Mutagenetix > Incidental Mutation

Incidental Mutation 'R1737:Nr6a1'

199755

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

039769-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1737 (G1)

Quality Score

214

Status

Validated

Chromosome

Chromosomal Location

38613381-38816473 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 38628955 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 356 (F356L)

Ref Sequence

ENSEMBL: ENSMUSP00000108498 (fasta)

Gene Model

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

AlphaFold

Q64249

Predicted Effect

probably benign
Transcript: ENSMUST00000076275
AA Change: F356L

PolyPhen 2 Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000075624
Gene: ENSMUSG00000063972
AA Change: F356L

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: F356L

PolyPhen 2 Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000108498
Gene: ENSMUSG00000063972
AA Change: F356L

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

noncoding transcript
Transcript: ENSMUST00000123342

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128688

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132636

Predicted Effect

probably benign
Transcript: ENSMUST00000142113

SMART Domains

Protein: ENSMUSP00000121234
Gene: ENSMUSG00000063972

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

Predicted Effect

probably benign
Transcript: ENSMUST00000142130

SMART Domains

Protein: ENSMUSP00000115164
Gene: ENSMUSG00000063972

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: F299L

PolyPhen 2 Score 0.019 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000126009
Gene: ENSMUSG00000063972
AA Change: F299L

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000203202

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156301

Meta Mutation Damage Score

0.0652

Coding Region Coverage

1x: 97.6%
3x: 96.9%
10x: 95.1%
20x: 91.4%

Validation Efficiency

100% (75/75)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts16	G	A	13: 70,927,637 (GRCm39)		probably benign	Het
Ak7	G	A	12: 105,708,591 (GRCm39)	V349M	probably damaging	Het
Aldh1a2	A	T	9: 71,192,453 (GRCm39)	E436V	possibly damaging	Het
Apc	C	A	18: 34,450,075 (GRCm39)	P2290T	probably damaging	Het
Atp10a	T	C	7: 58,476,986 (GRCm39)		probably benign	Het
Bahd1	T	C	2: 118,746,404 (GRCm39)	S8P	probably damaging	Het
BC049715	C	T	6: 136,817,306 (GRCm39)	P182L	probably damaging	Het
Capn10	T	C	1: 92,862,677 (GRCm39)	Y28H	probably benign	Het
Cdh10	A	T	15: 18,964,149 (GRCm39)	I104F	probably damaging	Het
Cep170b	A	G	12: 112,703,061 (GRCm39)	D508G	possibly damaging	Het
Ces2a	G	T	8: 105,467,456 (GRCm39)	A494S	probably damaging	Het
Ces4a	G	A	8: 105,864,729 (GRCm39)	G69S	probably damaging	Het
Cltc	G	A	11: 86,624,553 (GRCm39)	T123M	probably damaging	Het
Cnot1	A	G	8: 96,474,904 (GRCm39)	S1102P	probably damaging	Het
Col12a1	C	A	9: 79,610,733 (GRCm39)	D224Y	probably damaging	Het
Col14a1	T	A	15: 55,208,357 (GRCm39)		probably benign	Het
Cyp7a1	T	A	4: 6,272,848 (GRCm39)	T122S	probably benign	Het
Dock4	A	G	12: 40,857,000 (GRCm39)		probably null	Het
Eid2	T	C	7: 27,967,924 (GRCm39)	V182A	possibly damaging	Het
Eloa	A	T	4: 135,738,081 (GRCm39)	V293D	probably benign	Het
Enkur	G	A	2: 21,199,106 (GRCm39)	P143S	probably damaging	Het
Ep300	T	C	15: 81,510,548 (GRCm39)	Y99H	probably damaging	Het
Fbxw5	C	A	2: 25,393,596 (GRCm39)	L66I	probably benign	Het
Flg2	A	T	3: 93,110,928 (GRCm39)	R985S	unknown	Het
Fscb	A	T	12: 64,521,355 (GRCm39)	I37K	possibly damaging	Het
H2-M10.3	T	C	17: 36,679,296 (GRCm39)	N3S	probably benign	Het
H2-Q7	A	C	17: 35,658,602 (GRCm39)	Y80S	probably damaging	Het
H60c	A	T	10: 3,209,914 (GRCm39)	D124E	possibly damaging	Het
Hsd3b2	A	T	3: 98,618,862 (GRCm39)	V361E	probably damaging	Het
Ice1	A	C	13: 70,754,444 (GRCm39)	C547W	probably damaging	Het
Itprid1	A	T	6: 55,945,289 (GRCm39)	D670V	probably damaging	Het
Jmy	A	G	13: 93,635,303 (GRCm39)	V171A	probably damaging	Het
Klf7	C	A	1: 64,118,372 (GRCm39)	R75L	possibly damaging	Het
Klk1b1	A	T	7: 43,619,783 (GRCm39)	Q114L	probably benign	Het
Krt10	A	G	11: 99,278,213 (GRCm39)	M280T	possibly damaging	Het
Lama1	G	A	17: 68,109,916 (GRCm39)	R2179Q	probably benign	Het
Mbd3l1	C	T	9: 18,396,225 (GRCm39)	P117S	possibly damaging	Het
Med18	A	T	4: 132,187,420 (GRCm39)	S71R	probably damaging	Het
Mov10l1	T	A	15: 88,895,607 (GRCm39)	I643N	possibly damaging	Het
Nfib	T	C	4: 82,416,826 (GRCm39)	K70E	probably damaging	Het
Nr3c2	A	C	8: 77,634,958 (GRCm39)	S20R	probably benign	Het
Oca2	G	A	7: 55,978,533 (GRCm39)	R567H	probably damaging	Het
Or10k2	A	G	8: 84,268,045 (GRCm39)	S91G	probably benign	Het
Or1e35	T	A	11: 73,797,911 (GRCm39)	M136L	possibly damaging	Het
Or1p1	T	C	11: 74,179,637 (GRCm39)	L55P	probably damaging	Het
Or6c88	T	A	10: 129,406,697 (GRCm39)	Y58N	probably damaging	Het
Or8g33	T	C	9: 39,338,254 (GRCm39)	T38A	probably damaging	Het
Pcdhb10	A	G	18: 37,546,009 (GRCm39)	T362A	probably benign	Het
Pip5k1b	A	T	19: 24,374,404 (GRCm39)	V59E	probably damaging	Het
Pkhd1l1	G	A	15: 44,410,905 (GRCm39)		probably null	Het
Prr36	T	C	8: 4,264,370 (GRCm39)		probably benign	Het
Ptger2	A	G	14: 45,239,228 (GRCm39)	T289A	probably benign	Het
Rad18	A	G	6: 112,658,498 (GRCm39)	F136L	probably damaging	Het
Rhbg	T	A	3: 88,153,181 (GRCm39)	S258C	probably damaging	Het
Scgb2b27	T	C	7: 33,712,739 (GRCm39)	I34M	possibly damaging	Het
Senp7	C	A	16: 55,944,162 (GRCm39)	T135K	probably damaging	Het
Slc20a2	A	G	8: 23,035,582 (GRCm39)	I193M	probably damaging	Het
Slc27a1	G	A	8: 72,023,504 (GRCm39)	V47I	probably benign	Het
Slc9a5	G	A	8: 106,094,766 (GRCm39)	V786M	probably damaging	Het
Smyd1	A	G	6: 71,193,875 (GRCm39)	L350P	probably damaging	Het
Ston2	A	T	12: 91,614,681 (GRCm39)	F576I	probably damaging	Het
Sulf2	A	T	2: 165,924,598 (GRCm39)	V496E	probably benign	Het
Tcl1b3	C	A	12: 105,157,481 (GRCm39)	S41Y	probably damaging	Het
Tulp2	A	T	7: 45,169,201 (GRCm39)	N256I	probably damaging	Het
Uspl1	T	A	5: 149,138,668 (GRCm39)	C349S	probably damaging	Het
Vcl	T	C	14: 21,070,604 (GRCm39)	I730T	probably damaging	Het
Vmn1r61	A	T	7: 5,614,060 (GRCm39)	F85I	probably benign	Het
Zfp318	A	G	17: 46,710,403 (GRCm39)	T709A	probably benign	Het
Zfr2	T	C	10: 81,077,919 (GRCm39)	S249P	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
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
R6861:Nr6a1	UTSW	2	38,630,597 (GRCm39)	missense	possibly damaging	0.71
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'- TGACCACACAAAGCTAGTATGTGCC -3'
(R):5'- TGGAAATGACTCTGTCCTGTCCCTG -3'

Sequencing Primer
(F):5'- CCAGGGTAAGGGTTACAGTTTAG -3'
(R):5'- CCAGGTATGCTGTGACACAGG -3'

Posted On

2014-05-23