Incidental Mutation 'R0349:Stag1'
ID 36093
Institutional Source Beutler Lab
Gene Symbol Stag1
Ensembl Gene ENSMUSG00000037286
Gene Name STAG1 cohesin complex component
Synonyms SA-1, Scc3
MMRRC Submission 038556-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0349 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 100479762-100840597 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 100658837 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Lysine at position 141 (N141K)
Ref Sequence ENSEMBL: ENSMUSP00000119637 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000129269] [ENSMUST00000133388] [ENSMUST00000138405] [ENSMUST00000146312] [ENSMUST00000155108]
AlphaFold Q9D3E6
Predicted Effect probably benign
Transcript: ENSMUST00000041418
AA Change: N141K

PolyPhen 2 Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000040724
Gene: ENSMUSG00000037286
AA Change: N141K

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
AA Change: N141K

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000117879
Gene: ENSMUSG00000037286
AA Change: N141K

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 benign
Transcript: ENSMUST00000129269
AA Change: N141K

PolyPhen 2 Score 0.063 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286
AA Change: N141K

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: ENSMUST00000133388
AA Change: N141K

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000119637
Gene: ENSMUSG00000037286
AA Change: N141K

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000138405
AA Change: N141K

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
SMART Domains Protein: ENSMUSP00000116322
Gene: ENSMUSG00000037286
AA Change: N141K

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 probably benign
Transcript: ENSMUST00000146312
SMART Domains Protein: ENSMUSP00000116597
Gene: ENSMUSG00000037286

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 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: 99.3%
  • 3x: 98.7%
  • 10x: 97.1%
  • 20x: 95.3%
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: 84 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A1cf A T 19: 31,910,062 (GRCm39) S285C possibly damaging Het
Abcc9 A T 6: 142,610,351 (GRCm39) N604K probably benign Het
Acsbg3 T A 17: 57,192,169 (GRCm39) Y577* probably null Het
Adgrl3 A G 5: 81,919,491 (GRCm39) T1192A probably damaging Het
Aldh1l2 A T 10: 83,326,478 (GRCm39) Y800N probably damaging Het
Ano3 A T 2: 110,491,832 (GRCm39) V865D probably damaging Het
App A T 16: 84,810,568 (GRCm39) L545Q probably damaging Het
Atp10a A G 7: 58,453,215 (GRCm39) D798G probably damaging Het
B3galnt2 T C 13: 14,166,059 (GRCm39) V318A probably benign Het
Clcn3 T A 8: 61,394,382 (GRCm39) D49V possibly damaging Het
Clcn6 T A 4: 148,108,651 (GRCm39) K126M possibly damaging Het
Cntln T A 4: 84,914,722 (GRCm39) S510T probably damaging Het
Csk A C 9: 57,535,477 (GRCm39) C290W probably damaging Het
Dmxl1 T A 18: 50,012,349 (GRCm39) M1502K probably damaging Het
Dpy19l2 T A 9: 24,607,218 (GRCm39) N81I possibly damaging Het
Dpyd T A 3: 118,710,748 (GRCm39) C385* probably null Het
Dst G A 1: 34,238,634 (GRCm39) V1765I probably benign Het
Eif5b A G 1: 38,071,447 (GRCm39) S459G probably benign Het
Fam83d A G 2: 158,621,768 (GRCm39) I160V possibly damaging Het
Fat3 A G 9: 15,942,476 (GRCm39) F1299L probably damaging Het
Fmn1 A G 2: 113,196,141 (GRCm39) I614V unknown Het
Fsd1l T A 4: 53,679,854 (GRCm39) V184E probably damaging Het
Fyco1 A G 9: 123,626,727 (GRCm39) V1328A probably damaging Het
Ganab T A 19: 8,889,016 (GRCm39) N572K probably null Het
Gbp10 T A 5: 105,368,942 (GRCm39) D299V possibly damaging Het
Gpr83 T G 9: 14,779,563 (GRCm39) L205R probably damaging Het
Hapln2 G A 3: 87,930,936 (GRCm39) P152S probably damaging Het
Htatip2 T C 7: 49,423,140 (GRCm39) Y232H probably benign Het
Itga2b C T 11: 102,358,252 (GRCm39) V158I probably damaging Het
Kansl3 T C 1: 36,390,864 (GRCm39) D390G probably damaging Het
Kcnh2 T C 5: 24,556,235 (GRCm39) D16G probably benign Het
Kctd8 A T 5: 69,498,353 (GRCm39) F98I probably damaging Het
Kif21b A T 1: 136,077,049 (GRCm39) E357V probably damaging Het
Kmt5c C T 7: 4,749,594 (GRCm39) R371C probably damaging Het
Kndc1 T C 7: 139,490,220 (GRCm39) F241L probably benign Het
Lrba A G 3: 86,447,312 (GRCm39) D2052G probably damaging Het
Lsr T A 7: 30,658,698 (GRCm39) I54F probably damaging Het
Matk G T 10: 81,094,328 (GRCm39) L28F probably benign Het
Mdn1 T C 4: 32,750,318 (GRCm39) L4429P probably damaging Het
Med29 CCTGCTGCTGCTGCTGC CCTGCTGCTGCTGC 7: 28,091,935 (GRCm39) probably benign Het
Msln G T 17: 25,969,250 (GRCm39) Q407K possibly damaging Het
Msr1 C T 8: 40,034,868 (GRCm39) G428R probably damaging Het
Myof A G 19: 37,899,417 (GRCm39) I1040T probably damaging Het
Nckap5 A G 1: 125,954,171 (GRCm39) S794P probably benign Het
Nfkbiz C T 16: 55,639,354 (GRCm39) probably null Het
Nr2c1 C T 10: 94,031,044 (GRCm39) S535L probably damaging Het
Opn3 A C 1: 175,519,870 (GRCm39) L78R probably damaging Het
Or11h4b G A 14: 50,918,711 (GRCm39) R127C probably benign Het
Or52n3 A T 7: 104,530,199 (GRCm39) D95V possibly damaging Het
Or5b12 A T 19: 12,897,299 (GRCm39) C125S probably damaging Het
Otulinl T A 15: 27,664,876 (GRCm39) I27L probably benign Het
Pcdhb9 A G 18: 37,535,632 (GRCm39) N542S probably damaging Het
Pdc T A 1: 150,209,178 (GRCm39) N220K probably benign Het
Pde6c A T 19: 38,150,797 (GRCm39) N569Y probably damaging Het
Pgm1 A T 4: 99,820,814 (GRCm39) K219M probably damaging Het
Pitpnb C T 5: 111,494,992 (GRCm39) T99M possibly damaging Het
Pou6f2 T A 13: 18,326,589 (GRCm39) Q71L probably damaging Het
Pramel24 T G 4: 143,453,629 (GRCm39) W246G probably benign Het
Prkd1 C A 12: 50,413,139 (GRCm39) L677F probably damaging Het
Ranbp17 T C 11: 33,450,689 (GRCm39) I78V probably benign Het
Rnft2 T A 5: 118,339,450 (GRCm39) K362M possibly damaging Het
Rprd1a T A 18: 24,639,904 (GRCm39) E259V possibly damaging Het
Scara3 A T 14: 66,169,230 (GRCm39) I129N probably damaging Het
Scgb1a1 A T 19: 9,062,753 (GRCm39) probably null Het
Sec16b A T 1: 157,359,746 (GRCm39) probably null Het
Slc18a1 A T 8: 69,524,753 (GRCm39) M167K probably damaging Het
Slc6a15 C T 10: 103,254,086 (GRCm39) A674V probably benign Het
Slc6a3 T C 13: 73,715,676 (GRCm39) F437S probably damaging Het
Snrnp40 C G 4: 130,271,836 (GRCm39) probably null Het
Sun2 T C 15: 79,614,433 (GRCm39) E321G probably damaging Het
Taar2 C A 10: 23,817,327 (GRCm39) T289K possibly damaging Het
Taar2 T C 10: 23,817,407 (GRCm39) Y316H probably benign Het
Tbcd T A 11: 121,493,809 (GRCm39) probably null Het
Tecr G A 8: 84,298,904 (GRCm39) T106I probably damaging Het
Thoc2l T C 5: 104,667,842 (GRCm39) L788P possibly damaging Het
Tmem60 T G 5: 21,091,628 (GRCm39) V131G probably benign Het
Uimc1 A G 13: 55,223,804 (GRCm39) V156A probably benign Het
Usp28 G A 9: 48,921,581 (GRCm39) W266* probably null Het
Vmn2r17 T A 5: 109,576,202 (GRCm39) S358T probably damaging Het
Wwc2 T A 8: 48,321,701 (GRCm39) Y471F unknown Het
Ythdc1 C T 5: 86,983,579 (GRCm39) R675C probably damaging Het
Zfp30 T C 7: 29,493,029 (GRCm39) S428P probably damaging Het
Zfp462 T A 4: 55,008,768 (GRCm39) C245S probably benign Het
Zscan30 T C 18: 24,104,455 (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
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
R4652: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'- CCTTGGTCAGTGTAACCCAGCCT -3'
(R):5'- GCATTATGCCAACTTTAACTCATGCCAT -3'

Sequencing Primer
(F):5'- gggggtagaaaatggcttagtg -3'
(R):5'- CAACTTTAACTCATGCCATTATGAAC -3'
Posted On 2013-05-09