Incidental Mutation 'R1102:Shox2'
ID 98153
Institutional Source Beutler Lab
Gene Symbol Shox2
Ensembl Gene ENSMUSG00000027833
Gene Name SHOX homeobox 2
Synonyms Og12x, Prx3, 6330543G17Rik
MMRRC Submission 039175-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1102 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 66879060-66889104 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 66885628 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 149 (L149Q)
Ref Sequence ENSEMBL: ENSMUSP00000029422 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000029422] [ENSMUST00000162036] [ENSMUST00000162060] [ENSMUST00000162439] [ENSMUST00000195261]
AlphaFold P70390
Predicted Effect probably damaging
Transcript: ENSMUST00000029422
AA Change: L149Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000029422
Gene: ENSMUSG00000027833
AA Change: L149Q

DomainStartEndE-ValueType
low complexity region 57 90 N/A INTRINSIC
HOX 140 202 1.8e-28 SMART
low complexity region 258 273 N/A INTRINSIC
Pfam:OAR 310 327 3.3e-10 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000162036
SMART Domains Protein: ENSMUSP00000125468
Gene: ENSMUSG00000034544

DomainStartEndE-ValueType
low complexity region 3 95 N/A INTRINSIC
low complexity region 98 159 N/A INTRINSIC
coiled coil region 180 233 N/A INTRINSIC
low complexity region 265 278 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000162060
AA Change: L20Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000125031
Gene: ENSMUSG00000027833
AA Change: L20Q

DomainStartEndE-ValueType
HOX 11 73 1.8e-28 SMART
low complexity region 117 132 N/A INTRINSIC
Pfam:OAR 167 187 9.7e-11 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000162098
AA Change: L69Q
SMART Domains Protein: ENSMUSP00000123838
Gene: ENSMUSG00000027833
AA Change: L69Q

DomainStartEndE-ValueType
low complexity region 1 11 N/A INTRINSIC
HOX 61 123 1.8e-28 SMART
low complexity region 167 182 N/A INTRINSIC
Pfam:OAR 219 236 1e-10 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000162439
AA Change: L20Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000124924
Gene: ENSMUSG00000027833
AA Change: L20Q

DomainStartEndE-ValueType
HOX 11 73 1.8e-28 SMART
low complexity region 117 132 N/A INTRINSIC
Pfam:OAR 167 187 9.7e-11 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000195261
AA Change: L20Q

PolyPhen 2 Score 0.970 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000141625
Gene: ENSMUSG00000027833
AA Change: L20Q

DomainStartEndE-ValueType
HOX 11 73 9e-31 SMART
Meta Mutation Damage Score 0.2247 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 98.0%
  • 10x: 95.3%
  • 20x: 88.8%
Validation Efficiency 98% (60/61)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the homeobox family of genes that encode proteins containing a 60-amino acid residue motif that represents a DNA binding domain. Homeobox genes have been characterized extensively as transcriptional regulators involved in pattern formation in both invertebrate and vertebrate species. Several human genetic disorders are caused by aberrations in human homeobox genes. This locus represents a pseudoautosomal homeobox gene that is thought to be responsible for idiopathic short stature, and it is implicated in the short stature phenotype of Turner syndrome patients. This gene is considered to be a candidate gene for Cornelia de Lange syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]
PHENOTYPE: Homozygous null mice display incomplete penetrance of embryonic lethality during organogenesis and incomplete clefting of the anterior part of the palate. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700010I14Rik C T 17: 9,211,460 (GRCm39) T203M probably damaging Het
Acy3 C T 19: 4,037,850 (GRCm39) T119I probably damaging Het
Ccdc6 C A 10: 70,023,636 (GRCm39) H400Q possibly damaging Het
Ccna1 T C 3: 54,958,281 (GRCm39) D134G probably damaging Het
Cct2 A T 10: 116,896,545 (GRCm39) probably null Het
Cd36 A G 5: 18,019,211 (GRCm39) F170S possibly damaging Het
Cep350 G A 1: 155,807,264 (GRCm39) P718S probably damaging Het
Cimip1 T A 2: 173,364,516 (GRCm39) D20E probably damaging Het
Ctnna3 A T 10: 64,421,774 (GRCm39) I523L probably benign Het
Dnah1 G T 14: 31,018,414 (GRCm39) Y1405* probably null Het
Dnah8 T A 17: 31,073,738 (GRCm39) probably null Het
Drd3 T C 16: 43,582,846 (GRCm39) L113S probably damaging Het
Emsy T C 7: 98,251,796 (GRCm39) T735A probably damaging Het
Epha5 A G 5: 84,381,434 (GRCm39) probably benign Het
Ezhip GTCATCATCATCATC GTCATCATCATCATCATC X: 5,994,645 (GRCm39) probably benign Het
Fbxo10 A G 4: 45,043,672 (GRCm39) L717P probably damaging Het
Galnt10 T C 11: 57,671,871 (GRCm39) probably benign Het
Gle1 T G 2: 29,834,066 (GRCm39) I437M possibly damaging Het
Gpr137b T C 13: 13,539,616 (GRCm39) probably benign Het
Gsta1 T C 9: 78,149,777 (GRCm39) F197L probably damaging Het
Icam1 G A 9: 20,939,132 (GRCm39) V502M possibly damaging Het
Ido1 T A 8: 25,083,156 (GRCm39) I90F probably damaging Het
Il4ra G A 7: 125,173,889 (GRCm39) probably null Het
Med12l T A 3: 59,152,257 (GRCm39) M1014K probably damaging Het
Mmp13 A G 9: 7,272,952 (GRCm39) E104G possibly damaging Het
Mms19 T C 19: 41,939,284 (GRCm39) E495G possibly damaging Het
Mrc2 A G 11: 105,231,647 (GRCm39) I820V probably benign Het
Naip6 T C 13: 100,440,923 (GRCm39) K286E possibly damaging Het
Ndrg1 T C 15: 66,816,685 (GRCm39) Y110C probably damaging Het
Or1e1c G A 11: 73,265,700 (GRCm39) V45I probably benign Het
Or4a78 A T 2: 89,497,814 (GRCm39) C139S probably damaging Het
Or5b118 T C 19: 13,448,771 (GRCm39) C146R probably damaging Het
Or5b3 G A 19: 13,388,454 (GRCm39) V174M probably damaging Het
Oxtr C T 6: 112,454,138 (GRCm39) R42Q probably benign Het
Pdzd4 G A X: 72,839,052 (GRCm39) R419C probably damaging Het
Pnpla7 G T 2: 24,886,177 (GRCm39) M3I probably damaging Het
Popdc3 A G 10: 45,192,642 (GRCm39) probably benign Het
Ppp5c A G 7: 16,756,368 (GRCm39) F112S probably benign Het
Rbp3 A G 14: 33,678,313 (GRCm39) T754A possibly damaging Het
Reep6 A G 10: 80,171,080 (GRCm39) T319A probably benign Het
Rfx3 A G 19: 27,845,000 (GRCm39) V43A possibly damaging Het
Rint1 A G 5: 24,010,565 (GRCm39) probably benign Het
Sacm1l T G 9: 123,411,363 (GRCm39) V384G probably damaging Het
Sipa1 T C 19: 5,702,782 (GRCm39) H805R probably benign Het
Skic2 T C 17: 35,059,082 (GRCm39) D1095G probably benign Het
Slc5a3 G T 16: 91,874,765 (GRCm39) W274L probably damaging Het
Spata31e4 A G 13: 50,857,118 (GRCm39) T919A probably benign Het
Sptbn1 G T 11: 30,070,785 (GRCm39) H1524Q possibly damaging Het
Ssr1 G T 13: 38,171,591 (GRCm39) Q149K probably benign Het
Taf7l2 T C 10: 115,949,299 (GRCm39) S76G probably damaging Het
Thsd7a T C 6: 12,555,701 (GRCm39) D61G possibly damaging Het
Tmem245 T C 4: 56,903,200 (GRCm39) probably benign Het
Tmem74 T C 15: 43,730,186 (GRCm39) T286A probably benign Het
Tnc T C 4: 63,938,705 (GRCm39) N45D probably benign Het
Trdmt1 T G 2: 13,528,225 (GRCm39) probably benign Het
Uty A T Y: 1,174,741 (GRCm39) Y220N probably damaging Het
Vdr T C 15: 97,757,002 (GRCm39) Y290C probably damaging Het
Vmn2r19 T A 6: 123,313,132 (GRCm39) M734K probably benign Het
Vmn2r53 T C 7: 12,332,410 (GRCm39) D413G possibly damaging Het
Vps45 A G 3: 95,950,253 (GRCm39) probably benign Het
Other mutations in Shox2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00334:Shox2 APN 3 66,888,774 (GRCm39) missense possibly damaging 0.49
IGL00813:Shox2 APN 3 66,882,777 (GRCm39) missense probably damaging 1.00
IGL01534:Shox2 APN 3 66,885,696 (GRCm39) missense probably benign 0.01
IGL01583:Shox2 APN 3 66,881,104 (GRCm39) unclassified probably benign
R0306:Shox2 UTSW 3 66,881,167 (GRCm39) missense probably damaging 0.98
R0374:Shox2 UTSW 3 66,881,184 (GRCm39) missense probably damaging 0.98
R0625:Shox2 UTSW 3 66,888,877 (GRCm39) critical splice donor site probably null
R0774:Shox2 UTSW 3 66,881,144 (GRCm39) missense probably damaging 1.00
R1192:Shox2 UTSW 3 66,881,243 (GRCm39) nonsense probably null
R2354:Shox2 UTSW 3 66,888,822 (GRCm39) missense possibly damaging 0.94
R2518:Shox2 UTSW 3 66,885,692 (GRCm39) missense possibly damaging 0.83
R4163:Shox2 UTSW 3 66,881,104 (GRCm39) unclassified probably benign
R4976:Shox2 UTSW 3 66,881,008 (GRCm39) unclassified probably benign
R5423:Shox2 UTSW 3 66,881,087 (GRCm39) unclassified probably benign
R5493:Shox2 UTSW 3 66,888,796 (GRCm39) missense probably damaging 1.00
R6528:Shox2 UTSW 3 66,888,618 (GRCm39) missense probably benign 0.00
RF020:Shox2 UTSW 3 66,881,146 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGCACTCTGACTTTCAGGACCCAG -3'
(R):5'- GCAGCTATACAGACGAGACTTTGCG -3'

Sequencing Primer
(F):5'- TTCAGGACCCAGCCTCC -3'
(R):5'- TCTTCAGTGTCCCCTGAACT -3'
Posted On 2014-01-05