Incidental Mutation 'R6640:Hoxd1'
ID 543512
Institutional Source Beutler Lab
Gene Symbol Hoxd1
Ensembl Gene ENSMUSG00000042448
Gene Name homeobox D1
Synonyms Hox-4.9
MMRRC Submission 044761-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.375) question?
Stock # R6640 (G1)
Quality Score 50.0072
Status Validated
Chromosome 2
Chromosomal Location 74593324-74595486 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 74593606 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 54 (V54E)
Ref Sequence ENSEMBL: ENSMUSP00000043078 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047793]
AlphaFold Q01822
Predicted Effect probably damaging
Transcript: ENSMUST00000047793
AA Change: V54E

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000043078
Gene: ENSMUSG00000042448
AA Change: V54E

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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 97.9%
  • 20x: 93.6%
Validation Efficiency 97% (31/32)
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: 34 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2ml1 A T 6: 128,530,248 (GRCm39) N936K probably benign Het
Abca2 A T 2: 25,337,015 (GRCm39) Y2318F possibly damaging Het
Aldh1b1 A G 4: 45,803,868 (GRCm39) T469A possibly damaging Het
Aoc1l1 A G 6: 48,954,605 (GRCm39) D581G probably benign Het
Ccdc136 A G 6: 29,412,959 (GRCm39) D382G possibly damaging Het
Dapk1 A G 13: 60,864,628 (GRCm39) K141E probably damaging Het
Dnah6 A T 6: 73,001,276 (GRCm39) W3973R probably damaging Het
Dock10 G T 1: 80,511,555 (GRCm39) S1518* probably null Het
Elovl5 C A 9: 77,887,195 (GRCm39) Y195* probably null Het
Fbxl21 T A 13: 56,684,822 (GRCm39) W309R probably damaging Het
Gm10801 C CGTG 2: 98,494,152 (GRCm39) probably null Het
Gpx1 A G 9: 108,217,295 (GRCm39) D133G probably damaging Het
Kcnh3 T C 15: 99,139,649 (GRCm39) V876A probably benign Het
Klri2 G C 6: 129,709,158 (GRCm39) F231L probably benign Het
Mogat1 T G 1: 78,500,411 (GRCm39) S158R probably damaging Het
Myo1c C T 11: 75,562,461 (GRCm39) P918S probably benign Het
Or2ag13 T A 7: 106,313,247 (GRCm39) I214F probably damaging Het
Or8k16 T A 2: 85,520,279 (GRCm39) C169S probably damaging Het
Otog G A 7: 45,911,167 (GRCm39) A673T possibly damaging Het
Pigm T C 1: 172,205,254 (GRCm39) V330A probably damaging Het
Rab33b A G 3: 51,391,900 (GRCm39) T50A possibly damaging Het
Raver2 C T 4: 100,988,500 (GRCm39) P371L probably damaging Het
Rpl15-ps6 G T 15: 52,341,016 (GRCm39) noncoding transcript Het
Sh3rf2 T A 18: 42,234,705 (GRCm39) Y163N probably damaging Het
Slc1a1 T C 19: 28,871,970 (GRCm39) probably null Het
Slc6a18 T A 13: 73,812,401 (GRCm39) Y563F possibly damaging Het
Sp3 A G 2: 72,801,458 (GRCm39) L185P possibly damaging Het
Thbs2 T C 17: 14,893,630 (GRCm39) D850G possibly damaging Het
Tmem161b C A 13: 84,370,537 (GRCm39) probably benign Het
Tmtc2 T A 10: 105,409,610 (GRCm39) M1L probably benign Het
Trpm2 C T 10: 77,773,660 (GRCm39) R585Q probably benign Het
Trpm3 T A 19: 22,955,946 (GRCm39) I1126K probably damaging Het
Ugt1a6b A C 1: 88,035,516 (GRCm39) T285P probably benign Het
Vps13b A G 15: 35,617,842 (GRCm39) T1181A possibly 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
R5216:Hoxd1 UTSW 2 74,594,695 (GRCm39) missense probably damaging 0.97
R5242:Hoxd1 UTSW 2 74,593,792 (GRCm39) missense probably damaging 0.99
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'- ACTATTTACCTCGGGCTCGC -3'
(R):5'- GCCGCTGAGCAGGAATGATC -3'

Sequencing Primer
(F):5'- GCCTAGGTCGTGCGGAG -3'
(R):5'- CCGAGGTGGCATAGTGGAC -3'
Posted On 2019-02-13