Incidental Mutation 'R2124:Hoxd3'
ID 229634
Institutional Source Beutler Lab
Gene Symbol Hoxd3
Ensembl Gene ENSMUSG00000079277
Gene Name homeobox D3
Synonyms Hox-5.5, Hox-4.1
MMRRC Submission 040127-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.858) question?
Stock # R2124 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 74542337-74578615 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 74574578 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Threonine at position 75 (P75T)
Ref Sequence ENSEMBL: ENSMUSP00000107614 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047830] [ENSMUST00000053932] [ENSMUST00000111982] [ENSMUST00000111983] [ENSMUST00000140666] [ENSMUST00000144544]
AlphaFold P09027
Predicted Effect possibly damaging
Transcript: ENSMUST00000047830
AA Change: P75T

PolyPhen 2 Score 0.922 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000044809
Gene: ENSMUSG00000079277
AA Change: P75T

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 possibly damaging
Transcript: ENSMUST00000111982
AA Change: P75T

PolyPhen 2 Score 0.922 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000107613
Gene: ENSMUSG00000079277
AA Change: P75T

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 possibly damaging
Transcript: ENSMUST00000111983
AA Change: P75T

PolyPhen 2 Score 0.922 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000107614
Gene: ENSMUSG00000079277
AA Change: P75T

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 noncoding transcript
Transcript: ENSMUST00000190553
Predicted Effect probably benign
Transcript: ENSMUST00000144544
Meta Mutation Damage Score 0.0674 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.2%
Validation Efficiency 98% (80/82)
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: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933430I17Rik T A 4: 62,457,109 (GRCm39) L143M possibly damaging Het
Abca13 T C 11: 9,259,013 (GRCm39) probably benign Het
Abcg5 T A 17: 84,978,575 (GRCm39) E294D probably benign Het
Adgrg6 T C 10: 14,342,930 (GRCm39) D339G probably damaging Het
Ahctf1 C A 1: 179,597,017 (GRCm39) R43L probably damaging Het
Ambn T A 5: 88,608,617 (GRCm39) probably benign Het
Arap3 A C 18: 38,106,403 (GRCm39) L1480R probably damaging Het
Arhgef10 A G 8: 14,984,820 (GRCm39) D200G probably damaging Het
Aspg G A 12: 112,087,608 (GRCm39) V8I probably benign Het
Aven T A 2: 112,455,541 (GRCm39) W26R probably damaging Het
Car4 T A 11: 84,854,911 (GRCm39) probably benign Het
Cd163 C T 6: 124,295,815 (GRCm39) R720C probably damaging Het
Cdh1 A G 8: 107,390,842 (GRCm39) I653V probably benign Het
Cdh3 A T 8: 107,279,520 (GRCm39) H712L probably damaging Het
Cdr2 T C 7: 120,581,250 (GRCm39) E9G probably damaging Het
Cfap47 T C X: 78,553,927 (GRCm39) I267V probably benign Het
Chrnb2 T C 3: 89,676,648 (GRCm39) probably benign Het
Col4a2 C A 8: 11,466,070 (GRCm39) P443Q probably damaging Het
Cyp2a12 A G 7: 26,736,071 (GRCm39) *493W probably null Het
Ddias T C 7: 92,507,464 (GRCm39) Q817R probably benign Het
Ddx6 C T 9: 44,535,816 (GRCm39) Q182* probably null Het
Dhrs7 A G 12: 72,699,951 (GRCm39) I227T probably damaging Het
Dhx8 A T 11: 101,653,071 (GRCm39) M970L probably damaging Het
Dnah7a A T 1: 53,536,101 (GRCm39) D2647E possibly damaging Het
Dstyk G A 1: 132,380,857 (GRCm39) G451R possibly damaging Het
Ednrb T A 14: 104,059,204 (GRCm39) D274V probably benign Het
Efl1 C T 7: 82,342,121 (GRCm39) R510C probably damaging Het
Eif4g3 A G 4: 137,912,053 (GRCm39) E1409G probably damaging Het
Fam78b G A 1: 166,906,278 (GRCm39) V146M probably damaging Het
Fcgbp T C 7: 27,791,444 (GRCm39) Y902H probably benign Het
Fgf18 A C 11: 33,068,003 (GRCm39) F129C probably damaging Het
Gbp9 T A 5: 105,242,409 (GRCm39) D110V probably damaging Het
Gm10477 A G X: 55,570,192 (GRCm39) K31E probably damaging Het
Gm10542 T A 18: 44,334,355 (GRCm39) W9R probably null Het
Gpaa1 A G 15: 76,217,552 (GRCm39) Y330C probably damaging Het
Hectd4 T C 5: 121,456,702 (GRCm39) L689P probably damaging Het
Ikbkb A G 8: 23,156,036 (GRCm39) L570P probably damaging Het
Ikbkb T C 8: 23,157,233 (GRCm39) probably benign Het
Il1rap A T 16: 26,529,315 (GRCm39) H379L probably damaging Het
Ints6l T A X: 55,550,228 (GRCm39) S718T probably benign Het
Jaml T A 9: 45,012,362 (GRCm39) I283N probably damaging Het
Kidins220 G A 12: 25,091,302 (GRCm39) probably null Het
Kif1b T C 4: 149,306,753 (GRCm39) D869G probably benign Het
Loxl2 T C 14: 69,929,859 (GRCm39) Y746H probably benign Het
Ltbr A G 6: 125,286,440 (GRCm39) S249P probably benign Het
Mageb5 A G X: 90,823,701 (GRCm39) I226T probably damaging Het
Msantd2 C T 9: 37,434,227 (GRCm39) R357W probably damaging Het
Mtcl2 T C 2: 156,875,245 (GRCm39) E835G probably damaging Het
Neb A G 2: 52,154,076 (GRCm39) F2345S probably damaging Het
Or7e173 T G 9: 19,938,797 (GRCm39) I146L probably benign Het
Pabpc4l T C 3: 46,401,276 (GRCm39) T123A probably benign Het
Plekhg4 TAGTCGATGCCCGAGTC TAGTC 8: 106,103,084 (GRCm39) probably benign Het
Prkdc T C 16: 15,537,297 (GRCm39) V1716A probably benign Het
Prss37 G A 6: 40,492,294 (GRCm39) R186* probably null Het
Psg20 T A 7: 18,414,947 (GRCm39) Y316F probably benign Het
Rasgrp2 T A 19: 6,454,425 (GRCm39) M156K probably benign Het
Rims1 T A 1: 22,474,732 (GRCm39) R200* probably null Het
Rnf168 T G 16: 32,097,036 (GRCm39) L37R probably damaging Het
Sall3 C T 18: 81,015,012 (GRCm39) G972D probably benign Het
Sap18 T A 14: 58,036,011 (GRCm39) S66T probably damaging Het
Scamp5 C A 9: 57,354,508 (GRCm39) V49F possibly damaging Het
Sdk1 C A 5: 142,170,943 (GRCm39) D1935E possibly damaging Het
Setd2 A G 9: 110,378,932 (GRCm39) S632G probably benign Het
Syt16 T A 12: 74,285,009 (GRCm39) S401T probably damaging Het
Tas2r106 A T 6: 131,655,317 (GRCm39) L178H probably damaging Het
Tbcd A G 11: 121,494,146 (GRCm39) Y983C probably damaging Het
Tenm3 A G 8: 48,870,041 (GRCm39) probably null Het
Tll1 T C 8: 64,538,591 (GRCm39) E351G probably benign Het
Tmem44 T A 16: 30,366,262 (GRCm39) K55* probably null Het
Top2a T C 11: 98,895,054 (GRCm39) I849V probably benign Het
Ttn A G 2: 76,624,792 (GRCm39) V13516A probably damaging Het
Uxs1 A G 1: 43,814,006 (GRCm39) L77P probably damaging Het
Vmn2r121 A T X: 123,043,439 (GRCm39) probably null Het
Vmn2r84 A C 10: 130,227,100 (GRCm39) M246R probably damaging Het
Vps13b T A 15: 35,646,226 (GRCm39) N1443K probably benign Het
Wfdc6b C T 2: 164,459,363 (GRCm39) R142C probably benign Het
Zfp616 A G 11: 73,973,869 (GRCm39) probably null Het
Zmym1 T C 4: 126,943,363 (GRCm39) T244A probably benign Het
Other mutations in Hoxd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02636:Hoxd3 APN 2 74,577,298 (GRCm39) missense probably benign 0.32
IGL03017:Hoxd3 APN 2 74,577,050 (GRCm39) missense possibly damaging 0.68
candide UTSW 2 74,574,420 (GRCm39) missense probably damaging 1.00
compressed UTSW 2 74,574,650 (GRCm39) nonsense probably null
R1977:Hoxd3 UTSW 2 74,574,620 (GRCm39) missense possibly damaging 0.94
R2079:Hoxd3 UTSW 2 74,574,610 (GRCm39) missense probably damaging 0.97
R5143:Hoxd3 UTSW 2 74,576,716 (GRCm39) missense probably damaging 1.00
R5250:Hoxd3 UTSW 2 74,574,650 (GRCm39) nonsense probably null
R5256:Hoxd3 UTSW 2 74,577,211 (GRCm39) missense possibly damaging 0.88
R5943:Hoxd3 UTSW 2 74,577,173 (GRCm39) missense probably benign 0.00
R6300:Hoxd3 UTSW 2 74,574,420 (GRCm39) missense probably damaging 1.00
R7362:Hoxd3 UTSW 2 74,574,563 (GRCm39) missense possibly damaging 0.59
R9203:Hoxd3 UTSW 2 74,576,744 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- GAAGGCTGCATACTACGAGAAC -3'
(R):5'- TAGAAGCACTGAGTCCACCC -3'

Sequencing Primer
(F):5'- TACGAGAACCCAGGACTCTTTGG -3'
(R):5'- ACTCCACTTCCAGGATTGGTAGG -3'
Posted On 2014-09-17