Mutagenetix > Incidental Mutation

Incidental Mutation 'R4931:Nanog'

380555

Institutional Source

Beutler Lab

Gene Symbol

Nanog

Ensembl Gene

ENSMUSG00000012396

Gene Name

Nanog homeobox

Synonyms

ENK, 2410002E02Rik, ecat4

MMRRC Submission

042532-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4931 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

122684448-122691592 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 122684865 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 17 (A17T)

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: A42T

PolyPhen 2 Score 0.357 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000012540
Gene: ENSMUSG00000012396
AA Change: A42T

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

possibly damaging
Transcript: ENSMUST00000112580
AA Change: A17T

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000108199
Gene: ENSMUSG00000012396
AA Change: A17T

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000112581
AA Change: A17T

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000108200
Gene: ENSMUSG00000012396
AA Change: A17T

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

0.1795

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.4%
20x: 92.7%

Validation Efficiency

95% (78/82)

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
2410004B18Rik	A	G	3: 145,643,875 (GRCm39)	D21G	probably benign	Het
4930562C15Rik	T	C	16: 4,678,910 (GRCm39)	L68P	possibly damaging	Het
Ache	A	G	5: 137,290,176 (GRCm39)	I414V	probably benign	Het
Acy1	G	A	9: 106,310,390 (GRCm39)	H308Y	probably damaging	Het
Aldh1b1	A	C	4: 45,803,661 (GRCm39)	I400L	probably benign	Het
Ankrd40	T	A	11: 94,225,647 (GRCm39)	L226Q	probably benign	Het
B3gnt9	T	C	8: 105,980,876 (GRCm39)	T171A	probably benign	Het
Ccdc33	T	C	9: 57,977,134 (GRCm39)	Y289C	probably damaging	Het
Cd209f	A	T	8: 4,153,688 (GRCm39)	I187N	probably damaging	Het
Cers6	T	G	2: 68,935,456 (GRCm39)	S319A	probably damaging	Het
Chrna4	A	G	2: 180,670,665 (GRCm39)	S364P	probably benign	Het
Chrnb3	T	C	8: 27,884,258 (GRCm39)	S317P	probably damaging	Het
Dapk1	T	C	13: 60,908,774 (GRCm39)	V1129A	probably benign	Het
Dhx9	G	A	1: 153,348,419 (GRCm39)	P302L	probably benign	Het
Dnaaf9	A	G	2: 130,583,793 (GRCm39)	F496L	possibly damaging	Het
Dnah8	G	A	17: 30,967,542 (GRCm39)	D2585N	probably benign	Het
Duox2	T	C	2: 122,127,236 (GRCm39)	N147S	probably benign	Het
Dytn	T	G	1: 63,672,837 (GRCm39)	E522A	probably benign	Het
E130114P18Rik	T	C	4: 97,608,524 (GRCm39)	D27G	unknown	Het
Egf	A	G	3: 129,505,117 (GRCm39)	F118S	probably damaging	Het
Eif2d	T	A	1: 131,082,128 (GRCm39)	F73L	probably damaging	Het
Eps8l1	A	G	7: 4,474,240 (GRCm39)	E237G	possibly damaging	Het
Espl1	A	G	15: 102,214,165 (GRCm39)	E664G	probably benign	Het
Fbrsl1	A	T	5: 110,526,895 (GRCm39)	S373T	possibly damaging	Het
Fras1	T	A	5: 96,784,699 (GRCm39)	F894Y	probably benign	Het
Gpatch8	T	C	11: 102,372,050 (GRCm39)	E496G	unknown	Het
Gucy1a2	A	G	9: 3,759,588 (GRCm39)	K465E	probably damaging	Het
Igdcc4	A	G	9: 65,031,297 (GRCm39)	T459A	possibly damaging	Het
Itgad	A	T	7: 127,803,797 (GRCm39)	I64F	probably damaging	Het
Itgb2l	T	A	16: 96,238,649 (GRCm39)	N50I	probably damaging	Het
Kif13a	A	G	13: 46,962,531 (GRCm39)	I478T	probably damaging	Het
Krt31	G	A	11: 99,940,983 (GRCm39)	T109I	probably benign	Het
Ltbr	G	T	6: 125,284,437 (GRCm39)		probably null	Het
Magel2	A	G	7: 62,030,372 (GRCm39)	D1092G	unknown	Het
Minar1	T	C	9: 89,483,705 (GRCm39)	H564R	probably benign	Het
Mindy3	A	T	2: 12,401,024 (GRCm39)	N231K	probably damaging	Het
Mpnd	T	G	17: 56,319,362 (GRCm39)		probably benign	Het
Mtus2	C	T	5: 148,014,226 (GRCm39)	L340F	probably benign	Het
Ndufa9	G	T	6: 126,813,283 (GRCm39)	A181E	probably damaging	Het
Or52z14	T	G	7: 103,253,581 (GRCm39)	L240R	probably benign	Het
Or7e175	A	T	9: 20,048,858 (GRCm39)	I149F	probably benign	Het
Pprc1	ATCCTCCTCCTCCTCCTCCTC	ATCCTCCTCCTCCTCCTC	19: 46,059,755 (GRCm39)		probably benign	Het
Pramel18	T	C	4: 101,766,367 (GRCm39)	V17A	possibly damaging	Het
Prkacb	T	C	3: 146,453,732 (GRCm39)	I211V	possibly damaging	Het
Ptpn14	C	G	1: 189,583,474 (GRCm39)	L774V	probably benign	Het
Rad1	T	C	15: 10,492,848 (GRCm39)		probably benign	Het
Rims1	G	T	1: 22,573,028 (GRCm39)	P391Q	probably benign	Het
Rnd2	C	T	11: 101,359,825 (GRCm39)	L57F	probably damaging	Het
Sf3b3	C	T	8: 111,542,961 (GRCm39)	R832Q	probably benign	Het
Slc12a2	A	G	18: 58,068,035 (GRCm39)	D975G	possibly damaging	Het
Slitrk6	A	G	14: 110,987,811 (GRCm39)	L632P	probably damaging	Het
Spire2	A	G	8: 124,095,523 (GRCm39)	D542G	possibly damaging	Het
Sppl3	A	T	5: 115,220,373 (GRCm39)	Q95L	probably damaging	Het
Stat5b	C	A	11: 100,675,080 (GRCm39)	E710*	probably null	Het
Tcl1	G	T	12: 105,188,872 (GRCm39)	H14N	probably damaging	Het
Ten1	T	C	11: 116,096,555 (GRCm39)	F70L	probably benign	Het
Tnfrsf13b	A	T	11: 61,031,763 (GRCm39)	T35S	possibly damaging	Het
Tpcn2	G	A	7: 144,821,046 (GRCm39)	P336L	probably benign	Het
Trf	C	A	9: 103,105,247 (GRCm39)	D22Y	probably damaging	Het
Ttyh1	A	G	7: 4,136,943 (GRCm39)		probably benign	Het
Vmn2r103	A	T	17: 20,032,031 (GRCm39)	I602F	probably benign	Het
Zfp296	G	T	7: 19,313,637 (GRCm39)	C164F	possibly damaging	Het
Zfp352	A	G	4: 90,112,541 (GRCm39)	Y227C	probably damaging	Het
Zfp599	A	T	9: 22,169,419 (GRCm39)	W18R	probably damaging	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
R6010:Nanog	UTSW	6	122,690,255 (GRCm39)	missense	probably benign	0.16
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'- TGATCTTTCCTTCTAGACACTGAG -3'
(R):5'- TAGAAGGCCAACGTATCACCG -3'

Sequencing Primer
(F):5'- ACTGACATGAGTGTGGGT -3'
(R):5'- GGTCAAACTCAGAGGGGTTTCC -3'

Posted On

2016-04-15