Incidental Mutation 'R5216:Hoxd1'
ID 403463
Institutional Source Beutler Lab
Gene Symbol Hoxd1
Ensembl Gene ENSMUSG00000042448
Gene Name homeobox D1
Synonyms Hox-4.9
MMRRC Submission 042789-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.469) question?
Stock # R5216 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 74762980-74765142 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 74764351 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Asparagine to Tyrosine at position 317 (N317Y)
Ref Sequence ENSEMBL: ENSMUSP00000043078 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047793]
AlphaFold Q01822
Predicted Effect probably damaging
Transcript: ENSMUST00000047793
AA Change: N317Y

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000043078
Gene: ENSMUSG00000042448
AA Change: N317Y

low complexity region 13 25 N/A INTRINSIC
low complexity region 57 84 N/A INTRINSIC
low complexity region 140 150 N/A INTRINSIC
HOX 229 291 1.37e-24 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152462
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.5%
  • 20x: 95.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Antp homeobox family and encodes a protein with a homeobox DNA-binding domain. This nuclear protein functions as a sequence-specific transcription factor that is involved in differentiation and limb development. Mutations in this gene have been associated with severe developmental defects on the anterior-posterior (a-p) limb axis. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a reporter allele display abnormal cervical vertebrae. Mice homozygous for a knock-out allele exhibit abnormal nociceptor innervation of the skin, aberrant nociceptor axonal projections in the spinal cord, and deficits in pain sensitivity. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700097O09Rik A T 12: 55,061,162 V84D probably damaging Het
Abcb1b T C 5: 8,813,705 V220A probably benign Het
Actg1 A T 11: 120,347,754 M82K probably damaging Het
Ahi1 T C 10: 20,960,076 S103P probably benign Het
Aldh1b1 G T 4: 45,803,652 G397C probably damaging Het
Arhgef3 A G 14: 27,401,842 T507A probably benign Het
Atg7 A G 6: 114,724,949 D682G probably damaging Het
Atp13a3 A G 16: 30,340,284 I783T probably damaging Het
Atp9a T C 2: 168,674,888 I362V probably benign Het
BC067074 G A 13: 113,342,413 C1497Y probably benign Het
Birc6 T A 17: 74,613,470 I168K probably damaging Het
Brca2 T A 5: 150,542,980 Y2070N probably damaging Het
Cabp7 A G 11: 4,738,873 I199T probably damaging Het
Cacng5 A G 11: 107,877,489 F231L possibly damaging Het
Cngb3 T A 4: 19,415,729 V413D possibly damaging Het
Col24a1 G A 3: 145,315,310 E481K possibly damaging Het
Ctr9 T A 7: 111,045,458 I560N possibly damaging Het
Dip2b C T 15: 100,211,986 R1451C probably damaging Het
Fat3 T C 9: 16,377,537 D230G probably damaging Het
Gramd4 G A 15: 86,134,785 probably null Het
Grb14 C T 2: 64,917,309 V369I probably benign Het
Kcnc4 A G 3: 107,439,441 S623P probably benign Het
Klhl20 A G 1: 161,093,679 probably null Het
Lamc1 C A 1: 153,227,696 V1375L probably damaging Het
Lpin2 C T 17: 71,242,760 S640L probably damaging Het
Mgll T A 6: 88,766,329 C110* probably null Het
Mmp14 A G 14: 54,437,663 N251D possibly damaging Het
Olfr393 A T 11: 73,847,436 S230T probably damaging Het
Olfr552 A G 7: 102,604,821 T156A probably benign Het
Olfr857 T A 9: 19,713,289 V154E probably benign Het
Pfkl T G 10: 78,009,670 D5A probably damaging Het
Pik3c3 A G 18: 30,272,976 Y9C probably damaging Het
Pkhd1l1 T A 15: 44,495,647 Y417* probably null Het
Rptor G A 11: 119,843,713 G514D probably damaging Het
Sulf1 T A 1: 12,796,874 M94K probably benign Het
Synrg A G 11: 83,982,196 T157A probably damaging Het
Syt1 T C 10: 108,642,257 N102S probably benign Het
Tnip2 C T 5: 34,503,805 R101H probably damaging Het
Trmt2a A G 16: 18,252,184 D421G probably benign Het
Vmn1r67 A G 7: 10,447,163 D57G probably benign Het
Wnt2b A G 3: 104,961,345 L43P possibly damaging Het
Zfp113 C T 5: 138,150,715 D56N probably damaging Het
Zfp184 C T 13: 21,950,236 L69F probably damaging Het
Zyx T C 6: 42,356,532 V464A probably damaging Het
Other mutations in Hoxd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
R1699:Hoxd1 UTSW 2 74764282 missense probably benign 0.35
R1830:Hoxd1 UTSW 2 74763522 missense probably damaging 1.00
R2008:Hoxd1 UTSW 2 74764180 missense possibly damaging 0.91
R2067:Hoxd1 UTSW 2 74763366 missense probably benign 0.09
R2111:Hoxd1 UTSW 2 74763366 missense probably benign 0.09
R2273:Hoxd1 UTSW 2 74764157 missense probably damaging 1.00
R2274:Hoxd1 UTSW 2 74764157 missense probably damaging 1.00
R2275:Hoxd1 UTSW 2 74764157 missense probably damaging 1.00
R5242:Hoxd1 UTSW 2 74763448 missense probably damaging 0.99
R6640:Hoxd1 UTSW 2 74763262 missense probably damaging 0.98
R7359:Hoxd1 UTSW 2 74764103 missense probably damaging 1.00
R7442:Hoxd1 UTSW 2 74763559 missense probably damaging 1.00
R7836:Hoxd1 UTSW 2 74763472 missense probably benign 0.25
R7942:Hoxd1 UTSW 2 74764160 missense probably damaging 1.00
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2016-07-22