Mutagenetix > Incidental Mutation

Incidental Mutation 'R4770:Nanog'

367401

Institutional Source

Beutler Lab

Gene Symbol

Nanog

Ensembl Gene

ENSMUSG00000012396

Gene Name

Nanog homeobox

Synonyms

ENK, 2410002E02Rik, ecat4

MMRRC Submission

042410-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4770 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

122684448-122691592 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 122688550 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Alanine at position 44 (S44A)

Ref Sequence

ENSEMBL: ENSMUSP00000108200 (fasta)

Gene Model

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

AlphaFold

Q80Z64

Predicted Effect

possibly damaging
Transcript: ENSMUST00000012540
AA Change: S69A

PolyPhen 2 Score 0.626 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000012540
Gene: ENSMUSG00000012396
AA Change: S69A

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: S44A

PolyPhen 2 Score 0.626 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000108199
Gene: ENSMUSG00000012396
AA Change: S44A

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: S44A

PolyPhen 2 Score 0.626 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000108200
Gene: ENSMUSG00000012396
AA Change: S44A

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

0.1026

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.7%

Validation Efficiency

93% (89/96)

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8a	A	G	11: 109,962,341 (GRCm39)	V503A	possibly damaging	Het
Agps	T	A	2: 75,722,199 (GRCm39)	F463Y	possibly damaging	Het
Ajm1	G	A	2: 25,469,759 (GRCm39)	R51C	possibly damaging	Het
Amigo3	A	T	9: 107,930,734 (GRCm39)	L52F	probably damaging	Het
Anapc1	T	C	2: 128,527,980 (GRCm39)		probably benign	Het
Ankrd36	G	T	11: 5,540,870 (GRCm39)	C312F	possibly damaging	Het
Asic2	A	C	11: 80,862,318 (GRCm39)	D226E	probably benign	Het
Atp8b2	T	A	3: 89,864,374 (GRCm39)	Q197L	probably damaging	Het
C2cd3	A	G	7: 100,092,642 (GRCm39)	Y495C	probably damaging	Het
Ccdc51	A	G	9: 108,919,978 (GRCm39)	T125A	probably benign	Het
Ccser1	A	G	6: 61,288,485 (GRCm39)	Y216C	possibly damaging	Het
Cimap1b	A	G	15: 89,263,326 (GRCm39)	I19T	probably damaging	Het
Cntfr	A	T	4: 41,663,282 (GRCm39)	I175N	possibly damaging	Het
Cox10	G	A	11: 63,854,989 (GRCm39)	R431W	probably benign	Het
Cubn	T	C	2: 13,319,578 (GRCm39)	T2881A	possibly damaging	Het
Cyp2d9	T	A	15: 82,336,774 (GRCm39)	V41E	probably damaging	Het
Dmrtb1	C	T	4: 107,540,986 (GRCm39)	G125D	probably benign	Het
Dscaml1	C	T	9: 45,581,404 (GRCm39)	R408C	probably damaging	Het
Duox2	A	T	2: 122,115,397 (GRCm39)	S1052T	probably benign	Het
Ecm1	A	G	3: 95,645,273 (GRCm39)		probably benign	Het
Edrf1	G	T	7: 133,260,339 (GRCm39)	M83I	probably damaging	Het
Epb41l1	T	A	2: 156,371,344 (GRCm39)	M727K	probably benign	Het
Exosc9	T	C	3: 36,607,984 (GRCm39)	V64A	probably damaging	Het
Ezh2	A	T	6: 47,517,630 (GRCm39)	I564N	probably damaging	Het
Fam89b	C	A	19: 5,779,482 (GRCm39)	R25L	probably damaging	Het
Fgr	C	T	4: 132,714,602 (GRCm39)	T98M	probably damaging	Het
Fhip2b	T	A	14: 70,825,727 (GRCm39)	D351V	probably damaging	Het
Gapvd1	A	G	2: 34,581,193 (GRCm39)	S1089P	probably damaging	Het
Gbp5	A	T	3: 142,213,837 (GRCm39)	I544F	possibly damaging	Het
Gli2	C	A	1: 118,910,318 (GRCm39)		probably benign	Het
Gm9934	A	G	7: 92,702,192 (GRCm39)		noncoding transcript	Het
Greb1	A	T	12: 16,731,357 (GRCm39)	D1660E	probably benign	Het
Gtf2i	T	A	5: 134,272,414 (GRCm39)	N750I	possibly damaging	Het
H2-DMb2	G	C	17: 34,367,698 (GRCm39)	D171H	probably damaging	Het
Il11ra1	A	G	4: 41,768,187 (GRCm39)	E366G	probably damaging	Het
Itga2b	A	G	11: 102,351,582 (GRCm39)	F581S	probably damaging	Het
Itsn2	T	A	12: 4,677,892 (GRCm39)	M83K	probably damaging	Het
Kif27	G	A	13: 58,492,191 (GRCm39)	T316M	probably damaging	Het
Lad1	A	T	1: 135,753,531 (GRCm39)	Q26L	probably damaging	Het
Lrrn3	T	A	12: 41,502,442 (GRCm39)	H625L	probably benign	Het
Mast1	A	G	8: 85,655,875 (GRCm39)	V155A	probably benign	Het
Mast3	G	A	8: 71,238,864 (GRCm39)	T480M	probably damaging	Het
Mpc1	C	T	17: 8,512,377 (GRCm39)		probably benign	Het
Mycbp2	T	A	14: 103,457,380 (GRCm39)	M1606L	probably benign	Het
Myo1c	T	A	11: 75,551,139 (GRCm39)	L238*	probably null	Het
Neb	T	C	2: 52,039,165 (GRCm39)	Q6958R	probably benign	Het
Ngef	C	T	1: 87,405,283 (GRCm39)	R709H	probably damaging	Het
Nr1d1	A	G	11: 98,661,471 (GRCm39)	V265A	probably benign	Het
Nr3c2	A	G	8: 77,634,872 (GRCm39)		probably null	Het
Olfm5	A	G	7: 103,809,685 (GRCm39)	S164P	probably benign	Het
Parvb	T	C	15: 84,188,106 (GRCm39)		probably null	Het
Pde4dip	G	T	3: 97,674,400 (GRCm39)	A172D	probably damaging	Het
Phf2	A	G	13: 48,957,079 (GRCm39)	L1096P	probably damaging	Het
Pik3r6	T	A	11: 68,420,720 (GRCm39)	V155E	probably damaging	Het
Pinx1	T	G	14: 64,109,820 (GRCm39)	V124G	probably damaging	Het
Poglut1	A	G	16: 38,355,119 (GRCm39)	Y236H	probably damaging	Het
Pou4f2	T	A	8: 79,163,030 (GRCm39)	M2L	unknown	Het
Ppfia2	G	C	10: 106,597,978 (GRCm39)	L180F	probably damaging	Het
Pramel26	C	T	4: 143,538,519 (GRCm39)	E151K	probably damaging	Het
Prkaca	A	G	8: 84,717,499 (GRCm39)	N209S	probably benign	Het
Ring1	G	A	17: 34,242,361 (GRCm39)	P49S	probably damaging	Het
Rnf20	T	A	4: 49,633,412 (GRCm39)		probably null	Het
Rnf25	G	A	1: 74,633,099 (GRCm39)	R418C	probably damaging	Het
Ryr1	G	T	7: 28,808,707 (GRCm39)	P462Q	probably damaging	Het
Serpinb3d	A	G	1: 107,006,008 (GRCm39)	F360S	probably damaging	Het
Setd7	T	C	3: 51,428,843 (GRCm39)	E329G	probably damaging	Het
Slco2b1	C	T	7: 99,320,156 (GRCm39)		probably null	Het
Snap91	G	A	9: 86,655,654 (GRCm39)	T844I	possibly damaging	Het
Snhg5	C	T	9: 88,404,424 (GRCm39)		noncoding transcript	Het
Son	T	A	16: 91,455,756 (GRCm39)	V1501E	probably damaging	Het
Syncrip	T	A	9: 88,361,905 (GRCm39)	E70V	probably damaging	Het
Tas2r125	A	G	6: 132,886,750 (GRCm39)	D46G	probably damaging	Het
Tmem115	G	A	9: 107,412,156 (GRCm39)	R160Q	probably benign	Het
Trerf1	G	A	17: 47,630,581 (GRCm39)		noncoding transcript	Het
Tut7	A	G	13: 59,920,698 (GRCm39)		probably benign	Het
Uggt2	A	T	14: 119,266,466 (GRCm39)		probably null	Het
Ush2a	G	T	1: 188,282,076 (GRCm39)	V1864F	probably benign	Het
Xkr4	A	T	1: 3,286,714 (GRCm39)	V492D	probably damaging	Het
Zfp646	T	A	7: 127,482,649 (GRCm39)	S1609T	possibly damaging	Het
Zfp65	A	T	13: 67,856,477 (GRCm39)	H277Q	probably damaging	Het
Zfp69	A	G	4: 120,791,614 (GRCm39)	S176P	probably damaging	Het
Zfp747	C	T	7: 126,974,971 (GRCm39)	A10T	probably damaging	Het
Zfp850	T	C	7: 27,684,411 (GRCm39)		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
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
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'- GGGGTGACAAAGTATTCCAAGA -3'
(R):5'- TGCTGGAGGCTGAGGTAC -3'

Sequencing Primer
(F):5'- TTTGAACTCAGGACCTTCGGAAG -3'
(R):5'- GAGGTACTTCTGCTTCTGAAACCTG -3'

Posted On

2015-12-29