Incidental Mutation 'R5501:Sox9'
ID 430629
Institutional Source Beutler Lab
Gene Symbol Sox9
Ensembl Gene ENSMUSG00000000567
Gene Name SRY (sex determining region Y)-box 9
Synonyms 2010306G03Rik
MMRRC Submission 043062-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5501 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 112673050-112678586 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 112674685 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 161 (L161Q)
Ref Sequence ENSEMBL: ENSMUSP00000000579 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000579]
AlphaFold Q04887
Predicted Effect probably damaging
Transcript: ENSMUST00000000579
AA Change: L161Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000000579
Gene: ENSMUSG00000000567
AA Change: L161Q

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
Coding Region Coverage
  • 1x: 98.2%
  • 3x: 97.3%
  • 10x: 95.1%
  • 20x: 90.3%
Validation Efficiency
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam26a A C 8: 44,022,941 (GRCm39) L183* probably null Het
Alox12e G T 11: 70,207,055 (GRCm39) Q584K probably benign Het
Atp1a4 A G 1: 172,074,399 (GRCm39) S285P probably damaging Het
Cdt1 C T 8: 123,297,239 (GRCm39) R311W probably damaging Het
Col25a1 A G 3: 130,389,312 (GRCm39) T632A probably benign Het
Coro6 T C 11: 77,358,622 (GRCm39) F227S probably damaging Het
Diras2 C T 13: 52,661,786 (GRCm39) V174M probably benign Het
Dop1a A G 9: 86,389,783 (GRCm39) D569G probably benign Het
Dync1li2 A G 8: 105,167,104 (GRCm39) probably null Het
Dysf T C 6: 84,064,800 (GRCm39) V508A probably damaging Het
Edem1 T C 6: 108,820,061 (GRCm39) probably null Het
Eef2k A G 7: 120,488,471 (GRCm39) D452G probably benign Het
Espl1 A G 15: 102,225,565 (GRCm39) R1539G possibly damaging Het
Fat4 A G 3: 38,941,364 (GRCm39) S86G probably benign Het
Hpgd A T 8: 56,751,391 (GRCm39) D73V probably benign Het
Ltb4r1 A G 14: 56,005,539 (GRCm39) N281D probably damaging Het
Map7 T C 10: 20,151,948 (GRCm39) S638P unknown Het
Mical1 G A 10: 41,362,075 (GRCm39) A934T probably benign Het
Micu3 C A 8: 40,807,341 (GRCm39) probably null Het
Mmp24 T A 2: 155,640,056 (GRCm39) Y129N probably damaging Het
Mras A T 9: 99,293,599 (GRCm39) Y14N probably damaging Het
Msmo1 A T 8: 65,175,523 (GRCm39) I169N probably damaging Het
Mtrr G T 13: 68,727,766 (GRCm39) T60K probably damaging Het
Or4c113 A T 2: 88,885,230 (GRCm39) L180* probably null Het
Or5p6 G T 7: 107,631,360 (GRCm39) Y63* probably null Het
Or7g30 T A 9: 19,352,290 (GRCm39) I27N possibly damaging Het
Pam A T 1: 97,768,090 (GRCm39) C8* probably null Het
Phrf1 T G 7: 140,839,834 (GRCm39) S1169A possibly damaging Het
Pkd1l2 T C 8: 117,792,569 (GRCm39) T408A probably damaging Het
Plch1 G T 3: 63,615,162 (GRCm39) Q778K probably damaging Het
Ppp1r3a A G 6: 14,719,417 (GRCm39) V499A probably benign Het
Rnd2 C T 11: 101,359,825 (GRCm39) L57F probably damaging Het
Ryr3 C A 2: 112,492,849 (GRCm39) S3736I possibly damaging Het
Serpinb13 T C 1: 106,909,915 (GRCm39) F11L possibly damaging Het
Slc45a2 C T 15: 11,027,871 (GRCm39) T480I probably damaging Het
Smcp A G 3: 92,491,731 (GRCm39) C39R unknown Het
Tanc2 T C 11: 105,805,811 (GRCm39) probably null Het
Tlr3 C T 8: 45,851,851 (GRCm39) D349N possibly damaging Het
Tmem131l G T 3: 83,833,435 (GRCm39) N809K probably damaging Het
Tyk2 T C 9: 21,032,908 (GRCm39) Y285C probably damaging Het
Usp15 T A 10: 123,011,804 (GRCm39) N98Y probably 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
R5905:Sox9 UTSW 11 112,674,646 (GRCm39) missense probably damaging 1.00
R6707:Sox9 UTSW 11 112,673,698 (GRCm39) missense probably damaging 0.99
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'- GGGTTTCCAAAATAGGAGGCC -3'
(R):5'- CTTAAGAGTGTGCCAGGAGGAC -3'

Sequencing Primer
(F):5'- TCAGGTCGACTCTGAGCAC -3'
(R):5'- TTGCTCACCAGAGTGCTCG -3'
Posted On 2016-10-05