Incidental Mutation 'R1180:Hoxa3'
ID 101472
Institutional Source Beutler Lab
Gene Symbol Hoxa3
Ensembl Gene ENSMUSG00000079560
Gene Name homeobox A3
Synonyms Hox-1.5, Mo-10
MMRRC Submission 039252-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1180 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 52146042-52190316 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) A to C at 52147382 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Stop codon at position 290 (Y290*)
Ref Sequence ENSEMBL: ENSMUSP00000110077 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000114434] [ENSMUST00000128102] [ENSMUST00000134831]
AlphaFold P02831
Predicted Effect probably null
Transcript: ENSMUST00000114434
AA Change: Y290*
SMART Domains Protein: ENSMUSP00000110077
Gene: ENSMUSG00000079560
AA Change: Y290*

DomainStartEndE-ValueType
low complexity region 76 131 N/A INTRINSIC
HOX 192 254 3.35e-28 SMART
low complexity region 287 302 N/A INTRINSIC
low complexity region 304 326 N/A INTRINSIC
Pfam:DUF4074 377 441 9e-32 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000114435
Predicted Effect probably benign
Transcript: ENSMUST00000128102
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133723
Predicted Effect probably benign
Transcript: ENSMUST00000134831
Predicted Effect noncoding transcript
Transcript: ENSMUST00000136806
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139055
Predicted Effect noncoding transcript
Transcript: ENSMUST00000189230
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155922
Meta Mutation Damage Score 0.9714 question?
Coding Region Coverage
  • 1x: 98.8%
  • 3x: 97.8%
  • 10x: 94.5%
  • 20x: 87.5%
Validation Efficiency 98% (55/56)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted null mutations are athymic, aparathyroid, and exhibit reduced thyroid and submaxillary glands, defects of the IXth nerve, and frequently, heart and artery abnormalities. Mutants die neonatally. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610021A01Rik T A 7: 41,275,141 (GRCm39) D281E probably benign Het
Adam24 T G 8: 41,134,467 (GRCm39) V645G probably damaging Het
Apcdd1 A T 18: 63,070,168 (GRCm39) Y145F probably damaging Het
Cadps A G 14: 12,457,836 (GRCm38) probably benign Het
Camk1d A T 2: 5,366,836 (GRCm39) Y126* probably null Het
Chd8 A C 14: 52,458,565 (GRCm39) S848A probably damaging Het
Col6a3 T C 1: 90,709,577 (GRCm39) K1873R unknown Het
Cpd T C 11: 76,692,579 (GRCm39) T753A possibly damaging Het
Cxcr2 A T 1: 74,197,527 (GRCm39) D7V probably benign Het
Dock4 A G 12: 40,690,413 (GRCm39) E173G possibly damaging Het
EU599041 G A 7: 42,875,731 (GRCm39) noncoding transcript Het
Fer1l6 G A 15: 58,474,160 (GRCm39) probably benign Het
Flt3 T C 5: 147,278,048 (GRCm39) D842G probably damaging Het
Foxp4 G C 17: 48,191,278 (GRCm39) probably benign Het
Fsip2 T C 2: 82,805,570 (GRCm39) Y630H probably damaging Het
Gprin3 C A 6: 59,331,921 (GRCm39) V129F possibly damaging Het
Gstm1 A G 3: 107,922,127 (GRCm39) F170S probably damaging Het
Htra4 G T 8: 25,523,735 (GRCm39) L277I probably damaging Het
Jak2 A G 19: 29,259,899 (GRCm39) Y266C probably damaging Het
Kif6 T A 17: 50,139,284 (GRCm39) probably benign Het
Kiz C T 2: 146,811,927 (GRCm39) R679C unknown Het
Kyat3 A C 3: 142,443,531 (GRCm39) probably null Het
Mipep G A 14: 61,071,505 (GRCm39) V537I probably damaging Het
Mrpl44 T A 1: 79,755,677 (GRCm39) N94K probably damaging Het
Mstn A T 1: 53,103,167 (GRCm39) T168S possibly damaging Het
Mx2 G A 16: 97,357,209 (GRCm39) R434H probably damaging Het
Myh6 A G 14: 55,181,925 (GRCm39) I1792T possibly damaging Het
Myo16 T C 8: 10,446,908 (GRCm39) S450P probably damaging Het
Nherf4 T A 9: 44,160,543 (GRCm39) D284V probably benign Het
Nrbp1 T A 5: 31,403,157 (GRCm39) I210N probably damaging Het
Or3a1b A G 11: 74,012,406 (GRCm39) Y97C probably benign Het
Or5d16 G A 2: 87,773,490 (GRCm39) L161F probably benign Het
Pirb A T 7: 3,720,637 (GRCm39) L287Q probably benign Het
Pkhd1 C T 1: 20,655,381 (GRCm39) probably null Het
Psmd8 A T 7: 28,874,825 (GRCm39) V248E probably benign Het
Ranbp2 A G 10: 58,301,285 (GRCm39) Y646C probably damaging Het
Samsn1 C T 16: 75,670,536 (GRCm39) G189E probably damaging Het
Sec61g A C 11: 16,454,722 (GRCm39) probably benign Het
Sfmbt2 C T 2: 10,406,877 (GRCm39) H59Y probably damaging Het
Shb T C 4: 45,423,996 (GRCm39) I486V possibly damaging Het
Shf G A 2: 122,199,163 (GRCm39) P51S probably damaging Het
Spag16 G A 1: 69,962,817 (GRCm39) probably benign Het
Spink13 A G 18: 62,741,241 (GRCm39) probably benign Het
Tenm2 C T 11: 35,954,004 (GRCm39) G1236R possibly damaging Het
Tk1 A G 11: 117,712,921 (GRCm39) probably null Het
Tnni3k A T 3: 154,581,150 (GRCm39) H600Q probably damaging Het
Ttn A T 2: 76,800,047 (GRCm39) I387N probably damaging Het
Ube2q2 T C 9: 55,102,700 (GRCm39) probably benign Het
Utp14b C A 1: 78,643,162 (GRCm39) N353K probably damaging Het
Zfp474 C T 18: 52,771,814 (GRCm39) Q156* probably null Het
Other mutations in Hoxa3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01710:Hoxa3 APN 6 52,147,554 (GRCm39) unclassified probably benign
IGL02346:Hoxa3 APN 6 52,147,579 (GRCm39) unclassified probably benign
FR4342:Hoxa3 UTSW 6 52,147,110 (GRCm39) unclassified probably benign
IGL03052:Hoxa3 UTSW 6 52,147,267 (GRCm39) unclassified probably benign
PIT4515001:Hoxa3 UTSW 6 52,147,164 (GRCm39) missense unknown
R0197:Hoxa3 UTSW 6 52,147,123 (GRCm39) unclassified probably benign
R1017:Hoxa3 UTSW 6 52,149,386 (GRCm39) splice site probably null
R1927:Hoxa3 UTSW 6 52,146,979 (GRCm39) unclassified probably benign
R1999:Hoxa3 UTSW 6 52,147,382 (GRCm39) nonsense probably null
R4939:Hoxa3 UTSW 6 52,147,656 (GRCm39) unclassified probably benign
R5931:Hoxa3 UTSW 6 52,149,568 (GRCm39) missense probably damaging 1.00
R5995:Hoxa3 UTSW 6 52,147,263 (GRCm39) unclassified probably benign
R6658:Hoxa3 UTSW 6 52,147,058 (GRCm39) nonsense probably null
R7651:Hoxa3 UTSW 6 52,149,253 (GRCm39) missense unknown
R7853:Hoxa3 UTSW 6 52,147,267 (GRCm39) unclassified probably benign
R8274:Hoxa3 UTSW 6 52,147,524 (GRCm39) missense unknown
X0057:Hoxa3 UTSW 6 52,147,421 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- TTAGGCCAAAGAGTGGCCCAGAGTTG -3'
(R):5'- TGTTTCCGCAGACCAAGAGAGGAC -3'

Sequencing Primer
(F):5'- GGTCCCATAGCTGCCATTG -3'
(R):5'- AGCACTGAAGTCCTGCTCC -3'
Posted On 2014-01-15