Incidental Mutation 'R4709:Stag1'
ID 355494
Institutional Source Beutler Lab
Gene Symbol Stag1
Ensembl Gene ENSMUSG00000037286
Gene Name STAG1 cohesin complex component
Synonyms SA-1, Scc3
MMRRC Submission 042018-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4709 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 100479762-100840597 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 100620092 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Leucine at position 65 (R65L)
Ref Sequence ENSEMBL: ENSMUSP00000116597 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000124487] [ENSMUST00000129269] [ENSMUST00000133388] [ENSMUST00000138405] [ENSMUST00000146312] [ENSMUST00000155108]
AlphaFold Q9D3E6
Predicted Effect probably benign
Transcript: ENSMUST00000041418
AA Change: R65L

PolyPhen 2 Score 0.373 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000040724
Gene: ENSMUSG00000037286
AA Change: R65L

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 possibly damaging
Transcript: ENSMUST00000123302
AA Change: R65L

PolyPhen 2 Score 0.659 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000117879
Gene: ENSMUSG00000037286
AA Change: R65L

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: ENSMUST00000124487
SMART Domains Protein: ENSMUSP00000123595
Gene: ENSMUSG00000037286

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000129269
AA Change: R65L

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286
AA Change: R65L

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: ENSMUST00000133388
AA Change: R65L

PolyPhen 2 Score 0.256 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000119637
Gene: ENSMUSG00000037286
AA Change: R65L

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000138405
AA Change: R65L

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000116322
Gene: ENSMUSG00000037286
AA Change: R65L

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 noncoding transcript
Transcript: ENSMUST00000143816
Predicted Effect probably damaging
Transcript: ENSMUST00000146312
AA Change: R65L

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000116597
Gene: ENSMUSG00000037286
AA Change: R65L

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 possibly damaging
Transcript: ENSMUST00000155108
AA Change: R65L

PolyPhen 2 Score 0.836 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000118952
Gene: ENSMUSG00000037286
AA Change: R65L

DomainStartEndE-ValueType
low complexity region 32 44 N/A INTRINSIC
low complexity region 59 72 N/A INTRINSIC
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.9%
Validation Efficiency 97% (77/79)
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: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcf1 G A 17: 36,271,069 (GRCm39) T463M probably damaging Het
Arhgap35 C T 7: 16,297,511 (GRCm39) G518D probably damaging Het
Arhgdia A G 11: 120,470,517 (GRCm39) Y110H probably damaging Het
Atp8b3 T C 10: 80,372,604 (GRCm39) probably null Het
Bpifb6 T A 2: 153,750,436 (GRCm39) I309N possibly damaging Het
Cbr4 T C 8: 61,943,061 (GRCm39) V77A possibly damaging Het
Cers2 A G 3: 95,227,534 (GRCm39) Y54C possibly damaging Het
Cnbp A T 6: 87,821,120 (GRCm39) H145Q probably damaging Het
Csmd1 A T 8: 16,073,905 (GRCm39) I2030N possibly damaging Het
Csmd1 A G 8: 16,760,522 (GRCm39) probably null Het
Dhodh T C 8: 110,328,170 (GRCm39) probably null Het
Dnah11 T A 12: 117,982,495 (GRCm39) Y2558F probably benign Het
Dysf C A 6: 84,074,697 (GRCm39) D499E probably damaging Het
En1 A T 1: 120,534,872 (GRCm39) Y387F unknown Het
Ephb2 C A 4: 136,423,363 (GRCm39) C305F probably damaging Het
Fryl A G 5: 73,238,315 (GRCm39) V1477A probably benign Het
Gimap3 A T 6: 48,742,327 (GRCm39) L201Q probably benign Het
Gm10801 T G 2: 98,494,246 (GRCm39) probably null Het
Grhl1 A G 12: 24,636,132 (GRCm39) I283V possibly damaging Het
Grid2ip T A 5: 143,374,658 (GRCm39) L926H probably damaging Het
Gtf2h2 G T 13: 100,605,523 (GRCm39) C82* probably null Het
Gtf2ird1 T C 5: 134,433,588 (GRCm39) T280A probably benign Het
Gzmd T C 14: 56,367,698 (GRCm39) I192V probably null Het
Hectd1 A G 12: 51,834,695 (GRCm39) V855A possibly damaging Het
Hey1 A G 3: 8,730,963 (GRCm39) probably benign Het
Hpx A G 7: 105,249,243 (GRCm39) S19P probably benign Het
Incenp G A 19: 9,853,964 (GRCm39) R696W unknown Het
Itgam T C 7: 127,700,709 (GRCm39) V493A probably damaging Het
Ldlrad3 A G 2: 101,900,343 (GRCm39) I53T probably damaging Het
Map3k7 G T 4: 31,985,700 (GRCm39) E208* probably null Het
Myh9 A T 15: 77,671,717 (GRCm39) I458N probably damaging Het
Myo1c C T 11: 75,560,856 (GRCm39) R770* probably null Het
Nectin3 T A 16: 46,284,306 (GRCm39) Y126F possibly damaging Het
Nek5 A T 8: 22,573,443 (GRCm39) N504K probably damaging Het
Nlrp4c T A 7: 6,068,424 (GRCm39) H108Q probably benign Het
Or10d5 A T 9: 39,861,165 (GRCm39) L301M probably damaging Het
Or2ak4 T C 11: 58,649,013 (GRCm39) V174A possibly damaging Het
Or2at1 A T 7: 99,416,989 (GRCm39) I207F probably damaging Het
Or5h17 A T 16: 58,820,458 (GRCm39) T137S probably benign Het
Or9a2 G T 6: 41,748,442 (GRCm39) Q264K probably benign Het
Or9i14 T A 19: 13,792,814 (GRCm39) I47F possibly damaging Het
Parp6 T C 9: 59,549,052 (GRCm39) I507T probably damaging Het
Pcdhb12 A G 18: 37,570,548 (GRCm39) T565A probably benign Het
Pclo A G 5: 14,828,572 (GRCm39) N4676D unknown Het
Pdlim1 T A 19: 40,211,180 (GRCm39) H278L probably benign Het
Pfkfb3 G A 2: 11,498,719 (GRCm39) T46M probably damaging Het
Plscr2 A G 9: 92,173,067 (GRCm39) Y203C probably damaging Het
Plxna1 T C 6: 89,311,733 (GRCm39) D924G possibly damaging Het
Postn T A 3: 54,292,031 (GRCm39) probably benign Het
Ptpn23 A G 9: 110,217,924 (GRCm39) S674P possibly damaging Het
Ranbp6 C T 19: 29,788,984 (GRCm39) R456Q probably benign Het
Rbm43 A T 2: 51,819,728 (GRCm39) V46E probably damaging Het
Rlig1 T C 10: 100,414,243 (GRCm39) I139V probably benign Het
Rtn4r A G 16: 17,969,046 (GRCm39) Y158C probably damaging Het
Ryr2 A G 13: 11,731,884 (GRCm39) I2352T probably damaging Het
Sbk2 G T 7: 4,960,577 (GRCm39) R198S possibly damaging Het
Scube3 G A 17: 28,386,166 (GRCm39) probably null Het
Slc45a1 G A 4: 150,722,697 (GRCm39) P396S probably benign Het
Slc4a10 A G 2: 62,087,861 (GRCm39) D418G probably null Het
Smarcad1 A G 6: 65,052,099 (GRCm39) T411A probably benign Het
Smtn G A 11: 3,474,663 (GRCm39) S716F probably damaging Het
Stat1 A T 1: 52,165,680 (GRCm39) D92V probably damaging Het
Ttn A G 2: 76,582,428 (GRCm39) Y22822H probably damaging Het
Vmn1r172 A G 7: 23,359,606 (GRCm39) T164A probably benign Het
Vmn2r118 A T 17: 55,917,860 (GRCm39) D217E probably damaging Het
Vmn2r26 A G 6: 124,030,924 (GRCm39) E553G probably damaging Het
Vmn2r96 T C 17: 18,803,088 (GRCm39) F333L probably benign Het
Ypel5 G A 17: 73,155,726 (GRCm39) R98H probably benign Het
Zfp719 C T 7: 43,239,656 (GRCm39) H415Y probably damaging Het
Zyg11a T C 4: 108,062,268 (GRCm39) S176G probably benign 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
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
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'- AGGCTCTCAAATTGCAGGAG -3'
(R):5'- GCACATTCCATGCAGGTTAC -3'

Sequencing Primer
(F):5'- CTCAAATTGCAGGAGAGTATATTGAG -3'
(R):5'- AGGTTACTGACTGCCTTGC -3'
Posted On 2015-10-21