Incidental Mutation 'R4398:Stag1'
ID 325591
Institutional Source Beutler Lab
Gene Symbol Stag1
Ensembl Gene ENSMUSG00000037286
Gene Name STAG1 cohesin complex component
Synonyms SA-1, Scc3
MMRRC Submission 041130-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4398 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 100479762-100840597 bp(+) (GRCm39)
Type of Mutation utr 3 prime
DNA Base Change (assembly) A to G at 100838659 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000118952 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000129269] [ENSMUST00000155108]
AlphaFold Q9D3E6
Predicted Effect probably benign
Transcript: ENSMUST00000041418
SMART Domains Protein: ENSMUSP00000040724
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-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 benign
Transcript: ENSMUST00000129269
SMART Domains Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286

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: ENSMUST00000143955
SMART Domains Protein: ENSMUSP00000115460
Gene: ENSMUSG00000037286

DomainStartEndE-ValueType
low complexity region 232 251 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000146934
SMART Domains Protein: ENSMUSP00000120974
Gene: ENSMUSG00000037286

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 noncoding transcript
Transcript: ENSMUST00000191345
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: 98.6%
  • 10x: 97.1%
  • 20x: 94.7%
Validation Efficiency 96% (53/55)
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts20 C A 15: 94,231,576 (GRCm39) R871L possibly damaging Het
Adcy5 G A 16: 35,089,363 (GRCm39) C520Y probably damaging Het
AI661453 G A 17: 47,779,042 (GRCm39) probably benign Het
Bptf T C 11: 107,001,670 (GRCm39) K481E probably damaging Het
Cnot10 T A 9: 114,460,949 (GRCm39) K74* probably null Het
Ctc1 C T 11: 68,913,697 (GRCm39) P200S probably damaging Het
Dact1 T C 12: 71,363,959 (GRCm39) Y210H probably damaging Het
Dbn1 T C 13: 55,623,194 (GRCm39) T430A probably benign Het
Dmd A C X: 82,765,624 (GRCm39) T657P probably benign Het
Efnb2 C T 8: 8,670,832 (GRCm39) R256H possibly damaging Het
Eif4a1 T C 11: 69,560,070 (GRCm39) I116M possibly damaging Het
F730035P03Rik A T 7: 99,429,475 (GRCm39) noncoding transcript Het
Fbn1 C T 2: 125,239,701 (GRCm39) V329I probably benign Het
Gpr20 G A 15: 73,568,125 (GRCm39) T88I probably benign Het
Herc1 T G 9: 66,386,735 (GRCm39) V3783G probably benign Het
Khdc1a A G 1: 21,420,617 (GRCm39) D79G possibly damaging Het
Klk1b16 A T 7: 43,790,851 (GRCm39) I218F probably damaging Het
Malrd1 C T 2: 16,155,594 (GRCm39) T2001I unknown Het
Mia3 A G 1: 183,111,733 (GRCm39) S556P probably damaging Het
Myo3a T A 2: 22,467,854 (GRCm39) D369E probably benign Het
Nelfa T C 5: 34,058,623 (GRCm39) D279G possibly damaging Het
Ntrk3 A T 7: 77,900,517 (GRCm39) C607* probably null Het
Or13a20 T C 7: 140,232,741 (GRCm39) V283A possibly damaging Het
Pclo A T 5: 14,825,380 (GRCm39) Q1371L probably damaging Het
Pdzd2 A T 15: 12,376,061 (GRCm39) V1358E probably benign Het
Pgr T C 9: 8,903,750 (GRCm39) probably null Het
Prag1 A G 8: 36,570,809 (GRCm39) D464G probably damaging Het
Prickle4 A G 17: 48,001,456 (GRCm39) probably benign Het
Prim2 A G 1: 33,551,192 (GRCm39) Y309H probably damaging Het
Prkaa1 A G 15: 5,206,642 (GRCm39) Q464R possibly damaging Het
Rab36 G A 10: 74,880,328 (GRCm39) V63I probably damaging Het
Rint1 T A 5: 23,999,445 (GRCm39) I78K possibly damaging Het
Rnf130 T A 11: 49,962,205 (GRCm39) F217Y probably benign Het
Smad7 T C 18: 75,527,234 (GRCm39) V360A probably damaging Het
Sp110 A C 1: 85,505,050 (GRCm39) F434C probably benign Het
Tlr12 T A 4: 128,509,988 (GRCm39) D754V probably benign Het
Tmf1 G A 6: 97,155,857 (GRCm39) P43L probably damaging Het
Togaram1 A G 12: 65,027,630 (GRCm39) N873S probably benign Het
Tsn C T 1: 118,238,799 (GRCm39) probably benign Het
Ubn1 A G 16: 4,882,289 (GRCm39) K250R probably damaging Het
Vmn1r25 A T 6: 57,955,812 (GRCm39) V159D probably damaging Het
Vmn2r89 T C 14: 51,689,551 (GRCm39) L18P probably damaging Het
Vps8 T G 16: 21,323,216 (GRCm39) N689K probably damaging Het
Ythdc1 T A 5: 86,963,513 (GRCm39) D30E possibly damaging Het
Ythdc1 G T 5: 86,983,679 (GRCm39) probably benign Het
Zfp407 G A 18: 84,580,856 (GRCm39) Q86* probably null Het
Zfp521 C T 18: 13,979,601 (GRCm39) E271K 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
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'- CAGACTTCTTTGACTCTGCAGC -3'
(R):5'- CACATCTGTACTGAGATAAGTCCAAC -3'

Sequencing Primer
(F):5'- GACTCTGCAGCTATCATAGAAGATG -3'
(R):5'- CTGTACTGAGATAAGTCCAACATTAG -3'
Posted On 2015-07-06