Incidental Mutation 'IGL03403:Hoxd4'
ID421505
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Hoxd4
Ensembl Gene ENSMUSG00000101174
Gene Namehomeobox D4
SynonymsHox-4.2, Hox-5.1
Accession Numbers
Is this an essential gene? Possibly non essential (E-score: 0.292) question?
Stock #IGL03403
Quality Score
Status
Chromosome2
Chromosomal Location74711929-74729123 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to T at 74728337 bp
ZygosityHeterozygous
Amino Acid Change Glutamic Acid to Valine at position 168 (E168V)
Ref Sequence ENSEMBL: ENSMUSP00000107611 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047904] [ENSMUST00000053932] [ENSMUST00000111980] [ENSMUST00000111983] [ENSMUST00000144544]
Predicted Effect possibly damaging
Transcript: ENSMUST00000047904
AA Change: E168V

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000047949
Gene: ENSMUSG00000115956
AA Change: E168V

DomainStartEndE-ValueType
low complexity region 63 70 N/A INTRINSIC
low complexity region 91 110 N/A INTRINSIC
low complexity region 112 123 N/A INTRINSIC
HOX 152 214 2.46e-26 SMART
low complexity region 220 229 N/A INTRINSIC
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: ENSMUST00000083566
Predicted Effect possibly damaging
Transcript: ENSMUST00000111980
AA Change: E168V

PolyPhen 2 Score 0.931 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000107611
Gene: ENSMUSG00000101174
AA Change: E168V

DomainStartEndE-ValueType
low complexity region 63 70 N/A INTRINSIC
low complexity region 91 110 N/A INTRINSIC
low complexity region 112 123 N/A INTRINSIC
HOX 152 214 2.46e-26 SMART
low complexity region 220 229 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111983
SMART Domains Protein: ENSMUSP00000107614
Gene: ENSMUSG00000079277

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 noncoding transcript
Transcript: ENSMUST00000144040
Predicted Effect probably benign
Transcript: ENSMUST00000144544
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 determining positional values in developing limb buds. Alternatively spliced variants have been described but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Both homozygotes and heterozygotes for a targeted null mutation exhibit homeotic transformations of the second cervical vertebrae and malformed neural arches of C1 to C3 and of the basioccipital bone. Mutants show variable penetrance and expressivity. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2410089E03Rik A C 15: 8,201,342 K1034N probably damaging Het
Adamts12 T A 15: 11,241,488 I382N probably damaging Het
Adamts5 T C 16: 85,863,014 T797A probably damaging Het
Ahr A T 12: 35,504,326 V598E possibly damaging Het
Akap10 A G 11: 61,915,273 S210P probably benign Het
Asb5 G T 8: 54,583,547 probably benign Het
AU041133 T C 10: 82,138,344 V31A probably damaging Het
Bcar3 T C 3: 122,512,969 V197A probably benign Het
Bptf A G 11: 107,099,733 V510A possibly damaging Het
Ccar2 A T 14: 70,140,068 D712E probably damaging Het
Cenpt G A 8: 105,849,665 Q85* probably null Het
Ciita C A 16: 10,503,872 H98N probably damaging Het
Csn1s1 T A 5: 87,667,293 M16K probably benign Het
Fah A G 7: 84,593,209 I297T probably damaging Het
Fbxo25 A G 8: 13,929,423 N214D probably benign Het
Frem3 A C 8: 80,611,090 D4A probably benign Het
Gm12800 T C 4: 101,909,928 S125P probably benign Het
Gm3409 A G 5: 146,539,524 K162E probably benign Het
Gxylt1 T C 15: 93,261,775 D148G possibly damaging Het
Ifna6 A G 4: 88,827,458 S15G possibly damaging Het
Iqck T A 7: 118,876,271 H97Q probably benign Het
Kif16b T A 2: 142,711,869 E1003V probably damaging Het
Lrp1b G A 2: 40,702,824 P3761L probably benign Het
Mc4r C T 18: 66,859,526 C172Y possibly damaging Het
Olfr373 A G 8: 72,100,497 T246A probably benign Het
Oosp1 T A 19: 11,687,380 N104I probably damaging Het
Pram1 A T 17: 33,642,143 I513F probably damaging Het
Rasef A G 4: 73,734,534 S577P probably damaging Het
Rfx8 T C 1: 39,690,173 D144G possibly damaging Het
Rreb1 A C 13: 37,929,574 N303T possibly damaging Het
Rrn3 A T 16: 13,799,945 K351* probably null Het
Sox30 A T 11: 46,017,208 E734V probably damaging Het
Spns1 C T 7: 126,371,536 probably null Het
Tgfbr2 T A 9: 116,110,302 E177D probably benign Het
Tnfaip8l3 A G 9: 54,027,457 M78T possibly damaging Het
Vmn2r92 C T 17: 18,166,852 T151I probably damaging Het
Wwc1 A G 11: 35,915,284 Y41H possibly damaging Het
Zfp407 A T 18: 84,560,797 N730K probably damaging Het
Other mutations in Hoxd4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02034:Hoxd4 APN 2 74728406 missense probably damaging 0.98
R0153:Hoxd4 UTSW 2 74727457 missense probably damaging 0.96
R3424:Hoxd4 UTSW 2 74727313 missense probably damaging 1.00
R5447:Hoxd4 UTSW 2 74727343 missense probably damaging 1.00
R5715:Hoxd4 UTSW 2 74727364 missense probably damaging 1.00
R6197:Hoxd4 UTSW 2 74728463 missense possibly damaging 0.85
R6264:Hoxd4 UTSW 2 74727385 missense possibly damaging 0.53
R6310:Hoxd4 UTSW 2 74728390 missense possibly damaging 0.84
R6336:Hoxd4 UTSW 2 74727361 missense probably damaging 1.00
R6921:Hoxd4 UTSW 2 74728492 missense possibly damaging 0.73
Posted On2016-08-02