Incidental Mutation 'R4400:Hoxd13'
ID 326569
Institutional Source Beutler Lab
Gene Symbol Hoxd13
Ensembl Gene ENSMUSG00000001819
Gene Name homeobox D13
Synonyms spdh, Hox-4.8
MMRRC Submission 041131-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.590) question?
Stock # R4400 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 74498654-74501943 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 74500359 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 300 (D300V)
Ref Sequence ENSEMBL: ENSMUSP00000001872 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001872] [ENSMUST00000001878]
AlphaFold P70217
Predicted Effect probably damaging
Transcript: ENSMUST00000001872
AA Change: D300V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000001872
Gene: ENSMUSG00000001819
AA Change: D300V

DomainStartEndE-ValueType
low complexity region 14 34 N/A INTRINSIC
Pfam:HoxA13_N 75 177 4e-18 PFAM
HOX 272 334 4.33e-22 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000001878
SMART Domains Protein: ENSMUSP00000001878
Gene: ENSMUSG00000001823

DomainStartEndE-ValueType
HOX 200 262 4.57e-21 SMART
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.3%
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 in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. Mutations in this particular gene cause synpolydactyly. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for targeted and spontaneous mutations exhibit abnormalities of the axial skeleton, especially limbs, and of the male accessory organs, and agenesis of the preputial glands. Mutant males are sterile. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atp4b A G 8: 13,438,810 (GRCm39) F189L probably damaging Het
Atp8a1 A T 5: 67,922,221 (GRCm39) Y372N probably benign Het
Bves T C 10: 45,245,389 (GRCm39) V354A probably benign Het
Cd79b A T 11: 106,202,836 (GRCm39) Y195* probably null Het
Cog6 A C 3: 52,920,362 (GRCm39) D131E probably benign Het
Elp3 C T 14: 65,785,539 (GRCm39) E421K possibly damaging Het
Fbxw28 A T 9: 109,157,378 (GRCm39) F237Y probably damaging Het
Fezf1 T C 6: 23,247,709 (GRCm39) N122S probably benign Het
Galnt2 A G 8: 125,051,042 (GRCm39) K157E probably damaging Het
Git2 T C 5: 114,871,970 (GRCm39) E141G possibly damaging Het
Gm26888 T C 11: 119,044,853 (GRCm39) silent Het
Gnrhr T C 5: 86,330,108 (GRCm39) probably null Het
Hspg2 G A 4: 137,275,433 (GRCm39) A2748T probably benign Het
Hyal2 A G 9: 107,448,052 (GRCm39) N235S probably damaging Het
Itgam T G 7: 127,680,830 (GRCm39) L253R probably damaging Het
Kcnh8 GAGACCAACGAGCAGCTGATGCTTCAGA GAGA 17: 53,032,934 (GRCm39) 74 probably benign Het
Matr3 A T 18: 35,716,969 (GRCm39) K591N possibly damaging Het
Mep1a T A 17: 43,785,897 (GRCm39) I731F possibly damaging Het
Mrtfa G A 15: 80,905,124 (GRCm39) Q103* probably null Het
Muc5b A G 7: 141,415,124 (GRCm39) D2690G possibly damaging Het
Nlrc5 A G 8: 95,220,981 (GRCm39) Q1140R probably benign Het
Or14c39 A G 7: 86,343,798 (GRCm39) I45V probably benign Het
Or5ac23 C T 16: 59,148,961 (GRCm39) V304I probably benign Het
Or6b6 A G 7: 106,571,209 (GRCm39) L114P probably damaging Het
Plcl1 T C 1: 55,754,736 (GRCm39) F1028L probably damaging Het
Plpp2 A G 10: 79,363,327 (GRCm39) V106A possibly damaging Het
Prpf8 A G 11: 75,381,528 (GRCm39) T255A possibly damaging Het
Shoc2 A G 19: 54,019,660 (GRCm39) I568V probably benign Het
Spopl C T 2: 23,407,957 (GRCm39) V241M probably damaging Het
Ssrp1 A T 2: 84,868,285 (GRCm39) D9V probably damaging Het
Strn3 A T 12: 51,694,883 (GRCm39) D293E possibly damaging Het
Tbx3 G T 5: 119,818,636 (GRCm39) D404Y probably damaging Het
Tdrd7 T C 4: 46,005,540 (GRCm39) S416P possibly damaging Het
Trim60 G T 8: 65,453,864 (GRCm39) Y128* probably null Het
Tspoap1 T C 11: 87,666,429 (GRCm39) S947P probably damaging Het
Ttn A T 2: 76,612,739 (GRCm39) S17113R probably damaging Het
Ubqln1 T A 13: 58,341,202 (GRCm39) N183I probably damaging Het
Ubr4 A G 4: 139,189,167 (GRCm39) N3917D possibly damaging Het
Ucp2 A G 7: 100,148,557 (GRCm39) *310W probably null Het
Wdr76 A G 2: 121,359,314 (GRCm39) M218V probably damaging Het
Zranb3 A C 1: 127,884,392 (GRCm39) L998R possibly damaging Het
Zxdc G A 6: 90,346,792 (GRCm39) G51E probably damaging Het
Other mutations in Hoxd13
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03108:Hoxd13 APN 2 74,500,440 (GRCm39) missense probably damaging 1.00
R1722:Hoxd13 UTSW 2 74,500,389 (GRCm39) missense probably benign 0.34
R2163:Hoxd13 UTSW 2 74,499,413 (GRCm39) missense possibly damaging 0.82
R4116:Hoxd13 UTSW 2 74,498,832 (GRCm39) missense possibly damaging 0.93
R4424:Hoxd13 UTSW 2 74,500,301 (GRCm39) nonsense probably null
R4938:Hoxd13 UTSW 2 74,499,027 (GRCm39) missense probably benign 0.26
R5535:Hoxd13 UTSW 2 74,499,141 (GRCm39) missense probably damaging 0.99
R7054:Hoxd13 UTSW 2 74,499,369 (GRCm39) missense probably damaging 1.00
R7069:Hoxd13 UTSW 2 74,499,368 (GRCm39) missense probably damaging 1.00
R7677:Hoxd13 UTSW 2 74,498,909 (GRCm39) missense probably benign 0.39
R8329:Hoxd13 UTSW 2 74,498,661 (GRCm39) missense probably benign 0.06
R8906:Hoxd13 UTSW 2 74,500,266 (GRCm39) missense
R9130:Hoxd13 UTSW 2 74,499,382 (GRCm39) missense probably benign 0.02
R9386:Hoxd13 UTSW 2 74,499,327 (GRCm39) missense probably damaging 1.00
R9803:Hoxd13 UTSW 2 74,499,247 (GRCm39) missense possibly damaging 0.83
Predicted Primers PCR Primer
(F):5'- AGTATCCAGGCTAATGTTTCCC -3'
(R):5'- CACAATGCTTGCCTTTCTAGG -3'

Sequencing Primer
(F):5'- AGGCTAATGTTTCCCCTGCTG -3'
(R):5'- CCTTTCTAGGCAGGGAAGGG -3'
Posted On 2015-07-07