Incidental Mutation 'R1999:Hoxa3'
ID 224712
Institutional Source Beutler Lab
Gene Symbol Hoxa3
Ensembl Gene ENSMUSG00000079560
Gene Name homeobox A3
Synonyms Hox-1.5, Mo-10
MMRRC Submission 040009-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1999 (G1)
Quality Score 225
Status Not 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: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.0%
Validation Efficiency
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: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acot1 T A 12: 84,056,527 (GRCm39) W82R probably damaging Het
Adprm A G 11: 66,929,055 (GRCm39) V312A probably benign Het
Ambp C T 4: 63,067,666 (GRCm39) M181I possibly damaging Het
Anln A G 9: 22,244,348 (GRCm39) *1122Q probably null Het
Apc2 C T 10: 80,144,994 (GRCm39) T635I probably damaging Het
Arhgap32 A G 9: 32,027,436 (GRCm39) E2G possibly damaging Het
Bltp1 C T 3: 36,962,360 (GRCm39) T487I probably damaging Het
Ccdc63 C G 5: 122,265,628 (GRCm39) A71P possibly damaging Het
Ceacam5 A T 7: 17,481,172 (GRCm39) K306N possibly damaging Het
Cep295nl T C 11: 118,223,915 (GRCm39) R310G probably damaging Het
Ces2h A G 8: 105,746,977 (GRCm39) T538A probably benign Het
Dab2 T C 15: 6,446,398 (GRCm39) V5A probably benign Het
Diaph3 T A 14: 87,222,302 (GRCm39) D405V possibly damaging Het
Dync1h1 T C 12: 110,632,857 (GRCm39) probably null Het
Epha7 C T 4: 28,938,686 (GRCm39) Q514* probably null Het
Etfb C T 7: 43,103,987 (GRCm39) L141F probably benign Het
Fat1 T C 8: 45,405,430 (GRCm39) V727A probably damaging Het
Flt4 T C 11: 49,536,824 (GRCm39) Y1265H probably benign Het
Fndc3c1 C T X: 105,464,311 (GRCm39) E1276K probably benign Het
Ghdc T C 11: 100,660,018 (GRCm39) E243G probably benign Het
Gpld1 T C 13: 25,146,630 (GRCm39) V225A probably benign Het
Herc1 A G 9: 66,393,360 (GRCm39) T4080A probably benign Het
Htr5a G A 5: 28,055,887 (GRCm39) V293M possibly damaging Het
Itgb7 C T 15: 102,130,553 (GRCm39) V378M probably damaging Het
Kcnq5 T C 1: 21,472,428 (GRCm39) S811G probably null Het
Kcnt1 T A 2: 25,782,372 (GRCm39) H156Q probably benign Het
Kif1a T C 1: 92,988,517 (GRCm39) N507S probably damaging Het
Krt84 T C 15: 101,438,019 (GRCm39) E312G possibly damaging Het
Manea A G 4: 26,327,871 (GRCm39) L390P probably damaging Het
Mboat2 A G 12: 24,996,672 (GRCm39) D225G possibly damaging Het
Medag T A 5: 149,350,717 (GRCm39) F64Y probably damaging Het
Mtmr6 T A 14: 60,530,856 (GRCm39) S331R probably damaging Het
Myh1 A C 11: 67,113,234 (GRCm39) D1873A probably benign Het
Nek9 A G 12: 85,376,677 (GRCm39) W235R probably damaging Het
Nomo1 T C 7: 45,706,151 (GRCm39) S502P possibly damaging Het
Or10g6 A G 9: 39,933,985 (GRCm39) I99V probably benign Het
Or3a1b A G 11: 74,012,406 (GRCm39) Y97C probably benign Het
Or8k30 T A 2: 86,339,089 (GRCm39) Y95* probably null Het
Otof T A 5: 30,546,116 (GRCm39) E427D probably benign Het
Pclo T C 5: 14,727,094 (GRCm39) probably benign Het
Pkhd1l1 T G 15: 44,363,378 (GRCm39) probably null Het
Prl2c2 G C 13: 13,176,786 (GRCm39) T47R probably damaging Het
Pwwp4a G T X: 72,171,261 (GRCm39) G218C probably damaging Het
Rad21l T C 2: 151,496,621 (GRCm39) probably null Het
Rbbp6 T C 7: 122,589,575 (GRCm39) V459A probably damaging Het
Rsbn1l G A 5: 21,107,368 (GRCm39) H549Y probably damaging Het
Rsf1 CG CGACGGCGGTG 7: 97,229,115 (GRCm39) probably benign Het
Senp1 C T 15: 97,956,196 (GRCm39) V408I possibly damaging Het
Slc44a5 T C 3: 153,964,130 (GRCm39) F499L possibly damaging Het
Slitrk3 C T 3: 72,957,297 (GRCm39) V492I probably benign Het
Spef2 T A 15: 9,668,989 (GRCm39) probably null Het
Ssc5d A T 7: 4,945,713 (GRCm39) D915V possibly damaging Het
Stard9 A G 2: 120,523,349 (GRCm39) D668G probably damaging Het
Sycp2l A G 13: 41,271,780 (GRCm39) D73G probably benign Het
Tectb C G 19: 55,169,431 (GRCm39) probably benign Het
Tmem8b G A 4: 43,681,300 (GRCm39) C439Y probably damaging Het
Vmn1r195 C G 13: 22,462,934 (GRCm39) L135V possibly damaging Het
Vmn1r74 G T 7: 11,581,302 (GRCm39) V201F probably damaging Het
Vmn2r-ps158 A T 7: 42,696,883 (GRCm39) I647F probably damaging Het
Zfp956 G A 6: 47,940,805 (GRCm39) R388H probably damaging 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
R1180:Hoxa3 UTSW 6 52,147,382 (GRCm39) nonsense probably null
R1927:Hoxa3 UTSW 6 52,146,979 (GRCm39) unclassified probably benign
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'- TCATGGGCTCCACATAGCTG -3'
(R):5'- AGATGGCCAACCTGCTGAAC -3'

Sequencing Primer
(F):5'- GGTCCCATAGCTGCCATTG -3'
(R):5'- TGCTGAACCTCACCGAGC -3'
Posted On 2014-08-25