Incidental Mutation 'R3424:Hoxd4'
ID 267838
Institutional Source Beutler Lab
Gene Symbol Hoxd4
Ensembl Gene ENSMUSG00000101174
Gene Name homeobox D4
Synonyms Hox-5.1, Hox-4.2
MMRRC Submission 040642-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.452) question?
Stock # R3424 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 74552322-74559504 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 74557657 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 12 (Y12C)
Ref Sequence ENSEMBL: ENSMUSP00000051355 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047904] [ENSMUST00000053932] [ENSMUST00000111980] [ENSMUST00000111983]
AlphaFold P10628
Predicted Effect possibly damaging
Transcript: ENSMUST00000047904
AA Change: Y12C

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000047949
Gene: ENSMUSG00000115956
AA Change: Y12C

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 damaging
Transcript: ENSMUST00000053932
AA Change: Y12C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000051355
Gene: ENSMUSG00000100642
AA Change: Y12C

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: Y12C

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000107611
Gene: ENSMUSG00000101174
AA Change: Y12C

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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.4%
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: 28 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
6030469F06Rik G T 12: 31,234,632 (GRCm39) noncoding transcript Het
Atp8b3 T C 10: 80,372,181 (GRCm39) E16G probably benign Het
BC016579 T A 16: 45,449,846 (GRCm39) I191F probably damaging Het
Cdh23 T G 10: 60,212,660 (GRCm39) I1584L possibly damaging Het
Cep250 G A 2: 155,823,381 (GRCm39) D1011N probably benign Het
Coro2b A T 9: 62,336,590 (GRCm39) probably null Het
Csf3r A G 4: 125,937,549 (GRCm39) D811G probably damaging Het
Dst T G 1: 34,237,586 (GRCm39) probably benign Het
Gabrr1 T C 4: 33,158,058 (GRCm39) L227P probably damaging Het
Galnt10 T C 11: 57,536,539 (GRCm39) V52A probably benign Het
Golga4 A C 9: 118,363,715 (GRCm39) D229A probably benign Het
Heatr5b G A 17: 79,075,833 (GRCm39) T1495I possibly damaging Het
Hps1 A T 19: 42,748,952 (GRCm39) M522K possibly damaging Het
Lrrc8e A T 8: 4,284,611 (GRCm39) I279F probably damaging Het
Mettl24 C T 10: 40,559,637 (GRCm39) Q96* probably null Het
Muc2 A G 7: 141,279,595 (GRCm39) N193S probably damaging Het
Mysm1 A G 4: 94,853,558 (GRCm39) L347P probably benign Het
Or10g9 T A 9: 39,911,830 (GRCm39) E231V probably damaging Het
Oxtr G T 6: 112,454,191 (GRCm39) H24Q probably benign Het
Paxip1 A G 5: 27,980,671 (GRCm39) probably benign Het
Pclo C T 5: 14,730,432 (GRCm39) probably benign Het
Ros1 C A 10: 52,004,512 (GRCm39) probably null Het
Slc18b1 T G 10: 23,698,874 (GRCm39) M348R probably damaging Het
Slco4c1 A T 1: 96,768,976 (GRCm39) S295R probably benign Het
Tmeff2 A G 1: 51,018,776 (GRCm39) probably benign Het
Tspan31 T A 10: 126,904,371 (GRCm39) Q141L probably benign Het
Virma G T 4: 11,513,177 (GRCm39) E344* probably null Het
Zbtb17 G T 4: 141,192,299 (GRCm39) G415C probably damaging 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
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
R6310:Hoxd4 UTSW 2 74,558,734 (GRCm39) missense possibly damaging 0.84
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'- CCGGTGATAAACATGCTTTCTTCC -3'
(R):5'- ATCCAAGGGTAGACCACAGC -3'

Sequencing Primer
(F):5'- CTATTGGCTGGCCTGGTCAC -3'
(R):5'- ACCGTAATGACTTCCCGGG -3'
Posted On 2015-02-18