Incidental Mutation 'R5729:Stag3'
ID 452650
Institutional Source Beutler Lab
Gene Symbol Stag3
Ensembl Gene ENSMUSG00000036928
Gene Name STAG3 cohesin complex component
Synonyms SA-2, stromalin 3
MMRRC Submission 043346-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5729 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 138278502-138310655 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 138288485 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Threonine at position 140 (S140T)
Ref Sequence ENSEMBL: ENSMUSP00000125290 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000048028] [ENSMUST00000160729] [ENSMUST00000161691] [ENSMUST00000162245]
AlphaFold O70576
Predicted Effect probably benign
Transcript: ENSMUST00000048028
AA Change: S171T

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000040945
Gene: ENSMUSG00000036928
AA Change: S171T

DomainStartEndE-ValueType
low complexity region 6 26 N/A INTRINSIC
low complexity region 75 90 N/A INTRINSIC
Pfam:STAG 188 301 3.1e-38 PFAM
low complexity region 633 653 N/A INTRINSIC
low complexity region 1099 1114 N/A INTRINSIC
low complexity region 1141 1151 N/A INTRINSIC
low complexity region 1190 1208 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159483
Predicted Effect probably benign
Transcript: ENSMUST00000160729
AA Change: S171T

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000124170
Gene: ENSMUSG00000036928
AA Change: S171T

DomainStartEndE-ValueType
low complexity region 6 26 N/A INTRINSIC
low complexity region 75 90 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161113
Predicted Effect possibly damaging
Transcript: ENSMUST00000161691
AA Change: S140T

PolyPhen 2 Score 0.762 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000125290
Gene: ENSMUSG00000036928
AA Change: S140T

DomainStartEndE-ValueType
low complexity region 44 59 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000162245
AA Change: S171T

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000125523
Gene: ENSMUSG00000036928
AA Change: S171T

DomainStartEndE-ValueType
low complexity region 6 26 N/A INTRINSIC
low complexity region 75 90 N/A INTRINSIC
Pfam:STAG 185 304 4e-50 PFAM
low complexity region 633 653 N/A INTRINSIC
low complexity region 1099 1114 N/A INTRINSIC
low complexity region 1141 1151 N/A INTRINSIC
low complexity region 1190 1208 N/A INTRINSIC
Meta Mutation Damage Score 0.0608 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 95.2%
Validation Efficiency 97% (62/64)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is expressed in the nucleus and is a subunit of the cohesin complex which regulates the cohesion of sister chromatids during cell division. A mutation in this gene is associated with premature ovarian failure. Alternate splicing results in multiple transcript variants encoding distinct isoforms. This gene has multiple pseudogenes. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mice homozygous for a transgenic gene disruption exhibit azoospermia and lack oocytes. [provided by MGI curators]
Allele List at MGI

All alleles(4) : Targeted(2) Gene trapped(1) Transgenic(1)

Other mutations in this stock
Total: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adss2 A T 1: 177,623,824 (GRCm39) V46E possibly damaging Het
Aldoart2 T C 12: 55,612,690 (GRCm39) V205A probably benign Het
Atp1a2 A G 1: 172,120,938 (GRCm39) S45P probably damaging Het
Atp4a A G 7: 30,411,851 (GRCm39) K29E possibly damaging Het
AU040320 T A 4: 126,724,208 (GRCm39) D428E probably damaging Het
Bend7 T C 2: 4,768,085 (GRCm39) L347P probably damaging Het
Cacna2d1 T A 5: 16,140,037 (GRCm39) L9* probably null Het
Ccdc103 A T 11: 102,773,904 (GRCm39) I50F probably damaging Het
Cdc5l T C 17: 45,737,495 (GRCm39) I88V probably benign Het
Cracr2a T C 6: 127,584,199 (GRCm39) V86A possibly damaging Het
Cybb C G X: 9,316,989 (GRCm39) D246H probably benign Het
Dgkd C T 1: 87,864,054 (GRCm39) Q90* probably null Het
Dnajc21 A T 15: 10,449,682 (GRCm39) D446E probably benign Het
Fam13a T G 6: 58,916,292 (GRCm39) R648S probably damaging Het
Gabrg2 A G 11: 41,858,450 (GRCm39) V226A probably damaging Het
Gm5499 A T 17: 87,385,944 (GRCm39) noncoding transcript Het
Gprc5c G T 11: 114,755,093 (GRCm39) V257L possibly damaging Het
Irf2bp1 G T 7: 18,739,172 (GRCm39) E271* probably null Het
Krt86 T G 15: 101,374,429 (GRCm39) V274G probably benign Het
Lats2 A T 14: 57,960,192 (GRCm39) C151S probably benign Het
Mapk3 A T 7: 126,363,979 (GRCm39) T254S probably benign Het
Mat2b A T 11: 40,573,373 (GRCm39) M202K probably damaging Het
Mos A G 4: 3,870,971 (GRCm39) Y282H probably benign Het
Myo3b A G 2: 69,936,083 (GRCm39) K108R probably damaging Het
Naa16 A G 14: 79,593,220 (GRCm39) Y417H probably damaging Het
Oat A T 7: 132,159,984 (GRCm39) I412N probably damaging Het
Or4d11 A T 19: 12,013,272 (GRCm39) I278N probably damaging Het
Pcdh1 A T 18: 38,335,999 (GRCm39) V73D probably damaging Het
Pigv A T 4: 133,392,134 (GRCm39) Y345* probably null Het
Pitpnc1 G T 11: 107,228,264 (GRCm39) F34L probably benign Het
Plxnd1 A G 6: 115,942,838 (GRCm39) L1282P probably damaging Het
Ppp1r3a T C 6: 14,719,762 (GRCm39) D384G probably benign Het
Ppp2ca G A 11: 52,008,856 (GRCm39) E119K probably damaging Het
Psg29 A T 7: 16,944,459 (GRCm39) N323I probably damaging Het
Rasa4 T C 5: 136,122,016 (GRCm39) V108A probably benign Het
Rbm14 A G 19: 4,852,577 (GRCm39) probably benign Het
Rfc1 A T 5: 65,434,795 (GRCm39) V657E probably damaging Het
Rhcg A T 7: 79,250,371 (GRCm39) N237K probably damaging Het
Rpgrip1 A G 14: 52,397,617 (GRCm39) Q1302R probably benign Het
Rragc A G 4: 123,818,645 (GRCm39) M287V possibly damaging Het
Scn7a A G 2: 66,572,301 (GRCm39) probably null Het
Sema6a C T 18: 47,414,410 (GRCm39) C506Y probably damaging Het
Senp1 G T 15: 97,964,412 (GRCm39) H267Q possibly damaging Het
Skor2 A G 18: 76,946,578 (GRCm39) E100G unknown Het
Slc38a11 A T 2: 65,147,365 (GRCm39) C371S probably benign Het
Snai3 G A 8: 123,181,629 (GRCm39) A276V probably benign Het
Sp110 C G 1: 85,516,839 (GRCm39) E219D probably damaging Het
Spag6 C T 2: 18,720,525 (GRCm39) T99I probably benign Het
Spop A G 11: 95,376,675 (GRCm39) I243V possibly damaging Het
Sra1 A T 18: 36,800,496 (GRCm39) probably benign Het
Stx16 G A 2: 173,935,292 (GRCm39) G156R probably damaging Het
Tbc1d2b G C 9: 90,089,925 (GRCm39) A868G probably benign Het
Tead2 A G 7: 44,870,166 (GRCm39) probably benign Het
Tmem53 C A 4: 117,125,669 (GRCm39) H261N probably damaging Het
Ube4a A T 9: 44,844,627 (GRCm39) S932T probably damaging Het
Usp9y A T Y: 1,381,339 (GRCm39) D827E probably damaging Het
Vmn2r53 T C 7: 12,334,733 (GRCm39) E309G probably damaging Het
Wrn T C 8: 33,758,806 (GRCm39) S1026G probably benign Het
Zfp646 G A 7: 127,484,626 (GRCm39) A1760T probably damaging Het
Other mutations in Stag3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00095:Stag3 APN 5 138,297,400 (GRCm39) missense probably damaging 1.00
IGL00336:Stag3 APN 5 138,295,921 (GRCm39) missense probably benign 0.42
IGL00514:Stag3 APN 5 138,298,397 (GRCm39) missense probably damaging 1.00
IGL00961:Stag3 APN 5 138,296,611 (GRCm39) missense probably benign 0.01
IGL01923:Stag3 APN 5 138,287,492 (GRCm39) missense probably damaging 1.00
IGL02252:Stag3 APN 5 138,300,810 (GRCm39) missense probably damaging 1.00
IGL02424:Stag3 APN 5 138,289,628 (GRCm39) missense probably damaging 1.00
IGL02424:Stag3 APN 5 138,280,247 (GRCm39) nonsense probably null
IGL02869:Stag3 APN 5 138,280,955 (GRCm39) missense probably damaging 0.96
thor UTSW 5 138,299,298 (GRCm39) critical splice donor site probably null
R0016:Stag3 UTSW 5 138,289,643 (GRCm39) missense possibly damaging 0.50
R0038:Stag3 UTSW 5 138,299,298 (GRCm39) critical splice donor site probably null
R0038:Stag3 UTSW 5 138,299,298 (GRCm39) critical splice donor site probably null
R0046:Stag3 UTSW 5 138,281,285 (GRCm39) splice site probably benign
R0046:Stag3 UTSW 5 138,281,285 (GRCm39) splice site probably benign
R1455:Stag3 UTSW 5 138,309,997 (GRCm39) missense probably benign 0.00
R1512:Stag3 UTSW 5 138,296,247 (GRCm39) missense probably benign 0.32
R1530:Stag3 UTSW 5 138,295,674 (GRCm39) missense probably damaging 0.99
R1608:Stag3 UTSW 5 138,296,901 (GRCm39) splice site probably null
R1736:Stag3 UTSW 5 138,302,771 (GRCm39) splice site probably benign
R1969:Stag3 UTSW 5 138,298,400 (GRCm39) missense probably damaging 0.99
R2034:Stag3 UTSW 5 138,296,263 (GRCm39) missense possibly damaging 0.82
R2214:Stag3 UTSW 5 138,299,528 (GRCm39) missense possibly damaging 0.92
R2281:Stag3 UTSW 5 138,296,546 (GRCm39) missense probably damaging 1.00
R2411:Stag3 UTSW 5 138,281,290 (GRCm39) splice site probably benign
R3792:Stag3 UTSW 5 138,296,611 (GRCm39) missense probably benign 0.01
R3887:Stag3 UTSW 5 138,297,101 (GRCm39) missense probably damaging 0.99
R4255:Stag3 UTSW 5 138,289,143 (GRCm39) missense probably damaging 0.98
R4777:Stag3 UTSW 5 138,307,461 (GRCm39) unclassified probably benign
R4842:Stag3 UTSW 5 138,307,627 (GRCm39) splice site probably null
R4854:Stag3 UTSW 5 138,294,956 (GRCm39) splice site probably null
R5045:Stag3 UTSW 5 138,302,740 (GRCm39) missense probably damaging 1.00
R5631:Stag3 UTSW 5 138,294,139 (GRCm39) missense probably damaging 0.96
R5894:Stag3 UTSW 5 138,297,100 (GRCm39) missense probably damaging 0.99
R6004:Stag3 UTSW 5 138,287,468 (GRCm39) missense probably damaging 1.00
R6172:Stag3 UTSW 5 138,298,105 (GRCm39) missense probably benign 0.41
R6503:Stag3 UTSW 5 138,302,682 (GRCm39) missense probably damaging 0.96
R6545:Stag3 UTSW 5 138,296,614 (GRCm39) missense possibly damaging 0.84
R6736:Stag3 UTSW 5 138,299,761 (GRCm39) missense probably damaging 0.98
R6861:Stag3 UTSW 5 138,302,969 (GRCm39) missense possibly damaging 0.55
R7012:Stag3 UTSW 5 138,295,871 (GRCm39) splice site probably null
R7358:Stag3 UTSW 5 138,299,770 (GRCm39) missense probably damaging 1.00
R7378:Stag3 UTSW 5 138,280,222 (GRCm39) missense probably benign 0.00
R7392:Stag3 UTSW 5 138,289,628 (GRCm39) missense probably damaging 1.00
R7395:Stag3 UTSW 5 138,280,207 (GRCm39) missense probably benign 0.33
R7818:Stag3 UTSW 5 138,299,705 (GRCm39) missense probably benign 0.00
R8017:Stag3 UTSW 5 138,299,465 (GRCm39) missense possibly damaging 0.80
R8019:Stag3 UTSW 5 138,299,465 (GRCm39) missense possibly damaging 0.80
R8076:Stag3 UTSW 5 138,281,404 (GRCm39) missense probably damaging 0.96
R8393:Stag3 UTSW 5 138,295,017 (GRCm39) missense probably damaging 0.98
R8405:Stag3 UTSW 5 138,302,914 (GRCm39) missense probably damaging 0.99
R8417:Stag3 UTSW 5 138,306,850 (GRCm39) missense probably benign
R8734:Stag3 UTSW 5 138,310,050 (GRCm39) missense probably benign 0.36
R8848:Stag3 UTSW 5 138,288,528 (GRCm39) missense probably null 0.97
R8966:Stag3 UTSW 5 138,289,666 (GRCm39) missense probably damaging 0.99
R9029:Stag3 UTSW 5 138,296,296 (GRCm39) missense probably damaging 1.00
R9292:Stag3 UTSW 5 138,299,712 (GRCm39) missense probably benign 0.01
R9410:Stag3 UTSW 5 138,297,601 (GRCm39) missense possibly damaging 0.95
R9645:Stag3 UTSW 5 138,299,701 (GRCm39) missense possibly damaging 0.78
R9723:Stag3 UTSW 5 138,298,103 (GRCm39) missense probably benign
Z1177:Stag3 UTSW 5 138,299,554 (GRCm39) missense possibly damaging 0.65
Predicted Primers PCR Primer
(F):5'- AGTTGTACAAATGAATGACAGCCC -3'
(R):5'- CCTGTCAGCTAATTTCTGTAAGTC -3'

Sequencing Primer
(F):5'- TGTACAAATGAATGACAGCCCATAAC -3'
(R):5'- GATTTCTGAGTTCAAGGCCAGCC -3'
Posted On 2017-01-03