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: 0.411) question?
Stock # R5216 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 74593324-74595486 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 74594695 bp (GRCm39)
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

DomainStartEndE-ValueType
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: 55,107,947 (GRCm39) V84D probably damaging Het
Abcb1b T C 5: 8,863,705 (GRCm39) V220A probably benign Het
Actg1 A T 11: 120,238,580 (GRCm39) M82K probably damaging Het
Ahi1 T C 10: 20,835,975 (GRCm39) S103P probably benign Het
Aldh1b1 G T 4: 45,803,652 (GRCm39) G397C probably damaging Het
Arhgef3 A G 14: 27,123,799 (GRCm39) T507A probably benign Het
Atg7 A G 6: 114,701,910 (GRCm39) D682G probably damaging Het
Atp13a3 A G 16: 30,159,102 (GRCm39) I783T probably damaging Het
Atp9a T C 2: 168,516,808 (GRCm39) I362V probably benign Het
Birc6 T A 17: 74,920,465 (GRCm39) I168K probably damaging Het
Brca2 T A 5: 150,466,445 (GRCm39) Y2070N probably damaging Het
Cabp7 A G 11: 4,688,873 (GRCm39) I199T probably damaging Het
Cacng5 A G 11: 107,768,315 (GRCm39) F231L possibly damaging Het
Cngb3 T A 4: 19,415,729 (GRCm39) V413D possibly damaging Het
Col24a1 G A 3: 145,021,071 (GRCm39) E481K possibly damaging Het
Cspg4b G A 13: 113,478,947 (GRCm39) C1497Y probably benign Het
Ctr9 T A 7: 110,644,665 (GRCm39) I560N possibly damaging Het
Dip2b C T 15: 100,109,867 (GRCm39) R1451C probably damaging Het
Fat3 T C 9: 16,288,833 (GRCm39) D230G probably damaging Het
Gramd4 G A 15: 86,018,986 (GRCm39) probably null Het
Grb14 C T 2: 64,747,653 (GRCm39) V369I probably benign Het
Kcnc4 A G 3: 107,346,757 (GRCm39) S623P probably benign Het
Klhl20 A G 1: 160,921,249 (GRCm39) probably null Het
Lamc1 C A 1: 153,103,442 (GRCm39) V1375L probably damaging Het
Lpin2 C T 17: 71,549,755 (GRCm39) S640L probably damaging Het
Ltbp4 AATTCAGGCCAAGGCTGGGATTCAGGCCGAGGCCGGGATTCAGGCCTAGGCTGGGATTCAGGC AATTCAGGCCTAGGCTGGGATTCAGGC 7: 27,026,736 (GRCm39) probably benign Het
Mgll T A 6: 88,743,311 (GRCm39) C110* probably null Het
Mmp14 A G 14: 54,675,120 (GRCm39) N251D possibly damaging Het
Or1e33 A T 11: 73,738,262 (GRCm39) S230T probably damaging Het
Or52k2 A G 7: 102,254,028 (GRCm39) T156A probably benign Het
Or7e166 T A 9: 19,624,585 (GRCm39) V154E probably benign Het
Pfkl T G 10: 77,845,504 (GRCm39) D5A probably damaging Het
Pik3c3 A G 18: 30,406,029 (GRCm39) Y9C probably damaging Het
Pkhd1l1 T A 15: 44,359,043 (GRCm39) Y417* probably null Het
Rptor G A 11: 119,734,539 (GRCm39) G514D probably damaging Het
Sulf1 T A 1: 12,867,098 (GRCm39) M94K probably benign Het
Synrg A G 11: 83,873,022 (GRCm39) T157A probably damaging Het
Syt1 T C 10: 108,478,118 (GRCm39) N102S probably benign Het
Tnip2 C T 5: 34,661,149 (GRCm39) R101H probably damaging Het
Trmt2a A G 16: 18,070,048 (GRCm39) D421G probably benign Het
Vmn1r67 A G 7: 10,181,090 (GRCm39) D57G probably benign Het
Wnt2b A G 3: 104,868,661 (GRCm39) L43P possibly damaging Het
Zfp113 C T 5: 138,148,977 (GRCm39) D56N probably damaging Het
Zfp184 C T 13: 22,134,406 (GRCm39) L69F probably damaging Het
Zyx T C 6: 42,333,466 (GRCm39) V464A probably damaging Het
Other mutations in Hoxd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
R1699:Hoxd1 UTSW 2 74,594,626 (GRCm39) missense probably benign 0.35
R1830:Hoxd1 UTSW 2 74,593,866 (GRCm39) missense probably damaging 1.00
R2008:Hoxd1 UTSW 2 74,594,524 (GRCm39) missense possibly damaging 0.91
R2067:Hoxd1 UTSW 2 74,593,710 (GRCm39) missense probably benign 0.09
R2111:Hoxd1 UTSW 2 74,593,710 (GRCm39) missense probably benign 0.09
R2273:Hoxd1 UTSW 2 74,594,501 (GRCm39) missense probably damaging 1.00
R2274:Hoxd1 UTSW 2 74,594,501 (GRCm39) missense probably damaging 1.00
R2275:Hoxd1 UTSW 2 74,594,501 (GRCm39) missense probably damaging 1.00
R5242:Hoxd1 UTSW 2 74,593,792 (GRCm39) missense probably damaging 0.99
R6640:Hoxd1 UTSW 2 74,593,606 (GRCm39) missense probably damaging 0.98
R7359:Hoxd1 UTSW 2 74,594,447 (GRCm39) missense probably damaging 1.00
R7442:Hoxd1 UTSW 2 74,593,903 (GRCm39) missense probably damaging 1.00
R7836:Hoxd1 UTSW 2 74,593,816 (GRCm39) missense probably benign 0.25
R7942:Hoxd1 UTSW 2 74,594,504 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TAACTAGAGCCCGACGCATC -3'
(R):5'- ATACACAGCCTCTGGAACTCAG -3'

Sequencing Primer
(F):5'- GCATCGAGATAGCCAACTGTTTAC -3'
(R):5'- CTGGAACTCAGAAGCCAATTTAG -3'
Posted On 2016-07-22