Incidental Mutation 'R2275:Hoxd1'
ID 242702
Institutional Source Beutler Lab
Gene Symbol Hoxd1
Ensembl Gene ENSMUSG00000042448
Gene Name homeobox D1
Synonyms Hox-4.9
MMRRC Submission 040274-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.411) question?
Stock # R2275 (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 G at 74594501 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 252 (K252R)
Ref Sequence ENSEMBL: ENSMUSP00000043078 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047793]
AlphaFold Q01822
Predicted Effect probably damaging
Transcript: ENSMUST00000047793
AA Change: K252R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000043078
Gene: ENSMUSG00000042448
AA Change: K252R

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: 99.1%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.6%
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: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2300003K06Rik A T 11: 99,728,667 (GRCm39) C59S possibly damaging Het
Abca5 A T 11: 110,166,107 (GRCm39) N1556K possibly damaging Het
Ackr1 T C 1: 173,160,052 (GRCm39) N156D probably benign Het
Aco2 C T 15: 81,779,465 (GRCm39) R57C probably benign Het
Adamtsl3 A T 7: 82,255,766 (GRCm39) S1593C probably benign Het
Adgrb2 G A 4: 129,900,647 (GRCm39) G333D probably damaging Het
Arhgef7 T A 8: 11,865,010 (GRCm39) F374Y possibly damaging Het
Atxn7 T A 14: 14,013,268 (GRCm38) M62K possibly damaging Het
C87436 G A 6: 86,422,582 (GRCm39) R52H probably damaging Het
Cacna1g T A 11: 94,306,762 (GRCm39) E1842V probably damaging Het
Cdh4 T C 2: 179,532,640 (GRCm39) S701P probably damaging Het
Cdr2 A T 7: 120,557,732 (GRCm39) H264Q possibly damaging Het
Cecr2 C T 6: 120,733,702 (GRCm39) S563L probably benign Het
Cfap276 A G 3: 108,449,819 (GRCm39) N33D possibly damaging Het
Col12a1 A T 9: 79,542,709 (GRCm39) V2352E probably damaging Het
Col9a2 C G 4: 120,911,455 (GRCm39) R599G probably damaging Het
Crygs C T 16: 22,624,301 (GRCm39) G102D possibly damaging Het
Csad G T 15: 102,095,557 (GRCm39) R167S probably damaging Het
Dnlz A T 2: 26,241,483 (GRCm39) C82S probably damaging Het
Ehmt2 T A 17: 35,129,691 (GRCm39) N951K possibly damaging Het
Emilin1 C T 5: 31,075,082 (GRCm39) P441L possibly damaging Het
Enpp2 A C 15: 54,761,190 (GRCm39) Y221D probably damaging Het
Exoc3l A T 8: 106,017,079 (GRCm39) probably null Het
F11 T C 8: 45,705,184 (GRCm39) D119G possibly damaging Het
Faiml T C 9: 99,111,612 (GRCm39) Y149C probably benign Het
Fn1 C T 1: 71,653,102 (GRCm39) G1296R probably null Het
Glg1 A T 8: 111,895,353 (GRCm39) Y819* probably null Het
Gm11568 A G 11: 99,749,070 (GRCm39) S92G unknown Het
Gm28042 A C 2: 119,867,310 (GRCm39) Q465P probably damaging Het
Gpatch1 A T 7: 34,988,103 (GRCm39) S678T probably benign Het
Gpr158 A T 2: 21,831,674 (GRCm39) M925L probably benign Het
Hecw1 T C 13: 14,520,653 (GRCm39) T195A probably benign Het
Iqck G A 7: 118,498,880 (GRCm39) D173N possibly damaging Het
Kcnh1 T G 1: 192,019,829 (GRCm39) V358G probably damaging Het
Kifap3 T A 1: 163,696,327 (GRCm39) V652D possibly damaging Het
Knl1 C A 2: 118,902,762 (GRCm39) Q1488K probably damaging Het
Map4k1 T A 7: 28,701,382 (GRCm39) H729Q probably damaging Het
Marchf1 T A 8: 66,840,151 (GRCm39) N311K probably benign Het
Mypn A G 10: 62,966,848 (GRCm39) F943L probably damaging Het
Nkpd1 A G 7: 19,257,822 (GRCm39) I534V probably benign Het
Nrarp T C 2: 25,071,421 (GRCm39) V100A possibly damaging Het
Nt5c1a T C 4: 123,109,873 (GRCm39) F324S probably damaging Het
Ntrk2 T A 13: 59,009,165 (GRCm39) Y319N probably damaging Het
Odad2 C A 18: 7,223,676 (GRCm39) G456W probably benign Het
Or5d41 A G 2: 88,055,167 (GRCm39) F70L probably benign Het
Parg A G 14: 32,017,195 (GRCm39) D384G probably damaging Het
Pde7b T A 10: 20,276,165 (GRCm39) *460L probably null Het
Pigr G T 1: 130,774,207 (GRCm39) V396L probably benign Het
Pkhd1 A G 1: 20,271,073 (GRCm39) I3160T possibly damaging Het
Ppl T C 16: 4,912,416 (GRCm39) S722G probably benign Het
Ppp1r26 A G 2: 28,342,713 (GRCm39) E781G possibly damaging Het
Rptor T A 11: 119,647,148 (GRCm39) C246* probably null Het
Rusc2 G A 4: 43,416,260 (GRCm39) R522H probably damaging Het
Senp7 T C 16: 56,005,146 (GRCm39) S927P probably damaging Het
Serpinb6d A T 13: 33,855,411 (GRCm39) M362L probably benign Het
Setx GTGGCT GT 2: 29,044,073 (GRCm39) 1814 probably null Het
Slc12a3 T A 8: 95,059,915 (GRCm39) I187N possibly damaging Het
Slc46a1 T G 11: 78,357,249 (GRCm39) S101A probably benign Het
Slc4a8 A G 15: 100,705,283 (GRCm39) M830V probably benign Het
Slco4a1 T C 2: 180,106,529 (GRCm39) L237P possibly damaging Het
Sned1 T A 1: 93,209,364 (GRCm39) probably null Het
Tia1 A G 6: 86,404,659 (GRCm39) N298S probably benign Het
Tsr1 A T 11: 74,795,653 (GRCm39) probably null Het
Ttc6 G A 12: 57,749,084 (GRCm39) V1339I probably benign Het
Tyrp1 A T 4: 80,755,771 (GRCm39) E180V probably damaging Het
Ubr3 T C 2: 69,846,685 (GRCm39) V1636A probably benign Het
Usp1 T C 4: 98,818,079 (GRCm39) L139P probably damaging Het
Vmn1r228 A G 17: 20,996,807 (GRCm39) L237P probably damaging Het
Vmn1r232 A G 17: 21,134,465 (GRCm39) L45P probably benign Het
Vmn2r2 T C 3: 64,023,930 (GRCm39) R884G probably benign Het
Vmn2r60 T A 7: 41,786,251 (GRCm39) Y351* probably null Het
Zbtb7a G A 10: 80,980,831 (GRCm39) V342I possibly damaging Het
Zdhhc11 C A 13: 74,121,871 (GRCm39) N127K 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
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
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'- AGCGCTTCTTCTGGTTCAGC -3'
(R):5'- CTGACCGGGGAAGCTTAATC -3'

Sequencing Primer
(F):5'- AGCTGTGTCCATCACTCAGGAG -3'
(R):5'- AGCTTAATCGAGGCCACAG -3'
Posted On 2014-10-16