Incidental Mutation 'R2349:Nkx2-9'
ID 247405
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 040331-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R2349 (G1)
Quality Score 105
Status Validated
Chromosome 12
Chromosomal Location 56658174-56660069 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 56659007 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Proline at position 69 (L69P)
Ref Sequence ENSEMBL: ENSMUSP00000072425 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000072631]
AlphaFold O70584
Predicted Effect probably benign
Transcript: ENSMUST00000072631
AA Change: L69P

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000072425
Gene: ENSMUSG00000058669
AA Change: L69P

DomainStartEndE-ValueType
HOX 81 143 5.04e-23 SMART
low complexity region 162 177 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000182105
Predicted Effect noncoding transcript
Transcript: ENSMUST00000182733
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191707
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.6%
Validation Efficiency 100% (34/34)
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: 32 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam34 T C 8: 44,105,415 (GRCm39) K77E probably damaging Het
Arfgef2 T A 2: 166,693,948 (GRCm39) I507N probably damaging Het
Atg16l2 T C 7: 100,945,746 (GRCm39) K231E probably damaging Het
C1s1 C A 6: 124,518,432 (GRCm39) probably benign Het
Cdh15 G A 8: 123,583,374 (GRCm39) R59H probably benign Het
Cntrl A G 2: 35,066,263 (GRCm39) T1739A probably benign Het
Col15a1 G A 4: 47,306,742 (GRCm39) M289I probably damaging Het
Crebbp G A 16: 3,956,774 (GRCm39) R350C probably damaging Het
Dbx2 A G 15: 95,522,840 (GRCm39) V289A probably benign Het
Esam A C 9: 37,439,527 (GRCm39) Q4P probably benign Het
Galnt1 A G 18: 24,413,085 (GRCm39) M462V probably benign Het
Got1l1 T C 8: 27,687,959 (GRCm39) T357A probably benign Het
Gpr182 T A 10: 127,586,806 (GRCm39) K48N probably damaging Het
Hdlbp A G 1: 93,349,956 (GRCm39) probably benign Het
Ifi209 G A 1: 173,470,122 (GRCm39) V237M probably damaging Het
Igf2r A T 17: 12,941,198 (GRCm39) probably null Het
Jmjd1c T C 10: 67,091,279 (GRCm39) M2520T probably benign Het
Krt222 A G 11: 99,129,591 (GRCm39) probably benign Het
Papss1 A G 3: 131,305,627 (GRCm39) D203G probably benign Het
Pex13 A G 11: 23,605,789 (GRCm39) M147T probably damaging Het
Pkd1l1 A T 11: 8,776,819 (GRCm39) probably null Het
Rac2 A G 15: 78,449,675 (GRCm39) V85A possibly damaging Het
Rock2 A G 12: 17,027,616 (GRCm39) N127S probably benign Het
Sfswap C T 5: 129,646,802 (GRCm39) R875C possibly damaging Het
Slco5a1 C T 1: 12,991,376 (GRCm39) V438M probably damaging Het
Thsd4 A G 9: 59,879,798 (GRCm39) Y620H probably benign Het
Trip4 T C 9: 65,773,844 (GRCm39) D246G probably benign Het
Usp10 T C 8: 120,683,448 (GRCm39) *88R probably null Het
Vars1 A G 17: 35,234,728 (GRCm39) I1186V probably benign Het
Vps13c A G 9: 67,864,808 (GRCm39) D3039G possibly damaging Het
Wwp1 A T 4: 19,638,644 (GRCm39) N566K possibly damaging Het
Xpo6 A T 7: 125,712,875 (GRCm39) V701E probably benign 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
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
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'- TGCAGATCAGATGATGCTGCC -3'
(R):5'- AGCAAGAGAATTGGGACTCC -3'

Sequencing Primer
(F):5'- TGATGCTGCCATATCCGAAG -3'
(R):5'- GAATTGGGACTCCAGGTGG -3'
Posted On 2014-11-11