Mutagenetix > Incidental Mutation

Incidental Mutation 'R6861:Nr6a1'

535489

Institutional Source

Beutler Lab

Gene Symbol

Nr6a1

Ensembl Gene

ENSMUSG00000063972

Gene Name

nuclear receptor subfamily 6, group A, member 1

Synonyms

1700113M01Rik, NCNF, Gcnf

MMRRC Submission

044962-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6861 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

38613381-38816473 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 38630597 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Isoleucine at position 207 (F207I)

Ref Sequence

ENSEMBL: ENSMUSP00000115164 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000076275] [ENSMUST00000112877] [ENSMUST00000142113] [ENSMUST00000142130] [ENSMUST00000168098]

AlphaFold

Q64249

Predicted Effect

probably benign
Transcript: ENSMUST00000076275
AA Change: F222I

PolyPhen 2 Score 0.145 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000075624
Gene: ENSMUSG00000063972
AA Change: F222I

Domain	Start	End	E-Value	Type
low complexity region	23	31	N/A	INTRINSIC
ZnF_C4	72	143	9.35e-36	SMART
low complexity region	202	216	N/A	INTRINSIC
HOLI	304	466	3.19e-29	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112877
AA Change: F222I

PolyPhen 2 Score 0.145 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000108498
Gene: ENSMUSG00000063972
AA Change: F222I

Domain	Start	End	E-Value	Type
low complexity region	23	31	N/A	INTRINSIC
ZnF_C4	72	143	9.35e-36	SMART
low complexity region	202	216	N/A	INTRINSIC
HOLI	304	466	3.19e-29	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000142113
AA Change: F165I

PolyPhen 2 Score 0.185 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000121234
Gene: ENSMUSG00000063972
AA Change: F165I

Domain	Start	End	E-Value	Type
ZnF_C4	15	86	9.35e-36	SMART
Blast:HOLI	105	235	6e-67	BLAST

Predicted Effect

possibly damaging
Transcript: ENSMUST00000142130
AA Change: F207I

PolyPhen 2 Score 0.712 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000115164
Gene: ENSMUSG00000063972
AA Change: F207I

Domain	Start	End	E-Value	Type
low complexity region	23	31	N/A	INTRINSIC
ZnF_C4	57	128	9.35e-36	SMART
low complexity region	187	201	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000168098
AA Change: F165I

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000126009
Gene: ENSMUSG00000063972
AA Change: F165I

Domain	Start	End	E-Value	Type
ZnF_C4	15	86	9.35e-36	SMART
low complexity region	145	159	N/A	INTRINSIC
HOLI	247	409	3.19e-29	SMART

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 encodes an orphan nuclear receptor which is a member of the nuclear hormone receptor family. Its expression pattern suggests that it may be involved in neurogenesis and germ cell development. The protein can homodimerize and bind DNA, but in vivo targets have not been identified. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2013]
PHENOTYPE: Homozygotes for targeted null mutations have cardiovascular abnormalities, defective trunk development, impaired somite formation, failure to turn, open neural tube and hindgut, protrusion of the tailbud outside the yolk sac and die by embryonic day 10.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamtsl4	G	A	3: 95,588,194 (GRCm39)	R598C	probably damaging	Het
Adra2a	T	C	19: 54,034,818 (GRCm39)	L58P	probably damaging	Het
Ajm1	C	CTCTA	2: 25,469,733 (GRCm39)		probably null	Het
Alox5ap	A	G	5: 149,201,927 (GRCm39)	D2G	probably damaging	Het
Arid1b	G	A	17: 5,377,961 (GRCm39)	V1238M	possibly damaging	Het
Bank1	A	G	3: 135,960,764 (GRCm39)	V31A	probably benign	Het
Bptf	G	A	11: 106,953,391 (GRCm39)	T2117M	probably damaging	Het
Cadps	G	A	14: 12,522,401 (GRCm38)	R588*	probably null	Het
Cavin4	A	G	4: 48,672,214 (GRCm39)	I220V	probably benign	Het
Cep192	G	A	18: 67,974,699 (GRCm39)	M1267I	probably benign	Het
Cers5	G	A	15: 99,670,244 (GRCm39)		probably benign	Het
Cfap65	A	T	1: 74,964,274 (GRCm39)	I558N	probably damaging	Het
Cfh	A	T	1: 140,028,621 (GRCm39)	S1025T	probably benign	Het
Cftr	A	G	6: 18,268,107 (GRCm39)	I689V	probably benign	Het
Cgrrf1	T	C	14: 47,069,785 (GRCm39)	I18T	probably damaging	Het
CK137956	A	G	4: 127,864,519 (GRCm39)	S37P	probably damaging	Het
Clca4a	T	C	3: 144,676,416 (GRCm39)	D88G	probably benign	Het
Col11a1	G	A	3: 113,961,141 (GRCm39)	G1166D	probably damaging	Het
Col24a1	G	A	3: 145,166,589 (GRCm39)	G1075S	probably damaging	Het
Crispld2	C	T	8: 120,752,852 (GRCm39)	T299M	probably damaging	Het
Cyb561a3	T	A	19: 10,562,701 (GRCm39)	Y114N	probably damaging	Het
Cyp3a57	T	A	5: 145,307,773 (GRCm39)	W147R	possibly damaging	Het
Dnah2	C	A	11: 69,346,789 (GRCm39)	R2599L	possibly damaging	Het
Dock1	T	A	7: 134,373,207 (GRCm39)	S525T	probably benign	Het
Drc7	T	G	8: 95,789,025 (GRCm39)		probably null	Het
Efhd2	G	T	4: 141,587,192 (GRCm39)		probably null	Het
Epb41l1	A	T	2: 156,367,142 (GRCm39)	E658D	probably benign	Het
Evi5	C	T	5: 107,896,184 (GRCm39)	S753N	probably benign	Het
Exoc3	A	T	13: 74,337,319 (GRCm39)	D427E	probably benign	Het
Fbxw9	A	G	8: 85,792,740 (GRCm39)	D363G	probably damaging	Het
Fcer2a	T	C	8: 3,732,910 (GRCm39)	Y277C	probably damaging	Het
Fstl5	A	T	3: 76,229,523 (GRCm39)	Y108F	probably damaging	Het
Gcn1	A	G	5: 115,749,108 (GRCm39)	D1880G	probably benign	Het
Gm4924	T	A	10: 82,214,948 (GRCm39)	Y915*	probably null	Het
Gpr139	T	A	7: 118,743,875 (GRCm39)	I237F	probably benign	Het
Hao2	A	G	3: 98,784,498 (GRCm39)	L289S	probably damaging	Het
Hexim1	A	G	11: 103,007,793 (GRCm39)	S16G	probably benign	Het
Hmgcs1	T	A	13: 120,161,535 (GRCm39)	M109K	probably damaging	Het
Hs3st4	T	A	7: 123,996,052 (GRCm39)	N239K	possibly damaging	Het
Hsd3b5	T	A	3: 98,529,328 (GRCm39)	N101Y	probably damaging	Het
Idh2	G	A	7: 79,747,966 (GRCm39)	P245S	probably damaging	Het
Irx3	A	G	8: 92,525,530 (GRCm39)		probably benign	Het
Lilra5	A	T	7: 4,244,931 (GRCm39)	D234V	probably benign	Het
Lrfn5	G	A	12: 61,886,476 (GRCm39)	S88N	probably damaging	Het
Lrp2	A	T	2: 69,343,721 (GRCm39)	S879R	possibly damaging	Het
Lsm11	A	G	11: 45,824,781 (GRCm39)	S249P	probably benign	Het
Ltbp1	C	T	17: 75,534,187 (GRCm39)	A543V	possibly damaging	Het
Mbd1	GTCTGCATCTGCGTCTTCGTCTGCATCTGCATCTGCGTCTTCGTCTGCATCTGCATCTGC	GTCTGCATCTGCGTCTTCGTCTGCATCTGCATCTGC	18: 74,406,645 (GRCm39)			Het
Mier2	C	T	10: 79,376,990 (GRCm39)		probably benign	Het
Mup6	G	C	4: 60,004,093 (GRCm39)	G70A	probably benign	Het
Neb	A	G	2: 52,085,732 (GRCm39)	L5258P	probably damaging	Het
Nlrc5	G	A	8: 95,247,857 (GRCm39)		probably benign	Het
Or2y1	A	T	11: 49,385,632 (GRCm39)	T91S	probably benign	Het
Or5k17	A	T	16: 58,746,867 (GRCm39)	D22E	probably benign	Het
Or8b43	T	C	9: 38,360,731 (GRCm39)	C188R	probably damaging	Het
Osbp2	A	G	11: 3,665,191 (GRCm39)	V51A	possibly damaging	Het
Papln	G	T	12: 83,821,723 (GRCm39)	C317F	probably damaging	Het
Pdcd7	T	C	9: 65,265,904 (GRCm39)	S454P	probably damaging	Het
Pde4a	C	T	9: 21,116,597 (GRCm39)	T473I	probably damaging	Het
Peg10	CC	CCCCATCAGGC	6: 4,756,350 (GRCm39)		probably benign	Het
Peg10	C	CCCATCAGGA	6: 4,756,351 (GRCm39)		probably benign	Het
Peg3	G	T	7: 6,714,385 (GRCm39)	S279*	probably null	Het
Rbl1	A	G	2: 156,994,887 (GRCm39)	Y929H	probably damaging	Het
Rsf1	G	GACGGCGGCA	7: 97,229,116 (GRCm39)		probably benign	Het
Sall3	C	A	18: 81,017,590 (GRCm39)	E113*	probably null	Het
Scn5a	A	C	9: 119,359,089 (GRCm39)	F653V	probably damaging	Het
Selenok	T	A	14: 29,692,005 (GRCm39)	N14K	possibly damaging	Het
Slc22a20	T	C	19: 6,021,838 (GRCm39)	T426A	probably benign	Het
Slc4a2	T	A	5: 24,640,007 (GRCm39)	S563T	probably damaging	Het
Sspo	T	A	6: 48,464,889 (GRCm39)	S3798T	probably benign	Het
Stag3	G	T	5: 138,302,969 (GRCm39)	R63L	possibly damaging	Het
Stard9	A	T	2: 120,535,667 (GRCm39)	M3975L	probably benign	Het
Syne2	C	A	12: 75,956,040 (GRCm39)	T582K	probably damaging	Het
Synj1	G	A	16: 90,760,768 (GRCm39)	Q748*	probably null	Het
Tas2r109	T	C	6: 132,957,048 (GRCm39)	D294G	probably benign	Het
Tbl1xr1	C	T	3: 22,245,603 (GRCm39)	T203M	possibly damaging	Het
Tbl1xr1	T	A	3: 22,245,703 (GRCm39)		probably null	Het
Tcf7l2	A	G	19: 55,730,955 (GRCm39)	D19G	probably damaging	Het
Tecta	A	G	9: 42,248,633 (GRCm39)	V1923A	possibly damaging	Het
Tg	T	A	15: 66,560,740 (GRCm39)	M1034K	probably benign	Het
Ttf2	T	C	3: 100,876,941 (GRCm39)	E8G	possibly damaging	Het
Vps13b	T	A	15: 35,576,541 (GRCm39)	V983E	probably damaging	Het
Vps35l	A	G	7: 118,342,898 (GRCm39)	H32R	probably damaging	Het
Vwa2	T	C	19: 56,890,025 (GRCm39)	V210A	probably benign	Het
Xkr6	T	A	14: 64,057,093 (GRCm39)	Y335N	probably benign	Het
Zfp97	A	G	17: 17,365,437 (GRCm39)	H312R	probably damaging	Het

Other mutations in Nr6a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01566:Nr6a1	APN	2	38,617,901 (GRCm39)	missense	probably benign	0.06
IGL02245:Nr6a1	APN	2	38,630,565 (GRCm39)	missense	probably benign	0.04
IGL03195:Nr6a1	APN	2	38,632,948 (GRCm39)	missense	probably damaging	1.00
R0270:Nr6a1	UTSW	2	38,629,032 (GRCm39)	missense	possibly damaging	0.75
R0909:Nr6a1	UTSW	2	38,775,218 (GRCm39)	missense	probably benign	0.11
R1737:Nr6a1	UTSW	2	38,628,955 (GRCm39)	missense	probably benign	0.04
R5918:Nr6a1	UTSW	2	38,629,103 (GRCm39)	missense	probably damaging	1.00
R6210:Nr6a1	UTSW	2	38,619,509 (GRCm39)	missense	probably damaging	0.99
R6311:Nr6a1	UTSW	2	38,629,083 (GRCm39)	missense	possibly damaging	0.69
R6978:Nr6a1	UTSW	2	38,762,631 (GRCm39)	missense	probably benign
R7566:Nr6a1	UTSW	2	38,621,085 (GRCm39)	missense	possibly damaging	0.77
R8177:Nr6a1	UTSW	2	38,619,510 (GRCm39)	missense	probably benign	0.02
R8441:Nr6a1	UTSW	2	38,632,888 (GRCm39)	missense	probably benign	0.05
R8548:Nr6a1	UTSW	2	38,619,551 (GRCm39)	missense	probably damaging	1.00
R8548:Nr6a1	UTSW	2	38,619,550 (GRCm39)	missense	probably damaging	1.00
R8776:Nr6a1	UTSW	2	38,650,244 (GRCm39)	missense	probably damaging	1.00
R8776-TAIL:Nr6a1	UTSW	2	38,650,244 (GRCm39)	missense	probably damaging	1.00
R8933:Nr6a1	UTSW	2	38,650,400 (GRCm39)	missense	probably damaging	0.99
R8982:Nr6a1	UTSW	2	38,762,613 (GRCm39)	missense	probably benign	0.00
R9189:Nr6a1	UTSW	2	38,816,129 (GRCm39)	critical splice donor site	probably null
R9284:Nr6a1	UTSW	2	38,638,890 (GRCm39)	missense	probably damaging	1.00
R9505:Nr6a1	UTSW	2	38,630,485 (GRCm39)	missense	probably benign	0.24

Predicted Primers

PCR Primer
(F):5'- CAACATAGGTGTGCCCAATGG -3'
(R):5'- ACAGAATCCTTGTCTTGTGGG -3'

Sequencing Primer
(F):5'- AATGGCTCCAGGTCTTCGG -3'
(R):5'- TGTGGGTGGAATTTAATAGCATAGAC -3'

Posted On

2018-09-12