Incidental Mutation 'R6707:Sox9'
ID 528991
Institutional Source Beutler Lab
Gene Symbol Sox9
Ensembl Gene ENSMUSG00000000567
Gene Name SRY (sex determining region Y)-box 9
Synonyms 2010306G03Rik
MMRRC Submission 044825-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6707 (G1)
Quality Score 225.009
Status Validated
Chromosome 11
Chromosomal Location 112673050-112678586 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 112673698 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 96 (N96K)
Ref Sequence ENSEMBL: ENSMUSP00000000579 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000579]
AlphaFold Q04887
Predicted Effect probably damaging
Transcript: ENSMUST00000000579
AA Change: N96K

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000000579
Gene: ENSMUSG00000000567
AA Change: N96K

DomainStartEndE-ValueType
Pfam:Sox_N 22 94 9.6e-29 PFAM
HMG 104 174 2.34e-27 SMART
low complexity region 186 196 N/A INTRINSIC
low complexity region 234 241 N/A INTRINSIC
low complexity region 339 377 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137081
Meta Mutation Damage Score 0.1866 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.4%
  • 20x: 95.6%
Validation Efficiency 100% (42/42)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene recognizes the sequence CCTTGAG along with other members of the HMG-box class DNA-binding proteins. It acts during chondrocyte differentiation and, with steroidogenic factor 1, regulates transcription of the anti-Muellerian hormone (AMH) gene. Deficiencies lead to the skeletal malformation syndrome campomelic dysplasia, frequently with sex reversal. [provided by RefSeq, Jul 2008]
PHENOTYPE: Null mutant heterozygotes and conditional knockout mutants display perinatal lethality with cleft palate, hypoplasia and distortion of numerous cartilage-derived skeletal structures, and premature mineralization in many bones. Specific conditional knockout mutations are sex-reversed. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acss3 T C 10: 106,920,783 (GRCm39) Y109C probably damaging Het
Actg2 C T 6: 83,490,076 (GRCm39) W341* probably null Het
Adam29 C T 8: 56,325,135 (GRCm39) G440R probably damaging Het
Arfgef3 T C 10: 18,496,903 (GRCm39) D1153G probably benign Het
Arhgef28 T C 13: 98,211,624 (GRCm39) T120A possibly damaging Het
Arhgef28 G T 13: 98,073,224 (GRCm39) Q1371K probably damaging Het
BC051665 A T 13: 60,932,222 (GRCm39) D122E probably benign Het
Boc A T 16: 44,320,979 (GRCm39) I227N possibly damaging Het
Clca3b T A 3: 144,550,288 (GRCm39) Q219L probably benign Het
Cplane1 G A 15: 8,252,606 (GRCm39) V1943M probably benign Het
Cyp2c66 T A 19: 39,174,944 (GRCm39) F448Y probably damaging Het
Ddx5 A G 11: 106,673,058 (GRCm39) M489T probably benign Het
Dnm1 T C 2: 32,226,253 (GRCm39) D312G probably null Het
Ecpas T A 4: 58,879,101 (GRCm39) I63L possibly damaging Het
Eqtn T C 4: 94,796,056 (GRCm39) D215G probably benign Het
Evi5l A T 8: 4,256,322 (GRCm39) T706S probably benign Het
Gtf2f1 T C 17: 57,314,770 (GRCm39) E90G probably benign Het
Hpx A T 7: 105,244,682 (GRCm39) S168T probably benign Het
Ipo4 C A 14: 55,866,361 (GRCm39) V773L possibly damaging Het
Ireb2 C T 9: 54,811,245 (GRCm39) T716I probably damaging Het
Klhl21 A G 4: 152,096,784 (GRCm39) D350G possibly damaging Het
Myh13 A T 11: 67,241,086 (GRCm39) N821I probably damaging Het
Nipbl G T 15: 8,354,043 (GRCm39) T1698K probably benign Het
Nod2 A G 8: 89,391,817 (GRCm39) H686R probably benign Het
Ntf3 A G 6: 126,141,691 (GRCm39) probably null Het
Or6c215 G T 10: 129,637,689 (GRCm39) A235D probably damaging Het
Or6c69 T C 10: 129,747,608 (GRCm39) T180A probably benign Het
Parp9 A T 16: 35,768,303 (GRCm39) H161L probably damaging Het
Pkhd1l1 A G 15: 44,392,539 (GRCm39) N1625D probably benign Het
Rdx T C 9: 51,974,954 (GRCm39) F30S probably damaging Het
Smo T A 6: 29,736,173 (GRCm39) V55E probably benign Het
Spp2 T G 1: 88,345,016 (GRCm39) probably null Het
Tex46 A G 4: 136,340,161 (GRCm39) N82S probably benign Het
Timm22 C T 11: 76,298,151 (GRCm39) L41F possibly damaging Het
Tmem30a A T 9: 79,681,547 (GRCm39) Y207* probably null Het
Tmem70 T C 1: 16,747,531 (GRCm39) V216A probably damaging Het
Tspan18 T C 2: 93,040,302 (GRCm39) N151S probably benign Het
Vmn2r90 T C 17: 17,948,364 (GRCm39) C537R probably damaging Het
Vps50 A G 6: 3,545,583 (GRCm39) Y339C probably damaging Het
Zp2 C T 7: 119,733,145 (GRCm39) G599R possibly damaging Het
Other mutations in Sox9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01916:Sox9 APN 11 112,675,500 (GRCm39) missense probably benign 0.00
IGL02257:Sox9 APN 11 112,675,811 (GRCm39) missense possibly damaging 0.84
IGL02935:Sox9 APN 11 112,676,175 (GRCm39) missense probably damaging 0.99
R0350:Sox9 UTSW 11 112,675,702 (GRCm39) missense probably damaging 0.99
R0634:Sox9 UTSW 11 112,675,768 (GRCm39) missense probably damaging 0.98
R4273:Sox9 UTSW 11 112,675,980 (GRCm39) missense possibly damaging 0.60
R4692:Sox9 UTSW 11 112,673,803 (GRCm39) missense probably benign 0.01
R5328:Sox9 UTSW 11 112,673,484 (GRCm39) missense probably benign 0.39
R5501:Sox9 UTSW 11 112,674,685 (GRCm39) missense probably damaging 1.00
R5905:Sox9 UTSW 11 112,674,646 (GRCm39) missense probably damaging 1.00
R6834:Sox9 UTSW 11 112,674,826 (GRCm39) missense probably benign 0.01
R7897:Sox9 UTSW 11 112,675,635 (GRCm39) missense probably benign 0.22
R9037:Sox9 UTSW 11 112,675,650 (GRCm39) missense probably damaging 0.99
R9485:Sox9 UTSW 11 112,673,705 (GRCm39) missense probably benign 0.19
R9511:Sox9 UTSW 11 112,676,001 (GRCm39) missense possibly damaging 0.68
R9606:Sox9 UTSW 11 112,673,416 (GRCm39) missense probably damaging 0.99
Z1176:Sox9 UTSW 11 112,675,948 (GRCm39) missense possibly damaging 0.51
Z1177:Sox9 UTSW 11 112,675,629 (GRCm39) missense possibly damaging 0.57
Predicted Primers PCR Primer
(F):5'- CATGAAGATGACCGACGAGC -3'
(R):5'- TGCATCCTGGACCAAAGAC -3'

Sequencing Primer
(F):5'- ACCATGTCGGAGGACTCG -3'
(R):5'- AGGATGCACAACTCCGCG -3'
Posted On 2018-07-24