Incidental Mutation 'R4745:Sox5'
ID 356643
Institutional Source Beutler Lab
Gene Symbol Sox5
Ensembl Gene ENSMUSG00000041540
Gene Name SRY (sex determining region Y)-box 5
Synonyms A730017D01Rik
MMRRC Submission 042028-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4745 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 143774151-144727703 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to C at 143779214 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Aspartic acid at position 606 (H606D)
Ref Sequence ENSEMBL: ENSMUSP00000107378 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038815] [ENSMUST00000077160] [ENSMUST00000111748] [ENSMUST00000111749] [ENSMUST00000170367]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000038815
AA Change: H690D

PolyPhen 2 Score 0.312 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000047567
Gene: ENSMUSG00000041540
AA Change: H690D

DomainStartEndE-ValueType
low complexity region 167 178 N/A INTRINSIC
coiled coil region 193 272 N/A INTRINSIC
low complexity region 336 348 N/A INTRINSIC
low complexity region 431 445 N/A INTRINSIC
coiled coil region 449 483 N/A INTRINSIC
low complexity region 494 505 N/A INTRINSIC
HMG 555 625 2.84e-26 SMART
low complexity region 686 708 N/A INTRINSIC
low complexity region 729 750 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000077160
AA Change: H642D

PolyPhen 2 Score 0.312 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000076403
Gene: ENSMUSG00000041540
AA Change: H642D

DomainStartEndE-ValueType
low complexity region 167 178 N/A INTRINSIC
coiled coil region 193 277 N/A INTRINSIC
low complexity region 383 397 N/A INTRINSIC
coiled coil region 401 435 N/A INTRINSIC
low complexity region 446 457 N/A INTRINSIC
HMG 507 577 2.84e-26 SMART
low complexity region 638 660 N/A INTRINSIC
low complexity region 681 702 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000111748
AA Change: H319D

PolyPhen 2 Score 0.312 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000107377
Gene: ENSMUSG00000041540
AA Change: H319D

DomainStartEndE-ValueType
low complexity region 60 74 N/A INTRINSIC
coiled coil region 78 112 N/A INTRINSIC
low complexity region 123 134 N/A INTRINSIC
HMG 184 254 2.84e-26 SMART
low complexity region 315 337 N/A INTRINSIC
low complexity region 358 379 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000111749
AA Change: H606D

PolyPhen 2 Score 0.533 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000107378
Gene: ENSMUSG00000041540
AA Change: H606D

DomainStartEndE-ValueType
low complexity region 132 143 N/A INTRINSIC
coiled coil region 158 237 N/A INTRINSIC
low complexity region 347 361 N/A INTRINSIC
coiled coil region 365 399 N/A INTRINSIC
low complexity region 410 421 N/A INTRINSIC
HMG 471 541 2.84e-26 SMART
low complexity region 602 624 N/A INTRINSIC
low complexity region 645 666 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000170367
AA Change: H641D

PolyPhen 2 Score 0.312 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000133041
Gene: ENSMUSG00000041540
AA Change: H641D

DomainStartEndE-ValueType
low complexity region 167 178 N/A INTRINSIC
coiled coil region 193 272 N/A INTRINSIC
low complexity region 382 396 N/A INTRINSIC
coiled coil region 400 434 N/A INTRINSIC
low complexity region 445 456 N/A INTRINSIC
HMG 506 576 2.84e-26 SMART
low complexity region 637 659 N/A INTRINSIC
low complexity region 680 701 N/A INTRINSIC
Meta Mutation Damage Score 0.1218 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.8%
Validation Efficiency 97% (89/92)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The encoded protein may play a role in chondrogenesis. A pseudogene of this gene is located on chromosome 8. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous null mice fail to breathe and die at birth exhibiting a narrow thoracic cage, irregularly mineralized sternum, cleft secondary palate, and delayed bone mineralization. Homozygotes for a transposon induced insertion die shortly after birth exhibiting cyanosis and respiratory distress. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca17 T C 17: 24,526,427 (GRCm39) Y619C probably damaging Het
Adck1 A G 12: 88,368,949 (GRCm39) probably null Het
Agap3 A C 5: 24,656,123 (GRCm39) probably null Het
Ankib1 A T 5: 3,782,566 (GRCm39) H354Q probably damaging Het
Ankrd29 T G 18: 12,387,679 (GRCm39) N301T probably benign Het
Arhgef4 A G 1: 34,846,356 (GRCm39) T379A probably damaging Het
Arid1a A G 4: 133,480,417 (GRCm39) V169A probably benign Het
Bag2 T C 1: 33,787,417 (GRCm39) probably null Het
Bmt2 A C 6: 13,628,686 (GRCm39) Y332* probably null Het
Bpifb1 A T 2: 154,053,501 (GRCm39) K248* probably null Het
Caap1 C A 4: 94,444,751 (GRCm39) probably null Het
Calcr T A 6: 3,692,576 (GRCm39) Y389F probably damaging Het
Capn1 C T 19: 6,043,946 (GRCm39) V562I probably benign Het
Ccr1 T A 9: 123,763,985 (GRCm39) T182S probably benign Het
Ceacam15 T C 7: 16,407,259 (GRCm39) D86G probably benign Het
Cldnd1 C T 16: 58,550,006 (GRCm39) T63I probably benign Het
Col12a1 A T 9: 79,559,368 (GRCm39) probably null Het
Cystm1 A G 18: 36,526,348 (GRCm39) probably benign Het
Ddx55 T A 5: 124,705,028 (GRCm39) Y428* probably null Het
Ensa G A 3: 95,538,745 (GRCm39) G118D probably benign Het
Folh1 A T 7: 86,372,482 (GRCm39) probably null Het
Foxj2 C A 6: 122,814,948 (GRCm39) P328Q probably damaging Het
Fscn3 A G 6: 28,435,627 (GRCm39) I417V probably damaging Het
Galnt7 T C 8: 57,995,761 (GRCm39) probably benign Het
Gm11563 T A 11: 99,549,246 (GRCm39) *169C probably null Het
Hfm1 A T 5: 107,049,709 (GRCm39) D417E possibly damaging Het
Ighv15-2 A G 12: 114,528,230 (GRCm39) S107P probably damaging Het
Itsn2 A G 12: 4,711,944 (GRCm39) D904G probably damaging Het
Kif1b A T 4: 149,322,339 (GRCm39) L860* probably null Het
Krt79 T C 15: 101,839,119 (GRCm39) E450G probably damaging Het
Lama1 T C 17: 68,045,775 (GRCm39) S227P probably damaging Het
Lamp5 C A 2: 135,902,786 (GRCm39) H168Q probably benign Het
Lilra5 A T 7: 4,245,076 (GRCm39) Q240L possibly damaging Het
Lrp1 A T 10: 127,385,813 (GRCm39) C3521S probably benign Het
Mroh1 T A 15: 76,292,730 (GRCm39) probably null Het
Nlrp4g A T 9: 124,349,515 (GRCm38) noncoding transcript Het
Nr2f6 A T 8: 71,831,179 (GRCm39) I70N probably benign Het
Nr4a2 T A 2: 57,000,163 (GRCm39) D311V probably damaging Het
Odad2 G A 18: 7,286,763 (GRCm39) T156M probably benign Het
Or10w1 T A 19: 13,632,750 (GRCm39) M319K probably benign Het
Or10x4 T C 1: 174,219,442 (GRCm39) L269P probably damaging Het
Or52n20 T A 7: 104,320,711 (GRCm39) F267L probably damaging Het
Pcdhb6 C A 18: 37,468,426 (GRCm39) A449D possibly damaging Het
Pcgf6 A G 19: 47,036,545 (GRCm39) probably null Het
Prc1 C A 7: 79,962,911 (GRCm39) H131Q probably benign Het
Ptprq C A 10: 107,360,114 (GRCm39) R2187L probably damaging Het
Rasl2-9 C A 7: 5,128,702 (GRCm39) R76L possibly damaging Het
Rdh16f1 A T 10: 127,626,685 (GRCm39) Y246F probably benign Het
Rit1 T C 3: 88,624,982 (GRCm39) probably benign Het
Sash1 A G 10: 8,605,672 (GRCm39) V906A probably benign Het
Scnn1b T C 7: 121,501,509 (GRCm39) V108A probably benign Het
Sema4f A T 6: 82,895,265 (GRCm39) I356N probably damaging Het
Shc4 A T 2: 125,491,197 (GRCm39) L447Q probably damaging Het
Slc24a1 T C 9: 64,856,758 (GRCm39) M50V unknown Het
Slc28a3 T A 13: 58,722,077 (GRCm39) D269V possibly damaging Het
Slc35e1 A G 8: 73,246,166 (GRCm39) S89P possibly damaging Het
Smpd5 T A 15: 76,179,008 (GRCm39) H125Q probably benign Het
Snapc2 A G 8: 4,304,578 (GRCm39) T31A probably damaging Het
Spag6 A G 2: 18,742,107 (GRCm39) T367A possibly damaging Het
Spag8 T C 4: 43,651,636 (GRCm39) T413A probably damaging Het
Sptlc3 G A 2: 139,389,087 (GRCm39) G156R probably damaging Het
Stx19 A G 16: 62,642,783 (GRCm39) T200A probably benign Het
Tas2r116 A G 6: 132,832,668 (GRCm39) T90A probably benign Het
Tasor2 G A 13: 3,640,069 (GRCm39) T356I probably benign Het
Tbl3 A G 17: 24,924,304 (GRCm39) probably benign Het
Tekt5 G T 16: 10,213,058 (GRCm39) P76T probably damaging Het
Tjp2 C T 19: 24,074,030 (GRCm39) E1086K possibly damaging Het
Topbp1 T C 9: 103,200,770 (GRCm39) L601P probably damaging Het
Trav16 T A 14: 53,980,934 (GRCm39) M41K possibly damaging Het
Trav6-5 C A 14: 53,728,960 (GRCm39) N72K probably benign Het
Trpm3 C G 19: 22,692,659 (GRCm39) T250S possibly damaging Het
Vps35 A T 8: 85,987,891 (GRCm39) D753E probably benign Het
Vstm2a A T 11: 16,213,061 (GRCm39) N149Y probably damaging Het
Vwa2 G T 19: 56,895,318 (GRCm39) M497I probably benign Het
Zfat C A 15: 68,052,223 (GRCm39) V517L probably benign Het
Zfp169 C A 13: 48,643,708 (GRCm39) R473L possibly damaging Het
Zfp672 T C 11: 58,220,324 (GRCm39) probably benign Het
Zranb1 T C 7: 132,574,443 (GRCm39) V420A probably damaging Het
Other mutations in Sox5
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01364:Sox5 APN 6 144,062,198 (GRCm39) missense probably damaging 0.96
IGL03217:Sox5 APN 6 143,853,223 (GRCm39) missense probably damaging 1.00
Stocking UTSW 6 144,062,169 (GRCm39) critical splice donor site probably null
R0230:Sox5 UTSW 6 144,155,064 (GRCm39) missense probably benign 0.02
R0610:Sox5 UTSW 6 143,779,165 (GRCm39) missense possibly damaging 0.56
R1162:Sox5 UTSW 6 143,906,538 (GRCm39) missense probably damaging 1.00
R1857:Sox5 UTSW 6 143,906,541 (GRCm39) missense probably damaging 1.00
R1959:Sox5 UTSW 6 143,819,831 (GRCm39) missense possibly damaging 0.94
R4057:Sox5 UTSW 6 144,062,248 (GRCm39) missense probably damaging 1.00
R4164:Sox5 UTSW 6 144,062,206 (GRCm39) missense probably damaging 1.00
R4284:Sox5 UTSW 6 143,781,055 (GRCm39) missense probably damaging 1.00
R4430:Sox5 UTSW 6 143,987,000 (GRCm39) missense possibly damaging 0.57
R4470:Sox5 UTSW 6 143,790,491 (GRCm39) missense possibly damaging 0.54
R4471:Sox5 UTSW 6 143,790,491 (GRCm39) missense possibly damaging 0.54
R4672:Sox5 UTSW 6 143,779,075 (GRCm39) missense probably damaging 1.00
R4683:Sox5 UTSW 6 143,779,193 (GRCm39) missense probably damaging 0.99
R4693:Sox5 UTSW 6 143,781,042 (GRCm39) missense probably damaging 1.00
R4735:Sox5 UTSW 6 143,906,561 (GRCm39) missense probably damaging 1.00
R4762:Sox5 UTSW 6 143,807,109 (GRCm39) critical splice donor site probably null
R4996:Sox5 UTSW 6 143,974,070 (GRCm39) nonsense probably null
R5218:Sox5 UTSW 6 143,906,616 (GRCm39) missense possibly damaging 0.93
R5673:Sox5 UTSW 6 144,062,206 (GRCm39) missense probably damaging 1.00
R5856:Sox5 UTSW 6 144,155,088 (GRCm39) missense probably damaging 1.00
R6249:Sox5 UTSW 6 143,779,009 (GRCm39) missense probably benign 0.33
R6394:Sox5 UTSW 6 143,987,039 (GRCm39) missense probably damaging 1.00
R6703:Sox5 UTSW 6 143,779,191 (GRCm39) missense probably damaging 1.00
R6812:Sox5 UTSW 6 144,062,169 (GRCm39) critical splice donor site probably null
R7312:Sox5 UTSW 6 144,100,759 (GRCm39) missense probably benign
R7543:Sox5 UTSW 6 143,786,905 (GRCm39) missense probably damaging 0.96
R8110:Sox5 UTSW 6 144,062,200 (GRCm39) missense possibly damaging 0.92
R8231:Sox5 UTSW 6 143,974,014 (GRCm39) missense probably damaging 0.98
R8250:Sox5 UTSW 6 144,100,777 (GRCm39) missense possibly damaging 0.85
R8705:Sox5 UTSW 6 143,987,012 (GRCm39) missense possibly damaging 0.50
R8937:Sox5 UTSW 6 143,853,169 (GRCm39) missense probably benign 0.00
R9182:Sox5 UTSW 6 143,779,118 (GRCm39) missense possibly damaging 0.51
R9193:Sox5 UTSW 6 143,790,570 (GRCm39) missense probably benign 0.27
R9740:Sox5 UTSW 6 144,100,947 (GRCm39) missense probably damaging 0.98
R9762:Sox5 UTSW 6 143,819,842 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TCCCGCAATGTGGTTTTCG -3'
(R):5'- TGAACATGTTGGCTAATTGGGC -3'

Sequencing Primer
(F):5'- ATAATCCACATCCGGGTCCTC -3'
(R):5'- AACATGTTGGCTAATTGGGCGAATG -3'
Posted On 2015-11-11