Mutagenetix > Incidental Mutation

Incidental Mutation 'R7922:Rorc'

648424

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

045969-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.837) question?

Stock #

R7922 (G1)

Quality Score

163.009

Status

Not validated

Chromosome

Chromosomal Location

94280101-94305583 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 94298495 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 348 (I348V)

Ref Sequence

ENSEMBL: ENSMUSP00000029795 (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: I348V

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

SMART Domains

Protein: ENSMUSP00000029795
Gene: ENSMUSG00000028150
AA Change: I348V

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: I327V

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000143763
Gene: ENSMUSG00000028150
AA Change: I327V

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

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

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.] 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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700049A03Rik	C	T	12: 71,211,180 (GRCm39)	T638M	possibly damaging	Het
4930546C10Rik	A	G	18: 69,083,067 (GRCm39)		probably null	Het
Abi3	A	T	11: 95,723,619 (GRCm39)	Y342N	unknown	Het
Adk	G	A	14: 21,368,111 (GRCm39)	V195I	probably benign	Het
Ago2	C	T	15: 72,998,375 (GRCm39)	V268M	possibly damaging	Het
Apaf1	T	C	10: 90,835,615 (GRCm39)	I1077V	probably benign	Het
Arap1	A	T	7: 101,053,621 (GRCm39)	K1317*	probably null	Het
Auts2	T	A	5: 131,469,211 (GRCm39)	D493V		Het
Baz1b	A	T	5: 135,260,533 (GRCm39)	Q1110L	probably damaging	Het
Brsk2	T	A	7: 141,546,957 (GRCm39)	S467T	possibly damaging	Het
Btbd9	A	T	17: 30,493,858 (GRCm39)	M511K	probably benign	Het
Cdh23	T	A	10: 60,218,485 (GRCm39)	Y1385F	probably benign	Het
Cfap100	A	C	6: 90,380,962 (GRCm39)	L427V	unknown	Het
Cnga1	A	G	5: 72,762,225 (GRCm39)	F430L	possibly damaging	Het
Csnk2a1-ps3	A	T	1: 156,352,562 (GRCm39)	L254F	probably damaging	Het
Dnhd1	A	T	7: 105,317,721 (GRCm39)	D472V	probably damaging	Het
Dock2	T	A	11: 34,598,154 (GRCm39)	E339V	probably benign	Het
Eif3a	A	T	19: 60,764,280 (GRCm39)	V379E	probably damaging	Het
Erich4	T	A	7: 25,315,168 (GRCm39)	N36Y	probably damaging	Het
Frem2	T	C	3: 53,560,725 (GRCm39)	T1261A	probably damaging	Het
Fzd6	A	T	15: 38,894,503 (GRCm39)	D223V	probably damaging	Het
Gabra2	A	T	5: 71,165,315 (GRCm39)	Y218*	probably null	Het
Gcn1	G	T	5: 115,752,527 (GRCm39)	M2177I	probably benign	Het
Ghr	G	A	15: 3,370,556 (GRCm39)	T103I	possibly damaging	Het
Gipc1	T	C	8: 84,387,857 (GRCm39)	V79A	probably benign	Het
Gm13272	T	A	4: 88,698,577 (GRCm39)	V164D	probably damaging	Het
Gramd4	C	A	15: 86,016,159 (GRCm39)	H503Q	probably benign	Het
Gstm4	A	T	3: 107,951,987 (GRCm39)	M1K	probably null	Het
Heatr5b	T	A	17: 79,067,988 (GRCm39)	Q1800L	probably benign	Het
Hectd1	T	A	12: 51,836,978 (GRCm39)	K826*	probably null	Het
Hoxa9	T	C	6: 52,201,289 (GRCm39)	I251V	possibly damaging	Het
Il2ra	A	T	2: 11,679,177 (GRCm39)	I46F	possibly damaging	Het
Ints2	T	A	11: 86,135,453 (GRCm39)	R320S	probably benign	Het
Iscu	A	T	5: 113,912,343 (GRCm39)	N46I	probably damaging	Het
Iscu	G	A	5: 113,912,410 (GRCm39)	R60Q	unknown	Het
Kcnk3	A	T	5: 30,745,875 (GRCm39)	H72L	probably damaging	Het
Kmt2a	T	G	9: 44,754,157 (GRCm39)	S1228R	unknown	Het
Mbl2	T	A	19: 30,216,638 (GRCm39)	L150Q	probably damaging	Het
Med13	A	T	11: 86,161,831 (GRCm39)	F2166Y	probably damaging	Het
Mterf4	A	C	1: 93,229,275 (GRCm39)	L246*	probably null	Het
Muc16	T	C	9: 18,496,121 (GRCm39)	Q6690R	probably benign	Het
Myh10	T	A	11: 68,699,719 (GRCm39)	L1722Q	possibly damaging	Het
Neurod2	T	C	11: 98,218,454 (GRCm39)	M237V	probably benign	Het
Olfml1	A	G	7: 107,170,356 (GRCm39)	Y81C	probably damaging	Het
Or4q3	A	G	14: 50,583,872 (GRCm39)	V9A	probably benign	Het
Pcdhga7	A	T	18: 37,849,226 (GRCm39)	N411I	probably benign	Het
Pcdhgb8	T	C	18: 37,897,002 (GRCm39)	F691L	probably benign	Het
Pik3c2a	A	G	7: 115,990,517 (GRCm39)	V481A	probably damaging	Het
Pik3r6	A	T	11: 68,424,701 (GRCm39)	R435S	probably benign	Het
Pkd1l1	G	A	11: 8,799,013 (GRCm39)	H2250Y		Het
Pkd1l1	A	G	11: 8,859,857 (GRCm39)	S1034P		Het
Plcd1	C	A	9: 118,903,720 (GRCm39)	R400L	possibly damaging	Het
Ppp2r1a	A	G	17: 21,174,879 (GRCm39)	T58A	probably benign	Het
Ppp5c	T	C	7: 16,761,725 (GRCm39)	E5G	possibly damaging	Het
Pradc1	A	C	6: 85,424,950 (GRCm39)	F82L	probably benign	Het
Prkag3	A	T	1: 74,780,416 (GRCm39)	S416R	probably benign	Het
Rab3gap2	T	C	1: 184,982,117 (GRCm39)	C390R	probably benign	Het
Rhot1	A	G	11: 80,156,629 (GRCm39)	T655A	probably benign	Het
Ryr1	A	T	7: 28,796,649 (GRCm39)	V1051E	probably benign	Het
Sema5b	GCAC	GC	16: 35,478,626 (GRCm39)		probably null	Het
Serpinb3c	G	A	1: 107,199,744 (GRCm39)	T259I	probably damaging	Het
Sh3gl1	A	T	17: 56,326,438 (GRCm39)	M70K	probably damaging	Het
Sinhcaf	T	A	6: 148,827,644 (GRCm39)	T125S	probably benign	Het
Slc7a4	C	T	16: 17,391,230 (GRCm39)	V607I	probably benign	Het
Spop	A	T	11: 95,362,154 (GRCm39)	N62Y	probably damaging	Het
Spout1	A	G	2: 30,066,823 (GRCm39)	F130S	probably benign	Het
Tab1	A	G	15: 80,043,066 (GRCm39)	H420R	possibly damaging	Het
Tecpr2	CA	C	12: 110,899,076 (GRCm39)		probably null	Het
Tnxb	G	C	17: 34,933,577 (GRCm39)	K2332N	probably damaging	Het
Togaram1	T	C	12: 65,014,512 (GRCm39)	Y588H	probably damaging	Het
Trim71	G	A	9: 114,342,153 (GRCm39)	R710C	probably damaging	Het
Tsen54	C	T	11: 115,711,608 (GRCm39)	Q342*	probably null	Het
Ube2r2	T	A	4: 41,190,812 (GRCm39)	N235K	unknown	Het
Utrn	C	A	10: 12,543,271 (GRCm39)	K1792N	possibly damaging	Het
Vmn1r122	A	G	7: 20,867,587 (GRCm39)	I156T	possibly damaging	Het
Vmn1r94	T	C	7: 19,901,636 (GRCm39)	T223A	possibly damaging	Het
Vmn2r120	G	A	17: 57,831,683 (GRCm39)	R369W	probably damaging	Het
Vwa7	G	T	17: 35,243,409 (GRCm39)	A717S	possibly damaging	Het
Zc3h4	T	A	7: 16,159,647 (GRCm39)	C398S	unknown	Het
Zc3hc1	T	A	6: 30,390,874 (GRCm39)	E43V	possibly damaging	Het
Zfp101	A	T	17: 33,600,511 (GRCm39)	V415D	possibly damaging	Het
Zfp553	A	G	7: 126,835,768 (GRCm39)	H441R	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
R1915: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
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'- GGCTACATTTGTGCTAATAGGCTC -3'
(R):5'- GGGTAGGCCATGTTAAGCAG -3'

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

Posted On

2020-09-15