Incidental Mutation 'R6663:Nkx2-9'
ID 526878
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 044783-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6663 (G1)
Quality Score 84.0076
Status Validated
Chromosome 12
Chromosomal Location 56658174-56660069 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 56658723 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Serine at position 164 (R164S)
Ref Sequence ENSEMBL: ENSMUSP00000072425 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000072631]
AlphaFold O70584
Predicted Effect probably benign
Transcript: ENSMUST00000072631
AA Change: R164S

PolyPhen 2 Score 0.121 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000072425
Gene: ENSMUSG00000058669
AA Change: R164S

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 0.4954 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.9%
  • 20x: 94.0%
Validation Efficiency 100% (32/32)
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
Ankrd17 A G 5: 90,411,923 (GRCm39) S1314P probably damaging Het
Btbd3 T A 2: 138,121,003 (GRCm39) I59K probably benign Het
Clcn2 A G 16: 20,521,995 (GRCm39) *865R probably null Het
Col22a1 T C 15: 71,691,908 (GRCm39) Q749R unknown Het
Cpsf2 T C 12: 101,965,852 (GRCm39) Y606H probably damaging Het
Csn1s1 T C 5: 87,823,599 (GRCm39) V154A probably benign Het
Cux1 T A 5: 136,514,701 (GRCm39) E23V probably damaging Het
Cyp2j9 C A 4: 96,467,679 (GRCm39) W269L probably benign Het
Dbf4 T C 5: 8,453,184 (GRCm39) M273V probably benign Het
Dnhd1 A G 7: 105,334,899 (GRCm39) probably null Het
Fezf1 A G 6: 23,247,527 (GRCm39) S183P probably damaging Het
Irx2 A G 13: 72,777,248 (GRCm39) Y23C probably damaging Het
Itga1 A T 13: 115,110,641 (GRCm39) N983K probably benign Het
Kifc1 A G 17: 34,100,430 (GRCm39) probably benign Het
Lrrc14b T C 13: 74,509,480 (GRCm39) N309S probably damaging Het
Lyst A T 13: 13,838,701 (GRCm39) probably null Het
Map1b T C 13: 99,566,530 (GRCm39) T2064A unknown Het
Mark3 T A 12: 111,541,517 (GRCm39) N11K probably benign Het
Med6 T A 12: 81,628,649 (GRCm39) D80V possibly damaging Het
Mfhas1 A G 8: 36,056,272 (GRCm39) E249G probably damaging Het
Mroh2b A G 15: 4,977,417 (GRCm39) I1256M probably benign Het
Or4p20 T A 2: 88,253,694 (GRCm39) N225I probably benign Het
Phf10 T C 17: 15,179,774 (GRCm39) D33G probably null Het
Plekha5 A G 6: 140,523,016 (GRCm39) M719V probably damaging Het
Pln A G 10: 53,219,792 (GRCm39) probably benign Het
Prg4 G A 1: 150,330,852 (GRCm39) probably benign Het
Slc35b3 A G 13: 39,138,112 (GRCm39) L99P probably damaging Het
Tbccd1 AT ATGT 16: 22,652,778 (GRCm39) probably null Het
Ube2j1 C T 4: 33,045,198 (GRCm39) S157L probably damaging Het
Zfp462 A G 4: 55,008,933 (GRCm39) T300A possibly damaging Het
Zfp668 G A 7: 127,466,941 (GRCm39) R212C probably damaging Het
Zup1 A G 10: 33,825,431 (GRCm39) M17T 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
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'- CCAAGTCTAGGGTGGCTTTAGG -3'
(R):5'- AGAATTGGGACTCCAGGTGG -3'

Sequencing Primer
(F):5'- TTTAGGCACTCCGCAGCAG -3'
(R):5'- TGTTCTCCAAGGCCCAGAC -3'
Posted On 2018-07-23