Incidental Mutation 'R4652:Stag1'
ID 351405
Institutional Source Beutler Lab
Gene Symbol Stag1
Ensembl Gene ENSMUSG00000037286
Gene Name STAG1 cohesin complex component
Synonyms SA-1, Scc3
MMRRC Submission 041912-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4652 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 100479762-100840597 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 100678769 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 230 (M230K)
Ref Sequence ENSEMBL: ENSMUSP00000116322 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000129269] [ENSMUST00000138405] [ENSMUST00000146312] [ENSMUST00000155108]
AlphaFold Q9D3E6
Predicted Effect probably damaging
Transcript: ENSMUST00000041418
AA Change: M230K

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000040724
Gene: ENSMUSG00000037286
AA Change: M230K

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 damaging
Transcript: ENSMUST00000123302
AA Change: M230K

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000117879
Gene: ENSMUSG00000037286
AA Change: M230K

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: M230K

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286
AA Change: M230K

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 damaging
Transcript: ENSMUST00000138405
AA Change: M230K

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000116322
Gene: ENSMUSG00000037286
AA Change: M230K

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: ENSMUST00000146312
AA Change: M172K
SMART Domains Protein: ENSMUSP00000116597
Gene: ENSMUSG00000037286
AA Change: M172K

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Pfam:STAG 99 196 4.2e-46 PFAM
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
Meta Mutation Damage Score 0.8683 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.7%
Validation Efficiency 95% (111/117)
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: 105 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310022B05Rik T A 8: 125,366,350 (GRCm39) Q131L probably damaging Het
2700049A03Rik G T 12: 71,211,320 (GRCm39) E685* probably null Het
2700049A03Rik A T 12: 71,211,321 (GRCm39) E685V possibly damaging Het
4933409G03Rik G A 2: 68,436,559 (GRCm39) E168K unknown Het
A830018L16Rik C A 1: 11,607,566 (GRCm39) probably benign Het
Adam26b A G 8: 43,974,375 (GRCm39) V209A possibly damaging Het
Adh6a T A 3: 138,031,876 (GRCm39) M256K probably benign Het
Ahnak2 T G 12: 112,741,271 (GRCm39) S128R possibly damaging Het
Angptl2 G T 2: 33,133,895 (GRCm39) D406Y probably damaging Het
Ano10 A T 9: 122,090,181 (GRCm39) Y377* probably null Het
Arfgef1 C T 1: 10,243,487 (GRCm39) D1021N probably damaging Het
Arhgap17 G A 7: 122,885,841 (GRCm39) probably benign Het
Arsi G A 18: 61,049,723 (GRCm39) G202E probably benign Het
Atp10b G A 11: 43,085,472 (GRCm39) G284S probably damaging Het
Atp13a4 A T 16: 29,271,421 (GRCm39) D498E probably damaging Het
C4a T A 17: 35,029,108 (GRCm39) noncoding transcript Het
Cacna1d C T 14: 29,817,365 (GRCm39) M1232I probably benign Het
Camsap3 A C 8: 3,650,689 (GRCm39) K223T possibly damaging Het
Cast A G 13: 74,894,133 (GRCm39) S171P probably benign Het
Cdh8 T A 8: 99,751,491 (GRCm39) D742V probably benign Het
Ceacam12 A G 7: 17,801,359 (GRCm39) T113A probably damaging Het
Cers3 G A 7: 66,431,604 (GRCm39) probably null Het
Cipc T C 12: 87,008,864 (GRCm39) V241A probably benign Het
Cntn5 C A 9: 9,704,917 (GRCm39) K832N possibly damaging Het
Col12a1 A T 9: 79,520,228 (GRCm39) D2815E probably damaging Het
Ctf2 T C 7: 127,318,556 (GRCm39) T148A probably benign Het
Cttnbp2 A G 6: 18,434,037 (GRCm39) I607T possibly damaging Het
Cux1 A T 5: 136,596,083 (GRCm39) N4K probably damaging Het
Dhx36 A T 3: 62,408,419 (GRCm39) L140M probably benign Het
Dhx58 T A 11: 100,592,185 (GRCm39) N288Y probably damaging Het
Dlgap1 T A 17: 71,068,090 (GRCm39) Y554N probably damaging Het
Dnah10 T C 5: 124,806,207 (GRCm39) Y127H probably benign Het
Dnah6 T C 6: 73,047,580 (GRCm39) M3140V probably benign Het
Dnd1 G A 18: 36,898,114 (GRCm39) probably benign Het
Dpy19l1 A C 9: 24,393,350 (GRCm39) S140A possibly damaging Het
Dyrk1a C T 16: 94,492,924 (GRCm39) T719I probably benign Het
Erlin1 T A 19: 44,029,231 (GRCm39) K234* probably null Het
Fndc7 T C 3: 108,770,135 (GRCm39) N597S probably benign Het
Folh1 C A 7: 86,393,633 (GRCm39) G360* probably null Het
Frmd4b T C 6: 97,272,716 (GRCm39) H846R probably benign Het
Gm10375 C A 14: 43,844,326 (GRCm39) probably null Het
Gm27047 T C 6: 130,607,479 (GRCm39) noncoding transcript Het
Gm7168 A G 17: 14,170,069 (GRCm39) R479G possibly damaging Het
Gm9996 T A 10: 29,019,754 (GRCm39) probably benign Het
Gnat3 T A 5: 18,220,568 (GRCm39) L247H probably damaging Het
H2-D1 T G 17: 35,485,492 (GRCm39) probably null Het
Hpf1 T G 8: 61,346,764 (GRCm39) S26R possibly damaging Het
Ift80 T A 3: 68,822,273 (GRCm39) N627I probably benign Het
Inpp5d A G 1: 87,593,173 (GRCm39) K91R probably benign Het
Irgc C A 7: 24,132,238 (GRCm39) R193L probably damaging Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Lamc1 T G 1: 153,104,523 (GRCm39) S59R probably damaging Het
Lrrc9 T C 12: 72,524,160 (GRCm39) W790R probably damaging Het
Man1a2 A G 3: 100,539,877 (GRCm39) L188P probably damaging Het
Med8 A T 4: 118,268,089 (GRCm39) E5V probably damaging Het
Mefv A G 16: 3,535,682 (GRCm39) L82P probably damaging Het
Mettl25 A T 10: 105,615,509 (GRCm39) C498* probably null Het
Mettl3 T A 14: 52,532,549 (GRCm39) I545F probably damaging Het
Mvp T A 7: 126,592,721 (GRCm39) I397F probably damaging Het
Nlrp14 A T 7: 106,781,024 (GRCm39) I74F probably benign Het
Nudt5 G A 2: 5,860,876 (GRCm39) probably benign Het
Nyap2 T A 1: 81,314,444 (GRCm39) D713E probably damaging Het
Obscn G A 11: 58,929,703 (GRCm39) R5824C probably damaging Het
Or4f6 G T 2: 111,838,595 (GRCm39) S312Y probably damaging Het
Or6c214 T C 10: 129,591,287 (GRCm39) I11V probably benign Het
Orc4 A T 2: 48,826,762 (GRCm39) probably benign Het
Pde10a T A 17: 8,975,885 (GRCm39) N3K possibly damaging Het
Pgm3 T A 9: 86,440,523 (GRCm39) R389S probably benign Het
Piwil4 G A 9: 14,623,604 (GRCm39) R529* probably null Het
Pkd2l2 A T 18: 34,542,889 (GRCm39) R20* probably null Het
Ppp4r3a T A 12: 101,049,170 (GRCm39) probably benign Het
Prkcq T C 2: 11,284,333 (GRCm39) V501A possibly damaging Het
Prkg1 T C 19: 30,572,412 (GRCm39) T400A probably damaging Het
Prps2 T C X: 166,135,288 (GRCm39) D183G probably damaging Het
Prrc2c A T 1: 162,550,843 (GRCm39) H40Q probably damaging Het
Ptcd1 A T 5: 145,091,985 (GRCm39) H371Q probably benign Het
Ptprk T C 10: 28,139,686 (GRCm39) I137T probably damaging Het
R3hdm1 T C 1: 128,112,181 (GRCm39) S422P probably damaging Het
Rapgef5 G A 12: 117,677,863 (GRCm39) G366E probably damaging Het
Rsf1 GCGGCGGCG GCGGCGGCGTCGGCGGCG 7: 97,229,126 (GRCm39) probably benign Het
Setd2 A G 9: 110,423,200 (GRCm39) D2085G possibly damaging Het
Sfxn3 A G 19: 45,039,313 (GRCm39) probably null Het
Sgce T C 6: 4,689,560 (GRCm39) probably benign Het
Sipa1l1 T A 12: 82,469,245 (GRCm39) L1248* probably null Het
Skint7 T G 4: 111,839,309 (GRCm39) M201R probably damaging Het
Slc18a1 A G 8: 69,496,583 (GRCm39) M360T possibly damaging Het
Srp68 A T 11: 116,164,840 (GRCm39) S31R probably benign Het
Strc A T 2: 121,204,829 (GRCm39) D985E possibly damaging Het
Tars3 T A 7: 65,339,717 (GRCm39) V704E probably damaging Het
Tbc1d2b A G 9: 90,089,940 (GRCm39) F863S probably damaging Het
Tek T C 4: 94,669,121 (GRCm39) S41P probably damaging Het
Top1 T C 2: 160,554,637 (GRCm39) Y463H probably damaging Het
Trim24 T G 6: 37,934,774 (GRCm39) probably null Het
Ttn A G 2: 76,576,979 (GRCm39) V24638A possibly damaging Het
Ttn A G 2: 76,701,213 (GRCm39) probably benign Het
Txndc11 A G 16: 10,892,986 (GRCm39) S915P probably benign Het
Tyro3 G C 2: 119,647,349 (GRCm39) G826A probably benign Het
Ubxn4 T A 1: 128,202,587 (GRCm39) W410R probably benign Het
Vmn1r193 C T 13: 22,403,695 (GRCm39) G99D probably damaging Het
Vmn2r109 T A 17: 20,761,656 (GRCm39) K567M probably damaging Het
Vmn2r23 T C 6: 123,718,689 (GRCm39) F681L probably damaging Het
Vrk2 T C 11: 26,439,803 (GRCm39) D256G probably damaging Het
Vwa3a T A 7: 120,378,138 (GRCm39) I476N probably damaging Het
Wdr81 A G 11: 75,342,066 (GRCm39) V1067A probably damaging Het
Zcwpw2 A G 9: 117,843,119 (GRCm39) noncoding transcript Het
Other mutations in Stag1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00649:Stag1 APN 9 100,658,861 (GRCm39) missense probably damaging 1.00
IGL01010:Stag1 APN 9 100,827,986 (GRCm39) missense probably benign 0.06
IGL01012:Stag1 APN 9 100,737,912 (GRCm39) missense possibly damaging 0.47
IGL01025:Stag1 APN 9 100,833,710 (GRCm39) missense possibly damaging 0.95
IGL01307:Stag1 APN 9 100,833,841 (GRCm39) intron probably benign
IGL02149:Stag1 APN 9 100,769,442 (GRCm39) missense probably benign 0.09
IGL02608:Stag1 APN 9 100,639,822 (GRCm39) missense probably null 0.99
IGL03008:Stag1 APN 9 100,658,844 (GRCm39) missense probably damaging 1.00
IGL03210:Stag1 APN 9 100,727,129 (GRCm39) missense possibly damaging 0.63
eto_o UTSW 9 100,678,769 (GRCm39) missense probably damaging 1.00
PIT4280001:Stag1 UTSW 9 100,824,769 (GRCm39) missense possibly damaging 0.95
R0070:Stag1 UTSW 9 100,838,461 (GRCm39) missense probably null 1.00
R0070:Stag1 UTSW 9 100,838,461 (GRCm39) missense probably null 1.00
R0349:Stag1 UTSW 9 100,658,837 (GRCm39) missense probably damaging 0.98
R0479:Stag1 UTSW 9 100,810,144 (GRCm39) missense probably benign 0.00
R0531:Stag1 UTSW 9 100,836,300 (GRCm39) makesense probably null
R0962:Stag1 UTSW 9 100,678,880 (GRCm39) missense probably damaging 1.00
R0976:Stag1 UTSW 9 100,812,069 (GRCm39) critical splice donor site probably null
R0976:Stag1 UTSW 9 100,658,877 (GRCm39) missense probably damaging 0.98
R1170:Stag1 UTSW 9 100,770,506 (GRCm39) intron probably benign
R1499:Stag1 UTSW 9 100,769,426 (GRCm39) intron probably benign
R1499:Stag1 UTSW 9 100,737,885 (GRCm39) missense possibly damaging 0.77
R1644:Stag1 UTSW 9 100,762,953 (GRCm39) intron probably benign
R1747:Stag1 UTSW 9 100,770,353 (GRCm39) missense probably benign
R1799:Stag1 UTSW 9 100,835,515 (GRCm39) splice site probably null
R1807:Stag1 UTSW 9 100,790,719 (GRCm39) missense probably benign 0.34
R1978:Stag1 UTSW 9 100,770,139 (GRCm39) missense probably benign 0.03
R2029:Stag1 UTSW 9 100,668,740 (GRCm39) missense probably damaging 1.00
R2161:Stag1 UTSW 9 100,771,648 (GRCm39) missense probably damaging 1.00
R2300:Stag1 UTSW 9 100,594,553 (GRCm39) missense possibly damaging 0.92
R2327:Stag1 UTSW 9 100,668,666 (GRCm39) missense possibly damaging 0.81
R2426:Stag1 UTSW 9 100,727,169 (GRCm39) critical splice donor site probably null
R2448:Stag1 UTSW 9 100,770,462 (GRCm39) missense probably benign 0.42
R2504:Stag1 UTSW 9 100,748,263 (GRCm39) missense probably damaging 0.99
R3713:Stag1 UTSW 9 100,771,671 (GRCm39) missense probably benign 0.01
R3835:Stag1 UTSW 9 100,620,035 (GRCm39) missense probably damaging 0.97
R3862:Stag1 UTSW 9 100,826,838 (GRCm39) missense probably benign 0.02
R4398:Stag1 UTSW 9 100,838,659 (GRCm39) utr 3 prime probably benign
R4568:Stag1 UTSW 9 100,730,722 (GRCm39) missense probably damaging 1.00
R4651:Stag1 UTSW 9 100,678,769 (GRCm39) missense probably damaging 1.00
R4653:Stag1 UTSW 9 100,678,769 (GRCm39) missense probably damaging 1.00
R4675:Stag1 UTSW 9 100,730,758 (GRCm39) missense probably damaging 1.00
R4709:Stag1 UTSW 9 100,620,092 (GRCm39) missense probably damaging 0.99
R4924:Stag1 UTSW 9 100,678,808 (GRCm39) missense possibly damaging 0.67
R5018:Stag1 UTSW 9 100,833,672 (GRCm39) missense probably benign 0.00
R5435:Stag1 UTSW 9 100,835,603 (GRCm39) missense probably benign 0.03
R5460:Stag1 UTSW 9 100,838,506 (GRCm39) splice site probably null
R5805:Stag1 UTSW 9 100,678,831 (GRCm39) missense probably damaging 1.00
R6127:Stag1 UTSW 9 100,833,750 (GRCm39) missense probably benign 0.05
R6313:Stag1 UTSW 9 100,639,786 (GRCm39) missense probably damaging 1.00
R6597:Stag1 UTSW 9 100,769,473 (GRCm39) missense probably benign 0.01
R6807:Stag1 UTSW 9 100,826,903 (GRCm39) missense probably damaging 1.00
R7099:Stag1 UTSW 9 100,826,879 (GRCm39) missense probably benign 0.02
R7167:Stag1 UTSW 9 100,827,942 (GRCm39) missense probably benign 0.05
R7395:Stag1 UTSW 9 100,678,781 (GRCm39) missense probably damaging 0.99
R7504:Stag1 UTSW 9 100,770,381 (GRCm39) missense probably benign 0.09
R7663:Stag1 UTSW 9 100,620,191 (GRCm39) missense probably damaging 0.98
R7769:Stag1 UTSW 9 100,826,880 (GRCm39) missense possibly damaging 0.86
R8245:Stag1 UTSW 9 100,811,946 (GRCm39) missense probably benign 0.01
R8343:Stag1 UTSW 9 100,639,819 (GRCm39) missense possibly damaging 0.95
R8473:Stag1 UTSW 9 100,762,840 (GRCm39) missense probably damaging 1.00
R8709:Stag1 UTSW 9 100,772,975 (GRCm39) intron probably benign
R8925:Stag1 UTSW 9 100,587,298 (GRCm39) missense possibly damaging 0.46
R8927:Stag1 UTSW 9 100,587,298 (GRCm39) missense possibly damaging 0.46
R8951:Stag1 UTSW 9 100,762,854 (GRCm39) missense probably damaging 1.00
R9138:Stag1 UTSW 9 100,829,335 (GRCm39) missense probably benign 0.01
R9233:Stag1 UTSW 9 100,812,024 (GRCm39) missense probably benign 0.00
R9246:Stag1 UTSW 9 100,770,329 (GRCm39) missense probably benign 0.00
R9419:Stag1 UTSW 9 100,811,967 (GRCm39) missense probably benign
R9442:Stag1 UTSW 9 100,836,306 (GRCm39) missense probably damaging 1.00
R9694:Stag1 UTSW 9 100,810,151 (GRCm39) missense probably benign 0.05
R9740:Stag1 UTSW 9 100,587,288 (GRCm39) missense probably damaging 0.98
Predicted Primers PCR Primer
(F):5'- CAACTGAGATTAGTCTATTCCTGTCAG -3'
(R):5'- GACCCGTATGAATTTTCTATTGTCC -3'

Sequencing Primer
(F):5'- AGATTAGTCTATTCCTGTCAGTTACC -3'
(R):5'- AACTTTCTGTGCAGCCAAGG -3'
Posted On 2015-10-08