Incidental Mutation 'R7362:Hoxd3'
ID 571395
Institutional Source Beutler Lab
Gene Symbol Hoxd3
Ensembl Gene ENSMUSG00000079277
Gene Name homeobox D3
Synonyms Hox-5.5, Hox-4.1
MMRRC Submission 045375-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.858) question?
Stock # R7362 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 74542337-74578615 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 74574563 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 70 (I70V)
Ref Sequence ENSEMBL: ENSMUSP00000107614 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047830] [ENSMUST00000053932] [ENSMUST00000111982] [ENSMUST00000111983] [ENSMUST00000140666] [ENSMUST00000144544]
AlphaFold P09027
Predicted Effect possibly damaging
Transcript: ENSMUST00000047830
AA Change: I70V

PolyPhen 2 Score 0.588 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000044809
Gene: ENSMUSG00000079277
AA Change: I70V

DomainStartEndE-ValueType
low complexity region 93 135 N/A INTRINSIC
low complexity region 141 159 N/A INTRINSIC
HOX 195 257 5.83e-28 SMART
Pfam:DUF4074 369 431 8.9e-35 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000053932
SMART Domains Protein: ENSMUSP00000051355
Gene: ENSMUSG00000100642

DomainStartEndE-ValueType
low complexity region 93 135 N/A INTRINSIC
low complexity region 141 159 N/A INTRINSIC
HOX 195 257 5.83e-28 SMART
Pfam:DUF4074 370 431 1.4e-33 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000111982
AA Change: I70V

PolyPhen 2 Score 0.588 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000107613
Gene: ENSMUSG00000079277
AA Change: I70V

DomainStartEndE-ValueType
low complexity region 93 135 N/A INTRINSIC
low complexity region 141 159 N/A INTRINSIC
HOX 195 257 5.83e-28 SMART
Pfam:DUF4074 369 431 8.9e-35 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000111983
AA Change: I70V

PolyPhen 2 Score 0.588 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000107614
Gene: ENSMUSG00000079277
AA Change: I70V

DomainStartEndE-ValueType
low complexity region 93 135 N/A INTRINSIC
low complexity region 141 159 N/A INTRINSIC
HOX 195 257 5.83e-28 SMART
Pfam:DUF4074 369 431 8.9e-35 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000140666
SMART Domains Protein: ENSMUSP00000134616
Gene: ENSMUSG00000079277

DomainStartEndE-ValueType
HOX 35 97 5.83e-28 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000144544
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The protein encoded by this gene may play a role in the regulation of cell adhesion processes. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele show partial postnatal lethality, asymmetric rib-sternum attachment, and anterior transformations of the cervical vertebrae I (atlas) and II (axis). Mice homozygous for a different knock-out allele lack the anteriorarch of the atlas and the dens of the axis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adprhl1 C T 8: 13,295,534 (GRCm39) R193K probably damaging Het
Aoc1 G T 6: 48,882,345 (GRCm39) V74L probably benign Het
Bfsp1 G C 2: 143,668,795 (GRCm39) P601A probably benign Het
Bicd1 A C 6: 149,385,591 (GRCm39) K108T probably benign Het
Btbd18 C T 2: 84,491,887 (GRCm39) Q23* probably null Het
Ccser1 A G 6: 61,787,864 (GRCm39) I227M unknown Het
Cd151 G A 7: 141,049,502 (GRCm39) V70I probably benign Het
Cdh10 A G 15: 18,899,780 (GRCm39) T36A probably benign Het
Crb2 A G 2: 37,680,211 (GRCm39) T380A probably benign Het
Csmd3 A C 15: 47,619,388 (GRCm39) S1829A possibly damaging Het
Dgat2 A T 7: 98,803,843 (GRCm39) H359Q probably damaging Het
Dhdds T C 4: 133,698,441 (GRCm39) T298A probably benign Het
Egfem1 A G 3: 29,206,069 (GRCm39) Q102R probably benign Het
Eps15 T A 4: 109,223,439 (GRCm39) probably null Het
Ern1 T A 11: 106,327,949 (GRCm39) D61V probably damaging Het
Fcamr G A 1: 130,741,760 (GRCm39) R511Q possibly damaging Het
Grhpr T C 4: 44,987,255 (GRCm39) V213A probably benign Het
Gsx2 A G 5: 75,236,765 (GRCm39) D115G possibly damaging Het
Inpp5a A G 7: 139,158,296 (GRCm39) I408V probably benign Het
Kansl3 A T 1: 36,383,208 (GRCm39) D759E possibly damaging Het
Lrrc37a T G 11: 103,348,335 (GRCm39) T2787P unknown Het
Mier3 G A 13: 111,841,783 (GRCm39) G115S possibly damaging Het
Mkln1 T C 6: 31,445,103 (GRCm39) I333T probably benign Het
Myt1 T A 2: 181,439,033 (GRCm39) V227D probably benign Het
Or1a1 T C 11: 74,086,412 (GRCm39) F28L probably benign Het
Or52s1 T A 7: 102,861,861 (GRCm39) Y265N probably damaging Het
Or7e171-ps1 C T 9: 19,853,527 (GRCm39) D70N probably damaging Het
Pcf11 A G 7: 92,302,453 (GRCm39) L1219P possibly damaging Het
Pde6g T C 11: 120,338,950 (GRCm39) E80G probably damaging Het
Pkd1l3 GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA 8: 110,350,827 (GRCm39) probably benign Het
Ppp3cb T A 14: 20,573,719 (GRCm39) Q304L probably benign Het
Prr19 T C 7: 25,003,343 (GRCm39) L319P probably damaging Het
Prss23 C T 7: 89,158,972 (GRCm39) A366T probably damaging Het
Rock2 T C 12: 17,008,422 (GRCm39) L560P probably damaging Het
Simc1 A T 13: 54,687,517 (GRCm39) R95S probably damaging Het
Slc10a6 A T 5: 103,776,992 (GRCm39) V36E probably damaging Het
Slco1c1 A T 6: 141,515,189 (GRCm39) T695S probably benign Het
Spata31h1 T A 10: 82,128,831 (GRCm39) Q1393L possibly damaging Het
Ssh2 T C 11: 77,340,476 (GRCm39) F543L probably benign Het
Tecpr2 T A 12: 110,907,910 (GRCm39) V999D possibly damaging Het
Tnfsf10 A T 3: 27,389,497 (GRCm39) Y186F probably damaging Het
Tnk2 A T 16: 32,494,338 (GRCm39) probably null Het
Tram1 T C 1: 13,659,832 (GRCm39) M39V probably benign Het
Uck2 C T 1: 167,065,211 (GRCm39) V36I possibly damaging Het
Ugcg T A 4: 59,217,109 (GRCm39) M211K probably damaging Het
Vash2 A T 1: 190,692,496 (GRCm39) S226R probably damaging Het
Vmn1r172 T A 7: 23,359,841 (GRCm39) M242K probably damaging Het
Vmn2r82 A T 10: 79,232,451 (GRCm39) M817L probably benign Het
Vwa5b1 T C 4: 138,321,623 (GRCm39) N390S probably damaging Het
Wdr73 T A 7: 80,550,451 (GRCm39) D17V probably damaging Het
Wdr91 A T 6: 34,866,050 (GRCm39) S501T possibly damaging Het
Zfp454 A G 11: 50,777,194 (GRCm39) probably null Het
Other mutations in Hoxd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02636:Hoxd3 APN 2 74,577,298 (GRCm39) missense probably benign 0.32
IGL03017:Hoxd3 APN 2 74,577,050 (GRCm39) missense possibly damaging 0.68
candide UTSW 2 74,574,420 (GRCm39) missense probably damaging 1.00
compressed UTSW 2 74,574,650 (GRCm39) nonsense probably null
R1977:Hoxd3 UTSW 2 74,574,620 (GRCm39) missense possibly damaging 0.94
R2079:Hoxd3 UTSW 2 74,574,610 (GRCm39) missense probably damaging 0.97
R2124:Hoxd3 UTSW 2 74,574,578 (GRCm39) missense possibly damaging 0.92
R5143:Hoxd3 UTSW 2 74,576,716 (GRCm39) missense probably damaging 1.00
R5250:Hoxd3 UTSW 2 74,574,650 (GRCm39) nonsense probably null
R5256:Hoxd3 UTSW 2 74,577,211 (GRCm39) missense possibly damaging 0.88
R5943:Hoxd3 UTSW 2 74,577,173 (GRCm39) missense probably benign 0.00
R6300:Hoxd3 UTSW 2 74,574,420 (GRCm39) missense probably damaging 1.00
R9203:Hoxd3 UTSW 2 74,576,744 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- ACTTCCTGAGTGCACCATGC -3'
(R):5'- ACCCTTGGTCTTCTTGGCAG -3'

Sequencing Primer
(F):5'- GCACCATGCAGAAGGCTG -3'
(R):5'- ACTCCACTTCCAGGATTGGTAGG -3'
Posted On 2019-09-13