Incidental Mutation 'R7804:Nkx2-9'
ID 600686
Institutional Source Beutler Lab
Gene Symbol Nkx2-9
Ensembl Gene ENSMUSG00000058669
Gene Name NK2 homeobox 9
Synonyms tinman, Nkx-2.9, Nkx2.9
MMRRC Submission 045859-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7804 (G1)
Quality Score 225.009
Status Validated
Chromosome 12
Chromosomal Location 56658174-56660069 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 56658917 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 99 (R99H)
Ref Sequence ENSEMBL: ENSMUSP00000072425 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000072631]
AlphaFold O70584
Predicted Effect probably damaging
Transcript: ENSMUST00000072631
AA Change: R99H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000072425
Gene: ENSMUSG00000058669
AA Change: R99H

DomainStartEndE-ValueType
HOX 81 143 5.04e-23 SMART
low complexity region 162 177 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.4%
Validation Efficiency 95% (55/58)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a homeobox-containing developmental regulator associated with liver development. The encoded protein binds to the alpha-fetoprotein (AFP) gene promoter and increases the expression of AFP. This gene is overexpressed in some lung cancers and is linked to poor patient survival, possibly due to its resistance to cisplatin. This gene is aberrantly methylated in pancreatic cancer, deleted in squamous cell lung carcinomas, and acts as a tumor suppressor in esophageal cancer. Mutations in this gene may also be a cause of neural tube defects. [provided by RefSeq, Dec 2015]
PHENOTYPE: Mutant mice lacking both functional copies of the gene are viable and fertile but display abnormal development of the spinal accessory nerve. Another mutant exhibits progressive bronchial dysplasia leading to lung cancer in aged mutants. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933415A04Rik GTGTGTATGTGT GTGTGT 11: 43,478,241 (GRCm39) probably benign Het
Ago4 A T 4: 126,406,423 (GRCm39) C296S probably benign Het
Apbb1 A G 7: 105,215,807 (GRCm39) L401P probably damaging Het
Cacnb2 C A 2: 14,972,848 (GRCm39) P252T probably benign Het
Ctnna2 C T 6: 77,618,357 (GRCm39) V202I probably benign Het
Dapk1 A T 13: 60,873,153 (GRCm39) I352F probably benign Het
Dexi T C 16: 10,360,349 (GRCm39) D69G possibly damaging Het
Dlg5 T C 14: 24,215,388 (GRCm39) E645G possibly damaging Het
Dnah3 A G 7: 119,551,841 (GRCm39) I2826T probably damaging Het
Dnah3 A G 7: 119,610,235 (GRCm39) W1734R probably damaging Het
Dtna A G 18: 23,728,666 (GRCm39) K287R probably damaging Het
Elovl5 A G 9: 77,887,105 (GRCm39) probably null Het
Ess2 T A 16: 17,729,031 (GRCm39) I47F probably damaging Het
Fam222b C A 11: 78,044,979 (GRCm39) P180Q probably benign Het
Fat3 C T 9: 15,901,888 (GRCm39) V3046I probably benign Het
Fem1a A G 17: 56,565,068 (GRCm39) D387G probably damaging Het
Frmd5 A G 2: 121,422,225 (GRCm39) Y33H probably damaging Het
Gucy2g A T 19: 55,216,584 (GRCm39) L464H probably benign Het
Ints2 T C 11: 86,103,489 (GRCm39) E1189G possibly damaging Het
Itgb4 T C 11: 115,894,510 (GRCm39) V1355A probably damaging Het
Lepr A T 4: 101,639,783 (GRCm39) S750C probably damaging Het
Lingo1 T C 9: 56,526,798 (GRCm39) D603G probably benign Het
Map4k3 A C 17: 80,922,499 (GRCm39) V474G probably damaging Het
Myl4 T A 11: 104,475,787 (GRCm39) V167E probably damaging Het
Naa25 T C 5: 121,562,652 (GRCm39) V478A probably benign Het
Neurl4 T A 11: 69,796,700 (GRCm39) L487H probably benign Het
Or4c110 C G 2: 88,831,855 (GRCm39) R259P unknown Het
Or52x1 A T 7: 104,853,367 (GRCm39) M61K probably damaging Het
Or6c76 A G 10: 129,612,091 (GRCm39) I103V probably benign Het
Pcdhga9 A G 18: 37,871,132 (GRCm39) I320M probably damaging Het
Pi15 T A 1: 17,695,137 (GRCm39) C251* probably null Het
Pkhd1l1 A T 15: 44,460,534 (GRCm39) K4248* probably null Het
Prkg1 C T 19: 30,556,032 (GRCm39) V625I probably benign Het
Prkg1 G A 19: 30,602,170 (GRCm39) A362V possibly damaging Het
Prol1 C T 5: 88,476,264 (GRCm39) T218I unknown Het
Ptpro G A 6: 137,376,599 (GRCm39) probably null Het
Rev3l T A 10: 39,699,481 (GRCm39) I1326K probably benign Het
Shank1 C A 7: 43,962,308 (GRCm39) R60S unknown Het
Slc24a2 A G 4: 86,909,774 (GRCm39) V648A probably damaging Het
Slc35d3 T C 10: 19,725,116 (GRCm39) T247A probably damaging Het
Specc1 C T 11: 62,096,223 (GRCm39) T895I probably damaging Het
Spta1 A G 1: 174,023,471 (GRCm39) E626G possibly damaging Het
Syngr2 C A 11: 117,703,401 (GRCm39) S72R possibly damaging Het
Synj2 T A 17: 6,069,809 (GRCm39) L490Q unknown Het
Tbc1d9 T C 8: 83,963,341 (GRCm39) L351P possibly damaging Het
Tcof1 G C 18: 60,962,123 (GRCm39) A702G possibly damaging Het
Themis3 G A 17: 66,862,605 (GRCm39) T451I probably benign Het
Tia1 T C 6: 86,401,364 (GRCm39) S146P probably benign Het
Tpp2 T A 1: 44,022,441 (GRCm39) N946K probably benign Het
Tpr A T 1: 150,308,310 (GRCm39) R1688S probably damaging Het
Trav12-1 A G 14: 53,775,988 (GRCm39) Q47R possibly damaging Het
Ttll9 G A 2: 152,844,278 (GRCm39) probably null Het
Ttn G A 2: 76,537,585 (GRCm39) T34781M possibly damaging Het
V1ra8 A G 6: 90,180,298 (GRCm39) Y167C probably damaging Het
Vegfb T C 19: 6,963,707 (GRCm39) D84G probably damaging Het
Vmn2r14 A T 5: 109,368,324 (GRCm39) L223M probably benign Het
Wdr26 A G 1: 181,010,387 (GRCm39) I554T probably damaging Het
Other mutations in Nkx2-9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02806:Nkx2-9 APN 12 56,658,705 (GRCm39) missense probably damaging 1.00
R1633:Nkx2-9 UTSW 12 56,659,766 (GRCm39) missense probably benign 0.01
R2349:Nkx2-9 UTSW 12 56,659,007 (GRCm39) missense probably benign 0.00
R6663:Nkx2-9 UTSW 12 56,658,723 (GRCm39) missense probably benign 0.12
R6872:Nkx2-9 UTSW 12 56,658,674 (GRCm39) missense probably benign
R7898:Nkx2-9 UTSW 12 56,659,031 (GRCm39) missense probably benign 0.02
Predicted Primers PCR Primer
(F):5'- CAGATGATGCTGCCATATCCG -3'
(R):5'- AGAATTGGGACTCCAGGTGG -3'

Sequencing Primer
(F):5'- GAAGGCTCTGTGATCCCAG -3'
(R):5'- AGACACCCGTAGAGGCTG -3'
Posted On 2019-11-26