Incidental Mutation 'R2504:Stag1'
ID 252179
Institutional Source Beutler Lab
Gene Symbol Stag1
Ensembl Gene ENSMUSG00000037286
Gene Name stromal antigen 1
Synonyms Scc3, SA-1
MMRRC Submission 040412-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2504 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 100597798-100959375 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) G to T at 100866210 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Serine to Isoleucine at position 475 (S475I)
Ref Sequence ENSEMBL: ENSMUSP00000040724 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000129269] [ENSMUST00000138405] [ENSMUST00000155108]
AlphaFold Q9D3E6
Predicted Effect probably damaging
Transcript: ENSMUST00000041418
AA Change: S475I

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000040724
Gene: ENSMUSG00000037286
AA Change: S475I

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Pfam:STAG 157 276 1.5e-50 PFAM
SCOP:d1qbkb_ 279 850 4e-5 SMART
low complexity region 1062 1081 N/A INTRINSIC
low complexity region 1107 1120 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000123302
SMART Domains Protein: ENSMUSP00000117879
Gene: ENSMUSG00000037286

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Pfam:STAG 157 276 2.9e-51 PFAM
low complexity region 303 315 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000129269
AA Change: S475I

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286
AA Change: S475I

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Pfam:STAG 160 274 3.8e-41 PFAM
SCOP:d1qbkb_ 279 850 3e-5 SMART
low complexity region 1062 1081 N/A INTRINSIC
low complexity region 1107 1120 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000138405
SMART Domains Protein: ENSMUSP00000116322
Gene: ENSMUSG00000037286

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Pfam:STAG 157 276 1.5e-51 PFAM
Predicted Effect unknown
Transcript: ENSMUST00000146934
AA Change: S85I
SMART Domains Protein: ENSMUSP00000120974
Gene: ENSMUSG00000037286
AA Change: S85I

DomainStartEndE-ValueType
low complexity region 673 692 N/A INTRINSIC
low complexity region 718 731 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149771
Predicted Effect probably benign
Transcript: ENSMUST00000155108
SMART Domains Protein: ENSMUSP00000118952
Gene: ENSMUSG00000037286

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.4%
Validation Efficiency
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 SCC3 family and is expressed in the nucleus. It encodes a component of cohesin, a multisubunit protein complex that provides sister chromatid cohesion along the length of a chromosome from DNA replication through prophase and prometaphase, after which it is dissociated in preparation for segregation during anaphase. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mouse embryos homozygous for a null mutation show developmental delay and die before birth. Heterozygous animals have shorter lifespan and earlier onset of tumourigenesis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 113 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2410089E03Rik G A 15: 8,219,216 (GRCm38) E1750K probably damaging Het
4933425L06Rik A G 13: 105,109,742 (GRCm38) I270M probably benign Het
Aatk T C 11: 120,018,855 (GRCm38) D28G probably benign Het
Abcg1 T A 17: 31,092,395 (GRCm38) S125T probably damaging Het
Actbl2 T C 13: 111,256,183 (GRCm38) S351P possibly damaging Het
Ankrd34b A G 13: 92,439,061 (GRCm38) probably null Het
BC030867 T C 11: 102,255,296 (GRCm38) Y133H possibly damaging Het
BC051665 C T 13: 60,782,654 (GRCm38) V295I probably benign Het
C1qtnf2 A G 11: 43,491,156 (GRCm38) N265S probably damaging Het
Ccdc14 C T 16: 34,721,850 (GRCm38) R573* probably null Het
Cd55b A T 1: 130,409,875 (GRCm38) Y247N probably damaging Het
Celsr2 A T 3: 108,413,591 (GRCm38) V635E probably benign Het
Clec16a T C 16: 10,559,687 (GRCm38) probably benign Het
Clec4b1 A G 6: 123,065,945 (GRCm38) Y41C probably damaging Het
Cntn5 A T 9: 10,172,121 (GRCm38) D19E probably benign Het
Cop1 A G 1: 159,232,805 (GRCm38) N53S probably damaging Het
Csad A T 15: 102,188,667 (GRCm38) M1K probably null Het
Cyb5rl A G 4: 107,080,945 (GRCm38) I200V probably benign Het
Cyp26a1 A G 19: 37,698,342 (GRCm38) T81A probably damaging Het
Cyp2d12 A T 15: 82,559,036 (GRCm38) H433L probably benign Het
D7Ertd443e T A 7: 134,349,479 (GRCm38) probably null Het
Dennd1b A G 1: 139,170,170 (GRCm38) probably benign Het
Dmap1 G T 4: 117,675,298 (GRCm38) T357K probably damaging Het
Dzip1 G T 14: 118,881,044 (GRCm38) T759K probably benign Het
Elmo2 A G 2: 165,298,687 (GRCm38) V300A probably damaging Het
Eml5 T C 12: 98,844,105 (GRCm38) D864G possibly damaging Het
Ep400 A G 5: 110,668,645 (GRCm38) V2670A probably damaging Het
Epha3 T A 16: 63,603,625 (GRCm38) I534F probably damaging Het
Epha4 A C 1: 77,382,991 (GRCm38) Y742D probably damaging Het
Ergic2 A G 6: 148,204,774 (GRCm38) probably null Het
Ero1l A T 14: 45,299,088 (GRCm38) probably null Het
Fam229a A G 4: 129,491,486 (GRCm38) D70G probably damaging Het
Fbn2 C T 18: 58,093,359 (GRCm38) R781Q probably damaging Het
Fbxo16 A T 14: 65,270,714 (GRCm38) probably benign Het
Fbxo39 T A 11: 72,317,285 (GRCm38) S154R probably benign Het
Fer T A 17: 63,991,580 (GRCm38) probably null Het
Filip1l A T 16: 57,571,047 (GRCm38) D428V probably damaging Het
Filip1l A G 16: 57,570,662 (GRCm38) I538V possibly damaging Het
Fsip2 T C 2: 82,979,610 (GRCm38) I2091T possibly damaging Het
Glyat A C 19: 12,651,398 (GRCm38) T186P possibly damaging Het
Gm10604 A G 4: 11,980,083 (GRCm38) S74P unknown Het
Gm4787 T G 12: 81,379,137 (GRCm38) K82N possibly damaging Het
Hectd4 T C 5: 121,220,620 (GRCm38) I50T unknown Het
Hectd4 T C 5: 121,263,967 (GRCm38) S373P possibly damaging Het
Hmcn1 A T 1: 150,686,867 (GRCm38) C2313* probably null Het
Igfn1 A T 1: 135,969,316 (GRCm38) S1171T probably benign Het
Ints8 T C 4: 11,241,642 (GRCm38) D267G probably benign Het
Itln1 A G 1: 171,529,159 (GRCm38) C251R probably damaging Het
Jcad C T 18: 4,674,026 (GRCm38) T596M probably damaging Het
Kcnj16 C T 11: 111,025,583 (GRCm38) T357M probably benign Het
Kif13a G A 13: 46,814,200 (GRCm38) T346M probably damaging Het
Klhl24 G A 16: 20,120,167 (GRCm38) A491T probably benign Het
Kntc1 C T 5: 123,778,347 (GRCm38) Q748* probably null Het
Krt25 T A 11: 99,317,296 (GRCm38) K369* probably null Het
Krt75 C T 15: 101,568,031 (GRCm38) R433Q probably benign Het
Krt76 A G 15: 101,884,858 (GRCm38) F582L unknown Het
Lysmd1 G A 3: 95,138,397 (GRCm38) V182I probably benign Het
Mab21l2 T A 3: 86,547,555 (GRCm38) E46V probably damaging Het
Magi2 A T 5: 20,358,936 (GRCm38) K355N probably damaging Het
March10 T C 11: 105,385,572 (GRCm38) D630G probably damaging Het
Mast4 A T 13: 102,738,639 (GRCm38) I1215N probably damaging Het
Nckap1 G A 2: 80,530,218 (GRCm38) T523I probably benign Het
Nexmif T A X: 104,084,393 (GRCm38) D1306V probably damaging Het
Nfkb1 A C 3: 135,589,329 (GRCm38) I918R possibly damaging Het
Nup50 A T 15: 84,933,658 (GRCm38) T93S probably benign Het
Nwd2 T C 5: 63,804,374 (GRCm38) Y434H probably benign Het
Olfr61 T C 7: 140,638,484 (GRCm38) V261A probably benign Het
Osbpl1a C A 18: 12,905,031 (GRCm38) V288L probably benign Het
Pan3 A G 5: 147,527,036 (GRCm38) E562G possibly damaging Het
Pappa T A 4: 65,180,889 (GRCm38) Y548* probably null Het
Phf3 A T 1: 30,810,789 (GRCm38) L1181Q probably damaging Het
Phip T C 9: 82,915,339 (GRCm38) H537R possibly damaging Het
Pkhd1l1 T C 15: 44,485,428 (GRCm38) I240T probably damaging Het
Pole G A 5: 110,290,502 (GRCm38) probably null Het
Polq T A 16: 37,011,942 (GRCm38) S15T unknown Het
Prrt2 T C 7: 127,020,224 (GRCm38) E23G possibly damaging Het
Prss37 A T 6: 40,517,826 (GRCm38) probably null Het
Prune2 T C 19: 17,000,036 (GRCm38) L45P probably damaging Het
Psd A T 19: 46,324,913 (GRCm38) M6K possibly damaging Het
Psmd1 A G 1: 86,089,997 (GRCm38) E510G possibly damaging Het
Ptch1 T G 13: 63,524,959 (GRCm38) E944A probably benign Het
Pxdn T A 12: 30,003,406 (GRCm38) I1194N probably damaging Het
Rbp3 C T 14: 33,956,018 (GRCm38) T641M probably damaging Het
Rgmb C A 17: 15,807,647 (GRCm38) R270L probably benign Het
Rpgrip1l A G 8: 91,280,716 (GRCm38) probably null Het
Rps2 G A 17: 24,720,379 (GRCm38) probably benign Het
Rsbn1l G T 5: 20,902,366 (GRCm38) A550E probably damaging Het
S1pr4 C T 10: 81,499,304 (GRCm38) R112H probably benign Het
Scfd2 T C 5: 74,531,177 (GRCm38) N148S probably damaging Het
Scin C T 12: 40,081,706 (GRCm38) M276I probably benign Het
Sec24d T C 3: 123,353,606 (GRCm38) I708T possibly damaging Het
Skint11 T A 4: 114,228,812 (GRCm38) F41I possibly damaging Het
Slc15a4 A T 5: 127,617,239 (GRCm38) F44Y possibly damaging Het
Slc6a18 A G 13: 73,675,806 (GRCm38) Y72H probably benign Het
Slc7a11 A T 3: 50,377,746 (GRCm38) probably null Het
Slc7a14 G T 3: 31,237,501 (GRCm38) N209K possibly damaging Het
Sstr2 T C 11: 113,624,431 (GRCm38) C59R probably damaging Het
Stab1 A G 14: 31,163,040 (GRCm38) probably null Het
Stxbp5l A G 16: 37,115,667 (GRCm38) Y1183H probably damaging Het
Svep1 A T 4: 58,135,628 (GRCm38) probably null Het
Tm9sf2 A G 14: 122,158,684 (GRCm38) T653A probably benign Het
Tmeff1 T C 4: 48,662,059 (GRCm38) S366P possibly damaging Het
Tnnt2 G T 1: 135,852,065 (GRCm38) W300L probably damaging Het
Traj32 A G 14: 54,186,103 (GRCm38) probably benign Het
Trp53bp2 A T 1: 182,441,639 (GRCm38) M223L probably benign Het
Tsga10 G A 1: 37,815,677 (GRCm38) T246M probably damaging Het
Txn2 A T 15: 77,926,670 (GRCm38) probably benign Het
Ubr3 T A 2: 69,938,198 (GRCm38) F450I probably damaging Het
Usp47 T C 7: 112,104,470 (GRCm38) probably null Het
Vars2 C T 17: 35,664,793 (GRCm38) R244Q probably damaging Het
Xrra1 T A 7: 99,897,596 (GRCm38) F251L probably damaging Het
Zfp804a G A 2: 82,257,519 (GRCm38) R564Q probably benign Het
Zfp983 T C 17: 21,658,967 (GRCm38) C29R probably damaging Het
Other mutations in Stag1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00649:Stag1 APN 9 100,776,808 (GRCm38) missense probably damaging 1.00
IGL01010:Stag1 APN 9 100,945,933 (GRCm38) missense probably benign 0.06
IGL01012:Stag1 APN 9 100,855,859 (GRCm38) missense possibly damaging 0.47
IGL01025:Stag1 APN 9 100,951,657 (GRCm38) missense possibly damaging 0.95
IGL01307:Stag1 APN 9 100,951,788 (GRCm38) intron probably benign
IGL02149:Stag1 APN 9 100,887,389 (GRCm38) missense probably benign 0.09
IGL02608:Stag1 APN 9 100,757,769 (GRCm38) missense probably null 0.99
IGL03008:Stag1 APN 9 100,776,791 (GRCm38) missense probably damaging 1.00
IGL03210:Stag1 APN 9 100,845,076 (GRCm38) missense possibly damaging 0.63
eto_o UTSW 9 100,796,716 (GRCm38) missense probably damaging 1.00
PIT4280001:Stag1 UTSW 9 100,942,716 (GRCm38) missense possibly damaging 0.95
R0070:Stag1 UTSW 9 100,956,408 (GRCm38) missense probably null 1.00
R0070:Stag1 UTSW 9 100,956,408 (GRCm38) missense probably null 1.00
R0349:Stag1 UTSW 9 100,776,784 (GRCm38) missense probably damaging 0.98
R0479:Stag1 UTSW 9 100,928,091 (GRCm38) missense probably benign 0.00
R0531:Stag1 UTSW 9 100,954,247 (GRCm38) makesense probably null
R0962:Stag1 UTSW 9 100,796,827 (GRCm38) missense probably damaging 1.00
R0976:Stag1 UTSW 9 100,930,016 (GRCm38) critical splice donor site probably null
R0976:Stag1 UTSW 9 100,776,824 (GRCm38) missense probably damaging 0.98
R1170:Stag1 UTSW 9 100,888,453 (GRCm38) intron probably benign
R1499:Stag1 UTSW 9 100,887,373 (GRCm38) intron probably benign
R1499:Stag1 UTSW 9 100,855,832 (GRCm38) missense possibly damaging 0.77
R1644:Stag1 UTSW 9 100,880,900 (GRCm38) intron probably benign
R1747:Stag1 UTSW 9 100,888,300 (GRCm38) missense probably benign
R1799:Stag1 UTSW 9 100,953,462 (GRCm38) splice site probably null
R1807:Stag1 UTSW 9 100,908,666 (GRCm38) missense probably benign 0.34
R1978:Stag1 UTSW 9 100,888,086 (GRCm38) missense probably benign 0.03
R2029:Stag1 UTSW 9 100,786,687 (GRCm38) missense probably damaging 1.00
R2161:Stag1 UTSW 9 100,889,595 (GRCm38) missense probably damaging 1.00
R2300:Stag1 UTSW 9 100,712,500 (GRCm38) missense possibly damaging 0.92
R2327:Stag1 UTSW 9 100,786,613 (GRCm38) missense possibly damaging 0.81
R2426:Stag1 UTSW 9 100,845,116 (GRCm38) critical splice donor site probably null
R2448:Stag1 UTSW 9 100,888,409 (GRCm38) missense probably benign 0.42
R3713:Stag1 UTSW 9 100,889,618 (GRCm38) missense probably benign 0.01
R3835:Stag1 UTSW 9 100,737,982 (GRCm38) missense probably damaging 0.97
R3862:Stag1 UTSW 9 100,944,785 (GRCm38) missense probably benign 0.02
R4398:Stag1 UTSW 9 100,956,606 (GRCm38) utr 3 prime probably benign
R4568:Stag1 UTSW 9 100,848,669 (GRCm38) missense probably damaging 1.00
R4651:Stag1 UTSW 9 100,796,716 (GRCm38) missense probably damaging 1.00
R4652:Stag1 UTSW 9 100,796,716 (GRCm38) missense probably damaging 1.00
R4653:Stag1 UTSW 9 100,796,716 (GRCm38) missense probably damaging 1.00
R4675:Stag1 UTSW 9 100,848,705 (GRCm38) missense probably damaging 1.00
R4709:Stag1 UTSW 9 100,738,039 (GRCm38) missense probably damaging 0.99
R4924:Stag1 UTSW 9 100,796,755 (GRCm38) missense possibly damaging 0.67
R5018:Stag1 UTSW 9 100,951,619 (GRCm38) missense probably benign 0.00
R5435:Stag1 UTSW 9 100,953,550 (GRCm38) missense probably benign 0.03
R5460:Stag1 UTSW 9 100,956,453 (GRCm38) splice site probably null
R5805:Stag1 UTSW 9 100,796,778 (GRCm38) missense probably damaging 1.00
R6127:Stag1 UTSW 9 100,951,697 (GRCm38) missense probably benign 0.05
R6313:Stag1 UTSW 9 100,757,733 (GRCm38) missense probably damaging 1.00
R6597:Stag1 UTSW 9 100,887,420 (GRCm38) missense probably benign 0.01
R6807:Stag1 UTSW 9 100,944,850 (GRCm38) missense probably damaging 1.00
R7099:Stag1 UTSW 9 100,944,826 (GRCm38) missense probably benign 0.02
R7167:Stag1 UTSW 9 100,945,889 (GRCm38) missense probably benign 0.05
R7395:Stag1 UTSW 9 100,796,728 (GRCm38) missense probably damaging 0.99
R7504:Stag1 UTSW 9 100,888,328 (GRCm38) missense probably benign 0.09
R7663:Stag1 UTSW 9 100,738,138 (GRCm38) missense probably damaging 0.98
R7769:Stag1 UTSW 9 100,944,827 (GRCm38) missense possibly damaging 0.86
R8245:Stag1 UTSW 9 100,929,893 (GRCm38) missense probably benign 0.01
R8343:Stag1 UTSW 9 100,757,766 (GRCm38) missense possibly damaging 0.95
R8473:Stag1 UTSW 9 100,880,787 (GRCm38) missense probably damaging 1.00
R8709:Stag1 UTSW 9 100,890,922 (GRCm38) intron probably benign
R8925:Stag1 UTSW 9 100,705,245 (GRCm38) missense possibly damaging 0.46
R8927:Stag1 UTSW 9 100,705,245 (GRCm38) missense possibly damaging 0.46
R8951:Stag1 UTSW 9 100,880,801 (GRCm38) missense probably damaging 1.00
R9138:Stag1 UTSW 9 100,947,282 (GRCm38) missense probably benign 0.01
R9233:Stag1 UTSW 9 100,929,971 (GRCm38) missense probably benign 0.00
R9246:Stag1 UTSW 9 100,888,276 (GRCm38) missense probably benign 0.00
R9419:Stag1 UTSW 9 100,929,914 (GRCm38) missense probably benign
R9442:Stag1 UTSW 9 100,954,253 (GRCm38) missense probably damaging 1.00
R9694:Stag1 UTSW 9 100,928,098 (GRCm38) missense probably benign 0.05
R9740:Stag1 UTSW 9 100,705,235 (GRCm38) missense probably damaging 0.98
Predicted Primers PCR Primer
(F):5'- TTCCTCATGTTGAACTGTGTAAGA -3'
(R):5'- GCATGTAAAACTGGCATTCTATAAACA -3'

Sequencing Primer
(F):5'- TAGCATGTGACTGAAAGCTCAAC -3'
(R):5'- GGAAAAGGCTTGTTTTCCTAT -3'
Posted On 2014-12-04