Incidental Mutation 'IGL02636:Hoxd3'
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ID301509
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Hoxd3
Ensembl Gene ENSMUSG00000079277
Gene Namehomeobox D3
SynonymsHox-4.1, Hox-5.5
Accession Numbers
Is this an essential gene? Possibly essential (E-score: 0.729) question?
Stock #IGL02636
Quality Score
Status
Chromosome2
Chromosomal Location74711927-74748442 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) G to A at 74746954 bp
ZygosityHeterozygous
Amino Acid Change Alanine to Threonine at position 393 (A393T)
Ref Sequence ENSEMBL: ENSMUSP00000107614 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047830] [ENSMUST00000053932] [ENSMUST00000111982] [ENSMUST00000111983] [ENSMUST00000140666] [ENSMUST00000144544]
Predicted Effect probably benign
Transcript: ENSMUST00000047830
AA Change: A393T

PolyPhen 2 Score 0.319 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000044809
Gene: ENSMUSG00000079277
AA Change: A393T

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 noncoding transcript
Transcript: ENSMUST00000100000
Predicted Effect probably benign
Transcript: ENSMUST00000111982
AA Change: A393T

PolyPhen 2 Score 0.319 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000107613
Gene: ENSMUSG00000079277
AA Change: A393T

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: ENSMUST00000111983
AA Change: A393T

PolyPhen 2 Score 0.319 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000107614
Gene: ENSMUSG00000079277
AA Change: A393T

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152462
Predicted Effect noncoding transcript
Transcript: ENSMUST00000190553
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229136
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230341
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230511
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230540
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230704
Coding Region Coverage
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: 32 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Alms1 C A 6: 85,628,654 Q1960K probably benign Het
Arhgef40 T A 14: 51,997,408 V1056E probably damaging Het
Cdh26 T A 2: 178,449,962 F105I probably damaging Het
Cep162 A T 9: 87,248,379 D59E possibly damaging Het
Cngb3 A T 4: 19,396,690 T348S probably damaging Het
Eci3 A T 13: 34,946,980 probably null Het
Gapvd1 A G 2: 34,725,404 I409T probably benign Het
Golga2 T C 2: 32,296,723 probably null Het
Htr5a T C 5: 27,842,660 F71S probably damaging Het
Hyou1 T C 9: 44,381,410 probably null Het
Igsf6 C A 7: 121,067,280 probably benign Het
Klrb1c C A 6: 128,788,552 C25F probably benign Het
Lrguk C A 6: 34,090,188 T483K probably damaging Het
Lrpprc A T 17: 84,753,104 probably benign Het
Lrrk1 A T 7: 66,308,659 probably null Het
Megf8 G A 7: 25,358,432 G2098D probably damaging Het
Nfkbia T C 12: 55,491,173 Q165R possibly damaging Het
Nipsnap2 A G 5: 129,745,290 probably benign Het
Phykpl C T 11: 51,598,713 T382I probably damaging Het
Prdm10 A G 9: 31,329,681 D206G possibly damaging Het
Rab26 T C 17: 24,533,559 S9G probably benign Het
Sema3e C A 5: 14,225,656 N258K probably benign Het
Slfn10-ps T A 11: 83,030,145 noncoding transcript Het
Tgm5 A T 2: 121,076,796 C149S probably damaging Het
Timp4 C T 6: 115,249,824 probably null Het
Traf7 T C 17: 24,512,990 K251E probably benign Het
Ugcg G T 4: 59,207,763 R34L possibly damaging Het
Unc13d T C 11: 116,073,618 H300R probably damaging Het
Vmn1r20 G T 6: 57,431,761 C24F probably benign Het
Vmn2r13 T C 5: 109,192,017 R31G probably damaging Het
Vsig10l A G 7: 43,463,578 T87A possibly damaging Het
Zfp353-ps T A 8: 42,082,440 noncoding transcript Het
Other mutations in Hoxd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03017:Hoxd3 APN 2 74746706 missense possibly damaging 0.68
candide UTSW 2 74744076 missense probably damaging 1.00
compressed UTSW 2 74744306 nonsense probably null
R1977:Hoxd3 UTSW 2 74744276 missense possibly damaging 0.94
R2079:Hoxd3 UTSW 2 74744266 missense probably damaging 0.97
R2124:Hoxd3 UTSW 2 74744234 missense possibly damaging 0.92
R5143:Hoxd3 UTSW 2 74746372 missense probably damaging 1.00
R5250:Hoxd3 UTSW 2 74744306 nonsense probably null
R5256:Hoxd3 UTSW 2 74746867 missense possibly damaging 0.88
R5943:Hoxd3 UTSW 2 74746829 missense probably benign 0.00
R6300:Hoxd3 UTSW 2 74744076 missense probably damaging 1.00
R7362:Hoxd3 UTSW 2 74744219 missense possibly damaging 0.59
Posted On2015-04-16