Incidental Mutation 'R0280:Nanog'
ID 37449
Institutional Source Beutler Lab
Gene Symbol Nanog
Ensembl Gene ENSMUSG00000012396
Gene Name Nanog homeobox
Synonyms ENK, 2410002E02Rik, ecat4
MMRRC Submission 038502-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0280 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 122684448-122691592 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 122690357 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 229 (D229G)
Ref Sequence ENSEMBL: ENSMUSP00000108200 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000012540] [ENSMUST00000112580] [ENSMUST00000112581]
AlphaFold Q80Z64
Predicted Effect probably damaging
Transcript: ENSMUST00000012540
AA Change: D254G

PolyPhen 2 Score 0.958 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000012540
Gene: ENSMUSG00000012396
AA Change: D254G

DomainStartEndE-ValueType
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 damaging
Transcript: ENSMUST00000112580
AA Change: D229G

PolyPhen 2 Score 0.958 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000108199
Gene: ENSMUSG00000012396
AA Change: D229G

DomainStartEndE-ValueType
HOX 71 133 5.33e-22 SMART
low complexity region 181 205 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000112581
AA Change: D229G

PolyPhen 2 Score 0.958 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000108200
Gene: ENSMUSG00000012396
AA Change: D229G

DomainStartEndE-ValueType
HOX 71 133 5.33e-22 SMART
low complexity region 181 205 N/A INTRINSIC
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 96.9%
  • 20x: 94.6%
Validation Efficiency 96% (55/57)
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: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acsbg3 T A 17: 57,192,169 (GRCm39) Y577* probably null Het
Adam18 C T 8: 25,164,070 (GRCm39) G38R probably benign Het
Ankrd16 T G 2: 11,786,312 (GRCm39) V187G probably damaging Het
Ccdc110 A T 8: 46,396,487 (GRCm39) N793Y probably benign Het
Ccdc170 T C 10: 4,508,663 (GRCm39) I629T possibly damaging Het
Clcn6 A G 4: 148,093,172 (GRCm39) L836P probably damaging Het
Colgalt2 G T 1: 152,384,312 (GRCm39) A551S possibly damaging Het
Crocc T C 4: 140,755,737 (GRCm39) E1097G probably damaging Het
Csmd1 A T 8: 16,321,616 (GRCm39) V494E probably damaging Het
Drg1 A T 11: 3,206,537 (GRCm39) probably null Het
Dscam T C 16: 96,840,206 (GRCm39) K134E possibly damaging Het
Dyrk1b T C 7: 27,883,737 (GRCm39) Y198H probably damaging Het
Esr1 A G 10: 4,806,951 (GRCm39) D289G probably benign Het
Esr1 G T 10: 4,889,289 (GRCm39) V396F probably damaging Het
Evi5l T C 8: 4,243,133 (GRCm39) V339A probably damaging Het
Fat4 A T 3: 38,944,965 (GRCm39) Q1286L probably benign Het
Fcsk A T 8: 111,621,380 (GRCm39) V188D probably damaging Het
Frem1 T C 4: 82,887,681 (GRCm39) H1118R probably damaging Het
Fut9 C T 4: 25,619,852 (GRCm39) D321N probably benign Het
Gaa T G 11: 119,175,373 (GRCm39) V917G probably damaging Het
Gm973 GCC GC 1: 59,583,839 (GRCm39) probably null Het
Kidins220 A G 12: 25,060,140 (GRCm39) T767A probably damaging Het
Kif7 A G 7: 79,348,571 (GRCm39) S1257P probably benign Het
Ltn1 A G 16: 87,194,726 (GRCm39) L1391P probably damaging Het
Mast3 A G 8: 71,240,564 (GRCm39) V291A possibly damaging Het
Mast3 A G 8: 71,236,439 (GRCm39) Y681H probably damaging Het
Metrn C T 17: 26,014,109 (GRCm39) R239H probably benign Het
Mphosph10 C A 7: 64,026,451 (GRCm39) K666N possibly damaging Het
Mtbp C T 15: 55,449,857 (GRCm39) T433I probably benign Het
Mtmr2 A G 9: 13,710,545 (GRCm39) K365E probably damaging Het
Nkapd1 T C 9: 50,520,679 (GRCm39) T123A probably damaging Het
Npepps T C 11: 97,131,840 (GRCm39) N338S possibly damaging Het
Nphp4 T A 4: 152,636,393 (GRCm39) probably benign Het
Odad4 A T 11: 100,441,091 (GRCm39) K107N probably damaging Het
Or4g16 T C 2: 111,137,417 (GRCm39) F289S possibly damaging Het
Plcl2 A G 17: 50,914,062 (GRCm39) E357G probably damaging Het
Polb A T 8: 23,130,408 (GRCm39) Y173N probably damaging Het
R3hdm1 T A 1: 128,090,512 (GRCm39) S74T probably benign Het
Raet1d T A 10: 22,246,782 (GRCm39) C37S probably damaging Het
Reln G A 5: 22,432,511 (GRCm39) probably benign Het
Rps6kc1 T C 1: 190,541,197 (GRCm39) S369G probably damaging Het
Sgf29 A G 7: 126,270,743 (GRCm39) E108G probably benign Het
Sh3tc1 A G 5: 35,863,361 (GRCm39) L942P probably damaging Het
Slc22a27 A T 19: 7,874,187 (GRCm39) L188* probably null Het
Slc9a3 T A 13: 74,307,543 (GRCm39) I445N probably damaging Het
Sufu A T 19: 46,439,112 (GRCm39) probably benign Het
Tomm40 G A 7: 19,447,676 (GRCm39) T118I probably damaging Het
Ttn C T 2: 76,570,823 (GRCm39) R26690H probably damaging Het
Vmn2r16 A G 5: 109,488,005 (GRCm39) I293V possibly damaging Het
Vmn2r68 T A 7: 84,882,457 (GRCm39) probably benign Het
Vmn2r68 C G 7: 84,882,466 (GRCm39) probably null Het
Vsig8 A G 1: 172,389,105 (GRCm39) D119G probably benign Het
Other mutations in Nanog
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
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'- ACCTCTTTCAGAAGGGCTCAGCAC -3'
(R):5'- TCACCTGGTGGAGTCACAGAGTAG -3'

Sequencing Primer
(F):5'- GGAGTATCCCAGCATCCATTG -3'
(R):5'- GTTCAGGAATAATTCCAAGGCTTGTG -3'
Posted On 2013-05-23