Mutagenetix > Incidental Mutation

Incidental Mutation 'R6010:Nanog'

479705

Institutional Source

Beutler Lab

Gene Symbol

Nanog

Ensembl Gene

ENSMUSG00000012396

Gene Name

Nanog homeobox

Synonyms

ENK, 2410002E02Rik, ecat4

MMRRC Submission

044187-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6010 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

122684448-122691592 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 122690255 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Threonine at position 195 (N195T)

Ref Sequence

ENSEMBL: ENSMUSP00000108200 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000012540] [ENSMUST00000112580] [ENSMUST00000112581]

AlphaFold

Q80Z64

Predicted Effect

probably benign
Transcript: ENSMUST00000012540
AA Change: N220T

PolyPhen 2 Score 0.162 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000012540
Gene: ENSMUSG00000012396
AA Change: N220T

Domain	Start	End	E-Value	Type
low complexity region	13	25	N/A	INTRINSIC
HOX	96	158	5.33e-22	SMART
low complexity region	206	230	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112580
AA Change: N195T

PolyPhen 2 Score 0.162 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000108199
Gene: ENSMUSG00000012396
AA Change: N195T

Domain	Start	End	E-Value	Type
HOX	71	133	5.33e-22	SMART
low complexity region	181	205	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112581
AA Change: N195T

PolyPhen 2 Score 0.162 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000108200
Gene: ENSMUSG00000012396
AA Change: N195T

Domain	Start	End	E-Value	Type
HOX	71	133	5.33e-22	SMART
low complexity region	181	205	N/A	INTRINSIC

Meta Mutation Damage Score

0.1156

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.7%
20x: 92.9%

Validation Efficiency

100% (65/65)

MGI Phenotype

FUNCTION: The protein encoded by this gene is a DNA binding homeobox transcription factor involved in embryonic stem (ES) cell proliferation, renewal, and pluripotency. The encoded protein can block ES cell differentiation and can also autorepress its own expression in differentiating cells. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015]
PHENOTYPE: Mice homozygous for a disruption in this gene die between E3.5 and E5.5 with abnormal embryonic and extraembryonic tissue development. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actl7a	A	G	4: 56,743,870 (GRCm39)	I132M	possibly damaging	Het
Agap2	A	T	10: 126,926,779 (GRCm39)	I939F	probably damaging	Het
Ahctf1	A	G	1: 179,623,378 (GRCm39)	V80A	possibly damaging	Het
Atxn3	T	C	12: 101,914,285 (GRCm39)	D67G	probably damaging	Het
Avl9	G	A	6: 56,730,375 (GRCm39)	V573M	possibly damaging	Het
Baz1b	G	A	5: 135,246,305 (GRCm39)	E585K	possibly damaging	Het
Brms1l	T	C	12: 55,914,985 (GRCm39)	F298S	possibly damaging	Het
Camk2d	G	A	3: 126,591,363 (GRCm39)	V278I	possibly damaging	Het
Car10	A	G	11: 93,490,149 (GRCm39)	I297V	possibly damaging	Het
Cfap65	C	T	1: 74,962,190 (GRCm39)	C677Y	probably damaging	Het
Cfap74	T	A	4: 155,538,495 (GRCm39)	D872E	possibly damaging	Het
Cgrrf1	A	C	14: 47,091,158 (GRCm39)	Q227H	probably damaging	Het
Chil4	A	G	3: 106,121,711 (GRCm39)	I46T	probably damaging	Het
Chpf2	A	T	5: 24,796,917 (GRCm39)	H621L	probably damaging	Het
Cluap1	C	T	16: 3,755,437 (GRCm39)	R351W	possibly damaging	Het
Cnot6	A	T	11: 49,574,066 (GRCm39)	Y201*	probably null	Het
Col15a1	T	C	4: 47,245,630 (GRCm39)	V127A	probably benign	Het
Col6a3	C	T	1: 90,701,219 (GRCm39)	V2566I	unknown	Het
Cope	T	A	8: 70,761,162 (GRCm39)	M88K	probably damaging	Het
Cops4	A	G	5: 100,691,776 (GRCm39)	I358M	possibly damaging	Het
Coro7	T	C	16: 4,487,820 (GRCm39)	E130G	possibly damaging	Het
Csrp3	A	G	7: 48,485,213 (GRCm39)		probably null	Het
Cyp4f39	T	C	17: 32,701,160 (GRCm39)	F217L	probably damaging	Het
Dmac1	A	G	4: 75,196,473 (GRCm39)	S6P	unknown	Het
Drd4	A	T	7: 140,874,709 (GRCm39)	I367F	probably damaging	Het
Efcc1	T	A	6: 87,730,711 (GRCm39)		probably null	Het
Emid1	A	T	11: 5,085,389 (GRCm39)	M119K	possibly damaging	Het
Fbn2	C	T	18: 58,202,596 (GRCm39)	D1237N	probably benign	Het
Fbxl18	C	A	5: 142,858,153 (GRCm39)	R761L	probably damaging	Het
Gbp10	A	C	5: 105,372,205 (GRCm39)	L185R	probably damaging	Het
Gm7247	C	T	14: 51,601,805 (GRCm39)	S26F	probably benign	Het
Gucd1	G	T	10: 75,256,600 (GRCm39)		probably benign	Het
Helb	G	A	10: 119,941,788 (GRCm39)	T300M	probably damaging	Het
Ifna11	A	T	4: 88,738,278 (GRCm39)	H28L	probably benign	Het
Kalrn	T	A	16: 33,830,950 (GRCm39)	N723I	probably benign	Het
Kcnb2	C	T	1: 15,780,790 (GRCm39)	S554F	possibly damaging	Het
Med1	A	C	11: 98,049,188 (GRCm39)	V536G	probably damaging	Het
Neu1	C	T	17: 35,151,031 (GRCm39)	S94F	probably damaging	Het
Nop58	T	A	1: 59,740,071 (GRCm39)	S154R	probably damaging	Het
Npl	A	T	1: 153,388,314 (GRCm39)	L239*	probably null	Het
Nrg1	G	A	8: 32,308,600 (GRCm39)	T483M	probably damaging	Het
Nup98	G	T	7: 101,829,636 (GRCm39)	F391L	probably damaging	Het
Or4c122	A	T	2: 89,079,087 (GRCm39)	I305K	probably benign	Het
Or5ar1	T	C	2: 85,671,905 (GRCm39)	I77V	probably benign	Het
Or5d47	A	T	2: 87,804,886 (GRCm39)	V41E	probably damaging	Het
Or5g26	T	C	2: 85,494,374 (GRCm39)	I135V	probably benign	Het
Pacsin2	A	G	15: 83,266,020 (GRCm39)	V59A	possibly damaging	Het
Pcsk9	C	T	4: 106,311,469 (GRCm39)	R254H	possibly damaging	Het
Pierce2	A	T	9: 72,887,488 (GRCm39)		probably null	Het
Psme2	C	A	14: 55,824,980 (GRCm39)		probably null	Het
Ptprc	T	A	1: 138,028,794 (GRCm39)	H468L	probably benign	Het
Rbp3	T	A	14: 33,676,604 (GRCm39)	I184N	probably damaging	Het
Serpinb1c	A	G	13: 33,066,042 (GRCm39)	L301P	probably damaging	Het
Smim6	G	T	11: 115,804,219 (GRCm39)	G2V	probably damaging	Het
Snrpb2	A	G	2: 142,912,815 (GRCm39)	D146G	possibly damaging	Het
Svep1	T	A	4: 58,115,832 (GRCm39)	S954C	possibly damaging	Het
Telo2	G	T	17: 25,323,852 (GRCm39)	T568N	possibly damaging	Het
Tpp2	T	C	1: 43,990,373 (GRCm39)		probably null	Het
Upf1	A	G	8: 70,789,675 (GRCm39)	V720A	probably damaging	Het
Vmn1r81	T	C	7: 11,994,349 (GRCm39)	I86M	possibly damaging	Het
Vps8	T	A	16: 21,363,955 (GRCm39)		probably benign	Het
Wdr70	T	C	15: 7,916,900 (GRCm39)		probably null	Het
Zfp385c	A	T	11: 100,548,363 (GRCm39)	S30T	probably benign	Het
Zfp607a	T	A	7: 27,577,254 (GRCm39)	L108*	probably null	Het

Other mutations in Nanog

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00475:Nanog	APN	6	122,688,495 (GRCm39)	critical splice acceptor site	probably null
IGL03278:Nanog	APN	6	122,688,704 (GRCm39)	missense	probably damaging	1.00
IGL03387:Nanog	APN	6	122,688,731 (GRCm39)	missense	probably damaging	1.00
R0280:Nanog	UTSW	6	122,690,357 (GRCm39)	missense	probably damaging	0.96
R1443:Nanog	UTSW	6	122,688,734 (GRCm39)	missense	probably damaging	1.00
R2520:Nanog	UTSW	6	122,690,418 (GRCm39)	missense	probably benign	0.08
R3037:Nanog	UTSW	6	122,690,227 (GRCm39)	missense	possibly damaging	0.81
R4486:Nanog	UTSW	6	122,689,676 (GRCm39)	critical splice donor site	probably null
R4770:Nanog	UTSW	6	122,688,550 (GRCm39)	missense	possibly damaging	0.63
R4790:Nanog	UTSW	6	122,684,874 (GRCm39)	missense	probably benign	0.00
R4825:Nanog	UTSW	6	122,690,299 (GRCm39)	missense	probably benign	0.09
R4931:Nanog	UTSW	6	122,684,865 (GRCm39)	missense	possibly damaging	0.95
R6025:Nanog	UTSW	6	122,690,350 (GRCm39)	missense	possibly damaging	0.94
R7661:Nanog	UTSW	6	122,690,431 (GRCm39)	missense	probably damaging	0.96
R8236:Nanog	UTSW	6	122,690,131 (GRCm39)	missense	probably benign
R8272:Nanog	UTSW	6	122,688,736 (GRCm39)	missense	probably benign	0.00
R8520:Nanog	UTSW	6	122,690,475 (GRCm39)	missense	possibly damaging	0.94
R9500:Nanog	UTSW	6	122,690,219 (GRCm39)	missense	probably damaging	1.00
R9632:Nanog	UTSW	6	122,684,799 (GRCm39)	missense	probably benign	0.00
R9710:Nanog	UTSW	6	122,684,799 (GRCm39)	missense	probably benign	0.00
X0065:Nanog	UTSW	6	122,684,752 (GRCm39)	missense	probably benign
Z1176:Nanog	UTSW	6	122,690,190 (GRCm39)	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GCAGTTTACATCTTTAGAGTCCCC -3'
(R):5'- AATGCGCATGGCTTTCCCTAG -3'

Sequencing Primer
(F):5'- AGAGTCCCCTTTTCACTCATTG -3'
(R):5'- GTGGCTTCCAAATTCACCTCCAAATC -3'

Posted On

2017-06-26