Incidental Mutation 'R6872:Nkx2-9'
ID 536223
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 044969-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6872 (G1)
Quality Score 94.0077
Status Not validated
Chromosome 12
Chromosomal Location 56658174-56660069 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to G at 56658674 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Threonine at position 180 (N180T)
Ref Sequence ENSEMBL: ENSMUSP00000072425 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000072631]
AlphaFold O70584
Predicted Effect probably benign
Transcript: ENSMUST00000072631
AA Change: N180T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000072425
Gene: ENSMUSG00000058669
AA Change: N180T

DomainStartEndE-ValueType
HOX 81 143 5.04e-23 SMART
low complexity region 162 177 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.4%
  • 20x: 98.0%
Validation Efficiency
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadacl4 G A 4: 144,349,750 (GRCm39) V336I probably benign Het
Aadacl4fm4 A T 4: 144,397,216 (GRCm39) L172* probably null Het
Abcg3 T C 5: 105,083,860 (GRCm39) T637A probably benign Het
Ap3d1 G A 10: 80,550,156 (GRCm39) R692* probably null Het
Aqp2 C T 15: 99,481,885 (GRCm39) H260Y probably benign Het
Btbd2 C A 10: 80,480,166 (GRCm39) R383L probably damaging Het
Ccdc196 T A 12: 78,244,141 (GRCm39) D31E probably damaging Het
Ccdc24 T C 4: 117,727,123 (GRCm39) T196A probably benign Het
Cdc20b G A 13: 113,220,509 (GRCm39) G463S probably damaging Het
Ceacam5 A T 7: 17,486,212 (GRCm39) R570* probably null Het
Col12a1 A T 9: 79,584,516 (GRCm39) N1357K probably damaging Het
Cpa5 A T 6: 30,614,053 (GRCm39) Q65L probably benign Het
Ddo A C 10: 40,513,414 (GRCm39) M119L possibly damaging Het
Dnah8 G T 17: 30,981,653 (GRCm39) L3058F probably damaging Het
Dnajb8 A G 6: 88,200,022 (GRCm39) N186S probably damaging Het
Dock4 T C 12: 40,862,325 (GRCm39) probably null Het
Ear6 A G 14: 52,091,885 (GRCm39) Y144C probably damaging Het
Eng T A 2: 32,563,287 (GRCm39) I281N probably damaging Het
Fgf2 A G 3: 37,458,860 (GRCm39) K85E probably damaging Het
Fubp1 A T 3: 151,931,783 (GRCm39) Q37L probably benign Het
Gabra2 G T 5: 71,251,882 (GRCm39) P22T probably damaging Het
Gm10401 T C 5: 115,236,245 (GRCm39) probably benign Het
Gsdmc T C 15: 63,650,556 (GRCm39) D275G possibly damaging Het
Iglv3 A G 16: 19,060,034 (GRCm39) I98T probably damaging Het
Lmod1 G T 1: 135,292,879 (GRCm39) R578L probably damaging Het
Mindy2 A G 9: 70,524,044 (GRCm39) probably null Het
Neb G T 2: 52,183,657 (GRCm39) Q1004K probably damaging Het
Nlrp2 C T 7: 5,311,709 (GRCm39) R922H probably benign Het
Nol4l T C 2: 153,325,737 (GRCm39) E116G probably damaging Het
Or1af1 A T 2: 37,109,989 (GRCm39) M163L possibly damaging Het
Or5ac19 A G 16: 59,089,961 (GRCm39) L23P probably benign Het
Pcdhb20 A C 18: 37,639,218 (GRCm39) E581D probably benign Het
Pidd1 G T 7: 141,019,331 (GRCm39) T750K probably benign Het
Rab44 A G 17: 29,358,784 (GRCm39) E324G probably benign Het
Ramp3 T C 11: 6,624,768 (GRCm39) C21R possibly damaging Het
Rpap1 A C 2: 119,605,850 (GRCm39) M345R probably damaging Het
Serpina3k A C 12: 104,310,519 (GRCm39) K350Q probably benign Het
St13 C T 15: 81,250,547 (GRCm39) probably null Het
Stard9 A T 2: 120,544,549 (GRCm39) K4497* probably null Het
Tbx19 A T 1: 164,975,202 (GRCm39) probably null Het
Tgoln1 A G 6: 72,592,538 (GRCm39) V314A possibly damaging Het
Them4 A T 3: 94,231,678 (GRCm39) I172F probably damaging Het
Tmc7 T A 7: 118,146,846 (GRCm39) Y477F probably benign Het
Tmem132a A G 19: 10,840,669 (GRCm39) L421P probably damaging Het
Trim69 A G 2: 121,998,391 (GRCm39) E121G probably damaging Het
Vmn2r11 T G 5: 109,194,976 (GRCm39) R783S possibly damaging Het
Vmn2r62 T A 7: 42,438,412 (GRCm39) L141F probably benign Het
Zbtb7a A G 10: 80,983,905 (GRCm39) N449S possibly damaging Het
Zfhx3 C T 8: 109,527,273 (GRCm39) R1057W probably damaging Het
Zfp180 G T 7: 23,805,306 (GRCm39) C575F probably damaging Het
Zfp462 G A 4: 55,012,326 (GRCm39) A1431T probably benign Het
Zfp592 T C 7: 80,673,576 (GRCm39) V180A probably benign Het
Zfp605 C T 5: 110,275,311 (GRCm39) P143L probably benign Het
Zfp646 T C 7: 127,482,505 (GRCm39) S1561P probably benign Het
Zfp706 T C 15: 37,002,190 (GRCm39) T46A possibly 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
R7804:Nkx2-9 UTSW 12 56,658,917 (GRCm39) missense probably damaging 1.00
R7898:Nkx2-9 UTSW 12 56,659,031 (GRCm39) missense probably benign 0.02
Predicted Primers PCR Primer
(F):5'- CACCTCCTGACTTTGGTGTG -3'
(R):5'- CGCAGGTCAAGATCTGGTTC -3'

Sequencing Primer
(F):5'- CAATGTCCCAAGTCTAGGGTG -3'
(R):5'- CAGGTCAAGATCTGGTTCCAGAAC -3'
Posted On 2018-10-18