph nodes and Peyer's patches, reduced numbers of thymocytes, and increased apoptosis with loss of thymic expression of anti-apoptosic factor Bcl-xL. [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
Abca6	T	C	11: 110,103,036 (GRCm39)	R852G	probably benign	Het
Adam2	C	A	14: 66,275,006 (GRCm39)	V576F	possibly damaging	Het
Afmid	T	C	11: 117,726,625 (GRCm39)	F250L	possibly damaging	Het
Apc2	A	T	10: 80,151,701 (GRCm39)	I2252L	probably benign	Het
Bcar1	A	G	8: 112,442,030 (GRCm39)	V270A	probably damaging	Het
Btnl7-ps	T	A	17: 34,760,619 (GRCm39)		noncoding transcript	Het
Cdkn2aip	T	C	8: 48,164,961 (GRCm39)	T251A	probably benign	Het
Cdx1	A	G	18: 61,152,970 (GRCm39)	V212A	probably benign	Het
Cep95	C	T	11: 106,705,464 (GRCm39)	T483I	probably damaging	Het
Cfap100	T	C	6: 90,389,329 (GRCm39)		probably benign	Het
Cfap54	A	G	10: 92,720,564 (GRCm39)	V2630A	unknown	Het
Chia1	T	A	3: 106,035,875 (GRCm39)	N238K	probably benign	Het
Cldn23	T	A	8: 36,293,099 (GRCm39)	I130F	possibly damaging	Het
Cntrl	T	C	2: 35,052,873 (GRCm39)	M1126T	probably benign	Het
Col28a1	A	G	6: 8,176,333 (GRCm39)	F8S	probably benign	Het
Cpeb3	C	T	19: 37,031,665 (GRCm39)	R579Q	probably damaging	Het
Creld2	G	A	15: 88,704,834 (GRCm39)	W103*	probably null	Het
Dbh	A	G	2: 27,058,234 (GRCm39)	D134G	probably damaging	Het
Dcbld1	G	T	10: 52,193,131 (GRCm39)	C292F	probably damaging	Het
Dlgap5	T	C	14: 47,645,230 (GRCm39)	K304E	probably benign	Het
Dnajc2	A	G	5: 21,986,317 (GRCm39)		probably null	Het
Eps8l2	G	A	7: 140,941,765 (GRCm39)	V650M	probably damaging	Het
Erlin1	T	C	19: 44,047,504 (GRCm39)	Y139C	probably damaging	Het
Exoc3	A	G	13: 74,321,413 (GRCm39)		probably null	Het
F5	C	A	1: 164,010,486 (GRCm39)	R406S	probably damaging	Het
Fahd1	A	T	17: 25,068,622 (GRCm39)	W152R	possibly damaging	Het
Farp2	T	A	1: 93,456,424 (GRCm39)	S36T	probably benign	Het
Foxs1	A	G	2: 152,774,760 (GRCm39)	C98R	probably damaging	Het
Gal3st4	T	A	5: 138,263,672 (GRCm39)	K442N	probably benign	Het
Gm10644	G	A	8: 84,660,479 (GRCm39)		probably benign	Het
Gm8674	A	T	13: 50,054,889 (GRCm39)		noncoding transcript	Het
Gpr88	G	T	3: 116,046,073 (GRCm39)	S79R	possibly damaging	Het
Heatr9	T	G	11: 83,409,035 (GRCm39)	I171L	possibly damaging	Het
Hectd4	A	G	5: 121,460,357 (GRCm39)	T2209A	probably benign	Het
Hsh2d	A	G	8: 72,947,365 (GRCm39)	T21A	probably damaging	Het
Irf4	A	T	13: 30,945,445 (GRCm39)	Q397L	probably benign	Het
Itgae	T	A	11: 73,009,469 (GRCm39)		probably benign	Het
Jrkl	A	T	9: 13,245,609 (GRCm39)	D17E	possibly damaging	Het
Kcna4	T	C	2: 107,127,123 (GRCm39)	V619A	probably benign	Het
Kcnh6	T	A	11: 105,908,270 (GRCm39)	Y295*	probably null	Het
Kif1b	G	A	4: 149,351,673 (GRCm39)	T263I	probably damaging	Het
Large2	G	T	2: 92,196,170 (GRCm39)		probably benign	Het
Lcp1	T	A	14: 75,436,737 (GRCm39)	Y28N	possibly damaging	Het
Man1c1	G	C	4: 134,430,749 (GRCm39)	P11R	probably damaging	Het
Mccc2	T	C	13: 100,085,038 (GRCm39)		probably null	Het
Mlh3	T	C	12: 85,308,442 (GRCm39)	Y1115C	probably benign	Het
Mlst8	C	T	17: 24,696,264 (GRCm39)	W155*	probably null	Het
Myh10	T	C	11: 68,681,034 (GRCm39)	L1025P	probably damaging	Het
Myof	T	A	19: 37,966,141 (GRCm39)	N393I	probably damaging	Het
Nalcn	C	T	14: 123,540,181 (GRCm39)	V1140I	probably benign	Het
Ncald	C	T	15: 37,397,324 (GRCm39)	A119T	probably benign	Het
Nipbl	T	C	15: 8,373,114 (GRCm39)	E1044G	possibly damaging	Het
Nup58	T	C	14: 60,475,980 (GRCm39)	K279R	probably benign	Het
Oas1a	A	T	5: 121,043,876 (GRCm39)	N85K	possibly damaging	Het
Or11g1	C	T	14: 50,651,798 (GRCm39)	P266S	probably damaging	Het
Or8b12i	T	C	9: 20,082,324 (GRCm39)	Y181C	probably benign	Het
Or8k30	A	G	2: 86,339,343 (GRCm39)	D180G	probably damaging	Het
Pou2f2	C	T	7: 24,799,581 (GRCm39)	A92T	possibly damaging	Het
Ppp1r16a	T	C	15: 76,577,268 (GRCm39)	L212P	probably damaging	Het
Pram1	A	T	17: 33,860,131 (GRCm39)	I233F	probably benign	Het
Ptbp3	A	T	4: 59,517,635 (GRCm39)	L84Q	probably damaging	Het
Ptgr2	A	T	12: 84,349,096 (GRCm39)	Q145L	probably benign	Het
Ptpn23	A	T	9: 110,215,575 (GRCm39)	D1396E	probably damaging	Het
Pudp	T	C	18: 50,701,278 (GRCm39)	N152D	probably benign	Het
Rbm20	T	A	19: 53,852,518 (GRCm39)	L1166Q	probably damaging	Het
Rictor	T	G	15: 6,789,053 (GRCm39)	I223R	probably damaging	Het
Ripor1	A	T	8: 106,343,518 (GRCm39)	E270D	probably damaging	Het
Rpgrip1l	T	C	8: 91,959,552 (GRCm39)	D1116G	probably benign	Het
Rsf1	GCG	GCGACGGCGACG	7: 97,229,114 (GRCm39)		probably benign	Het
Sptan1	C	G	2: 29,901,048 (GRCm39)	Q1425E	probably benign	Het
Srd5a3	G	A	5: 76,295,552 (GRCm39)	V81I	probably benign	Het
Stk36	T	A	1: 74,673,346 (GRCm39)	S1080T	probably benign	Het
Sugp2	T	A	8: 70,706,310 (GRCm39)	I790K	probably damaging	Het
Syde2	T	G	3: 145,720,071 (GRCm39)	Y764*	probably null	Het
Tmem130	A	G	5: 144,674,666 (GRCm39)	F353S	probably damaging	Het
Tmem131	T	A	1: 36,835,347 (GRCm39)	K1591N	probably damaging	Het
Urb2	C	A	8: 124,756,537 (GRCm39)	T748K	possibly damaging	Het
Uri1	A	T	7: 37,661,103 (GRCm39)	I480K	probably damaging	Het
Zcchc3	A	C	2: 152,255,601 (GRCm39)	V366G	probably benign	Het
Zfp292	G	A	4: 34,805,100 (GRCm39)	S2648F	possibly damaging	Het
Zfp54	T	C	17: 21,654,414 (GRCm39)	Y303H	probably benign	Het
Zfp729b	A	G	13: 67,741,339 (GRCm39)	F319L	probably damaging	Het
Zfp934	G	A	13: 62,665,769 (GRCm39)	H291Y	probably damaging	Het

Other mutations in Rorc

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01626:Rorc	APN	3	94,296,094 (GRCm39)	missense	probably damaging	1.00
beto	UTSW	3	94,284,915 (GRCm39)	splice site	probably null
brazil	UTSW	3	94,296,826 (GRCm39)	missense	probably damaging	1.00
cashew	UTSW	3	94,298,460 (GRCm39)	missense	probably damaging	1.00
chestnut	UTSW	3	94,284,916 (GRCm39)	splice site	probably benign
macadamias	UTSW	3	94,304,609 (GRCm39)	nonsense	probably null
macadamias2	UTSW	3	94,294,500 (GRCm39)	missense	probably damaging	1.00
R0014:Rorc	UTSW	3	94,284,920 (GRCm39)	splice site	probably benign
R0115:Rorc	UTSW	3	94,284,916 (GRCm39)	splice site	probably benign
R0365:Rorc	UTSW	3	94,296,069 (GRCm39)	missense	probably damaging	1.00
R1470:Rorc	UTSW	3	94,304,609 (GRCm39)	nonsense	probably null
R1470:Rorc	UTSW	3	94,304,609 (GRCm39)	nonsense	probably null
R1914:Rorc	UTSW	3	94,298,480 (GRCm39)	missense	probably damaging	1.00
R2142:Rorc	UTSW	3	94,296,833 (GRCm39)	missense	probably benign	0.04
R2510:Rorc	UTSW	3	94,296,427 (GRCm39)	missense	probably benign	0.30
R4135:Rorc	UTSW	3	94,296,826 (GRCm39)	missense	probably damaging	1.00
R4181:Rorc	UTSW	3	94,294,500 (GRCm39)	missense	probably damaging	1.00
R4574:Rorc	UTSW	3	94,296,291 (GRCm39)	missense	probably benign	0.00
R4701:Rorc	UTSW	3	94,299,017 (GRCm39)	missense	probably null	1.00
R5014:Rorc	UTSW	3	94,298,460 (GRCm39)	missense	probably damaging	1.00
R5233:Rorc	UTSW	3	94,304,632 (GRCm39)	missense	probably benign	0.26
R6758:Rorc	UTSW	3	94,294,825 (GRCm39)	missense	possibly damaging	0.90
R7069:Rorc	UTSW	3	94,280,214 (GRCm39)	nonsense	probably null
R7162:Rorc	UTSW	3	94,284,915 (GRCm39)	splice site	probably null
R7169:Rorc	UTSW	3	94,296,487 (GRCm39)	missense	probably benign	0.00
R7730:Rorc	UTSW	3	94,300,421 (GRCm39)	missense	probably benign	0.43
R7922:Rorc	UTSW	3	94,298,495 (GRCm39)	missense	probably damaging	0.98
R8365:Rorc	UTSW	3	94,282,366 (GRCm39)	missense	probably benign	0.01
R9354:Rorc	UTSW	3	94,280,170 (GRCm39)	unclassified	probably benign
X0063:Rorc	UTSW	3	94,299,058 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TGACCCTGGCTACATTTGTG -3'
(R):5'- CCATGTTAAGCAGAGCCAGTG -3'

Sequencing Primer
(F):5'- GACCCTGGCTACATTTGTGCTAATAG -3'
(R):5'- CAGAGCCAGTGTCTTGTTAAGCC -3'

Posted On

2014-07-14