Incidental Mutation 'R6310:Hoxd4'
ID 509520
Institutional Source Beutler Lab
Gene Symbol Hoxd4
Ensembl Gene ENSMUSG00000101174
Gene Name homeobox D4
Synonyms Hox-5.1, Hox-4.2
MMRRC Submission 044414-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.495) question?
Stock # R6310 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 74552322-74559504 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 74558734 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Serine at position 186 (A186S)
Ref Sequence ENSEMBL: ENSMUSP00000107611 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047904] [ENSMUST00000053932] [ENSMUST00000111980] [ENSMUST00000111983] [ENSMUST00000144544]
AlphaFold P10628
Predicted Effect possibly damaging
Transcript: ENSMUST00000047904
AA Change: A186S

PolyPhen 2 Score 0.837 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000047949
Gene: ENSMUSG00000115956
AA Change: A186S

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: A186S

PolyPhen 2 Score 0.837 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000107611
Gene: ENSMUSG00000101174
AA Change: A186S

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
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.2%
  • 20x: 97.5%
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acly C G 11: 100,373,046 (GRCm39) G856A possibly damaging Het
Adgrb3 T A 1: 25,150,799 (GRCm39) M1145L probably benign Het
Akap13 A T 7: 75,398,941 (GRCm39) H2673L probably damaging Het
Bmpr1b A G 3: 141,570,297 (GRCm39) S131P probably damaging Het
Cep72 A C 13: 74,201,144 (GRCm39) S175A possibly damaging Het
Chd2 C T 7: 73,102,912 (GRCm39) E1358K probably damaging Het
Cmip T C 8: 118,156,549 (GRCm39) I308T possibly damaging Het
Cps1 A T 1: 67,182,140 (GRCm39) N118I probably benign Het
Cux1 C T 5: 136,304,018 (GRCm39) G1265D probably benign Het
Ddx24 C A 12: 103,390,166 (GRCm39) R275L probably damaging Het
Dhx58 T C 11: 100,590,193 (GRCm39) S364G probably benign Het
Dis3l A C 9: 64,229,857 (GRCm39) V274G probably benign Het
Fryl A T 5: 73,349,104 (GRCm39) probably benign Het
Gbf1 A G 19: 46,268,444 (GRCm39) H1272R probably damaging Het
Gjb3 A G 4: 127,220,433 (GRCm39) V33A probably damaging Het
Gm11595 G A 11: 99,663,381 (GRCm39) R100C unknown Het
Gm9964 T C 11: 79,187,476 (GRCm39) probably benign Het
Grk5 T C 19: 61,069,349 (GRCm39) I342T probably damaging Het
Hnf1b T A 11: 83,795,737 (GRCm39) C527S probably damaging Het
Ighv1-78 G A 12: 115,832,584 (GRCm39) H54Y probably benign Het
Intu T A 3: 40,655,721 (GRCm39) L936* probably null Het
Kcp G A 6: 29,493,257 (GRCm39) R89W probably damaging Het
Kctd3 T C 1: 188,704,435 (GRCm39) T779A probably benign Het
Muc16 G A 9: 18,553,246 (GRCm39) P4349L probably benign Het
Nedd9 T C 13: 41,471,928 (GRCm39) T178A probably benign Het
Nuak2 G T 1: 132,257,699 (GRCm39) A204S probably damaging Het
Or51f1 T A 7: 102,506,412 (GRCm39) I26F probably benign Het
Or6c214 T C 10: 129,590,528 (GRCm39) R264G probably benign Het
Pcdhac2 C A 18: 37,278,824 (GRCm39) Y601* probably null Het
Pla2g4a T A 1: 149,717,977 (GRCm39) D624V possibly damaging Het
Plxnb1 T C 9: 108,938,796 (GRCm39) V1386A probably damaging Het
Plxnd1 T A 6: 115,953,697 (GRCm39) L623F possibly damaging Het
Pms2 T A 5: 143,860,401 (GRCm39) S71R probably benign Het
Prkg1 T C 19: 30,546,651 (GRCm39) D683G probably damaging Het
Rasgrp3 T A 17: 75,801,204 (GRCm39) Y45N probably damaging Het
Rfc4 T C 16: 22,933,459 (GRCm39) I233M probably benign Het
Sema3a G A 5: 13,606,986 (GRCm39) G274S probably damaging Het
Sesn1 T C 10: 41,772,074 (GRCm39) L201P probably damaging Het
Setx G A 2: 29,066,947 (GRCm39) V2363I possibly damaging Het
Sh3glb1 A G 3: 144,403,228 (GRCm39) S81P probably damaging Het
Sik3 A G 9: 46,089,784 (GRCm39) S218G probably damaging Het
Slc12a2 C G 18: 58,048,578 (GRCm39) F781L probably damaging Het
Slc12a6 A T 2: 112,166,184 (GRCm39) I188F probably damaging Het
Slc34a2 A G 5: 53,222,139 (GRCm39) probably null Het
Slc35f4 A G 14: 49,559,914 (GRCm39) C44R probably damaging Het
Sytl1 G A 4: 132,988,309 (GRCm39) P16S probably benign Het
Taok3 C T 5: 117,394,003 (GRCm39) T592M possibly damaging Het
Tgfb1i1 T C 7: 127,852,009 (GRCm39) F303L probably damaging Het
Txk T C 5: 72,893,760 (GRCm39) S7G probably benign Het
Utp4 T C 8: 107,645,253 (GRCm39) V550A probably benign Het
Vmn1r229 G A 17: 21,034,976 (GRCm39) D74N probably benign Het
Zfp638 A G 6: 83,844,212 (GRCm39) D25G possibly damaging Het
Zfp646 T C 7: 127,483,079 (GRCm39) V1752A probably benign Het
Other mutations in Hoxd4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02034:Hoxd4 APN 2 74,558,750 (GRCm39) missense probably damaging 0.98
IGL03403:Hoxd4 APN 2 74,558,681 (GRCm39) missense possibly damaging 0.93
R0153:Hoxd4 UTSW 2 74,557,801 (GRCm39) missense probably damaging 0.96
R3424:Hoxd4 UTSW 2 74,557,657 (GRCm39) missense probably damaging 1.00
R5447:Hoxd4 UTSW 2 74,557,687 (GRCm39) missense probably damaging 1.00
R5715:Hoxd4 UTSW 2 74,557,708 (GRCm39) missense probably damaging 1.00
R6197:Hoxd4 UTSW 2 74,558,807 (GRCm39) missense possibly damaging 0.85
R6264:Hoxd4 UTSW 2 74,557,729 (GRCm39) missense possibly damaging 0.53
R6336:Hoxd4 UTSW 2 74,557,705 (GRCm39) missense probably damaging 1.00
R6921:Hoxd4 UTSW 2 74,558,836 (GRCm39) missense possibly damaging 0.73
R9246:Hoxd4 UTSW 2 74,558,747 (GRCm39) missense possibly damaging 0.86
Predicted Primers PCR Primer
(F):5'- GAGAACCTTTGAGGAGGACC -3'
(R):5'- AAGGTCGTCAGGTCCGTATG -3'

Sequencing Primer
(F):5'- TGGGGCCTAACTAGTGGC -3'
(R):5'- CAGGTCCGTATGGTGGTCC -3'
Posted On 2018-04-02