Incidental Mutation 'R1978:Stag1'
ID 222024
Institutional Source Beutler Lab
Gene Symbol Stag1
Ensembl Gene ENSMUSG00000037286
Gene Name STAG1 cohesin complex component
Synonyms SA-1, Scc3
MMRRC Submission 039991-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1978 (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 G at 100770139 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Serine at position 603 (I603S)
Ref Sequence ENSEMBL: ENSMUSP00000116205 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000129269] [ENSMUST00000155108]
AlphaFold Q9D3E6
Predicted Effect probably benign
Transcript: ENSMUST00000041418
AA Change: I603S

PolyPhen 2 Score 0.018 (Sensitivity: 0.95; Specificity: 0.80)
SMART Domains Protein: ENSMUSP00000040724
Gene: ENSMUSG00000037286
AA Change: I603S

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
AA Change: I603S

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286
AA Change: I603S

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 unknown
Transcript: ENSMUST00000146934
AA Change: I213S
SMART Domains Protein: ENSMUSP00000120974
Gene: ENSMUSG00000037286
AA Change: I213S

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: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.9%
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610040J01Rik T A 5: 64,055,880 (GRCm39) C205* probably null Het
4921539E11Rik T A 4: 103,127,961 (GRCm39) T55S possibly damaging Het
Akap12 A G 10: 4,263,855 (GRCm39) D88G probably benign Het
Ankrd53 C A 6: 83,740,185 (GRCm39) F84L probably damaging Het
Apol7b A C 15: 77,307,539 (GRCm39) F319V probably damaging Het
Bsn A G 9: 107,991,748 (GRCm39) S1335P probably benign Het
Cep192 T C 18: 67,936,228 (GRCm39) probably null Het
Cfap57 A G 4: 118,450,329 (GRCm39) S598P probably benign Het
Commd8 T C 5: 72,322,842 (GRCm39) H25R probably damaging Het
Crisp4 T C 1: 18,198,889 (GRCm39) I143V probably benign Het
Cyp4a12b A T 4: 115,295,342 (GRCm39) T483S probably benign Het
Dbx2 C T 15: 95,530,234 (GRCm39) M244I probably damaging Het
Dnah6 T G 6: 73,098,953 (GRCm39) H1982P possibly damaging Het
Fam220a C A 5: 143,548,882 (GRCm39) P98Q probably damaging Het
Ggnbp1 A G 17: 27,248,517 (GRCm39) K29E possibly damaging Het
Gm14569 A C X: 35,695,781 (GRCm39) M976R probably benign Het
Hck G T 2: 152,971,776 (GRCm39) W112C probably damaging Het
Heatr5a A T 12: 51,986,441 (GRCm39) S591T possibly damaging Het
Hhat A G 1: 192,399,415 (GRCm39) S242P probably benign Het
Hnrnpll A G 17: 80,351,947 (GRCm39) S333P probably benign Het
Hoxc6 T C 15: 102,918,439 (GRCm39) probably null Het
Inpp5j G A 11: 3,452,150 (GRCm39) P367S probably damaging Het
Lamc2 A G 1: 153,009,343 (GRCm39) probably null Het
Loxhd1 T A 18: 77,409,338 (GRCm39) I194N possibly damaging Het
Miga1 CCAGGGCAG CCAG 3: 152,040,941 (GRCm39) probably null Het
Mkln1 C T 6: 31,467,465 (GRCm39) Q60* probably null Het
Muc21 T A 17: 35,933,857 (GRCm39) probably benign Het
Mybph C A 1: 134,124,734 (GRCm39) H185N probably benign Het
Myo1g T C 11: 6,470,829 (GRCm39) D9G possibly damaging Het
Myo6 A T 9: 80,136,207 (GRCm39) D110V probably damaging Het
Ncoa7 A G 10: 30,567,295 (GRCm39) V412A probably benign Het
Neb T C 2: 52,177,357 (GRCm39) K1328R probably damaging Het
Olfm5 T A 7: 103,813,948 (GRCm39) Q22L unknown Het
Or10ak7 A T 4: 118,791,381 (GRCm39) Y221* probably null Het
Or4d11 T C 19: 12,013,705 (GRCm39) T134A probably benign Het
Or5j1 C T 2: 86,879,179 (GRCm39) V134M possibly damaging Het
Or6b3 C A 1: 92,439,499 (GRCm39) G84C probably damaging Het
Or6p1 T A 1: 174,258,657 (GRCm39) I221N probably damaging Het
Or7a39 A G 10: 78,715,114 (GRCm39) Y36C probably damaging Het
P3h1 A T 4: 119,105,173 (GRCm39) Q717L probably null Het
Pclo T C 5: 14,763,809 (GRCm39) I4094T unknown Het
Pfdn6 G A 17: 34,158,051 (GRCm39) R73W probably benign Het
Phyhipl A C 10: 70,395,591 (GRCm39) M205R possibly damaging Het
Pitpnm1 C T 19: 4,157,973 (GRCm39) probably null Het
Plcg1 A G 2: 160,594,498 (GRCm39) probably null Het
Pnldc1 A G 17: 13,125,392 (GRCm39) S81P possibly damaging Het
Pno1 T C 11: 17,154,519 (GRCm39) I221V possibly damaging Het
Porcn A G X: 8,070,540 (GRCm39) V75A probably damaging Het
Prkcg T A 7: 3,353,862 (GRCm39) C69S probably damaging Het
Rbbp6 G T 7: 122,598,711 (GRCm39) probably benign Het
Resf1 T A 6: 149,227,930 (GRCm39) N325K probably benign Het
Rif1 GCCACCA GCCA 2: 52,000,336 (GRCm39) probably benign Het
Scly A G 1: 91,247,891 (GRCm39) D413G probably damaging Het
Scn11a G A 9: 119,609,861 (GRCm39) R996* probably null Het
Skic3 T C 13: 76,282,934 (GRCm39) V752A probably benign Het
Slc6a13 A T 6: 121,309,332 (GRCm39) D281V probably damaging Het
Slfn5 T C 11: 82,847,442 (GRCm39) V109A probably benign Het
Smyd1 A T 6: 71,289,703 (GRCm39) probably null Het
Snx29 T A 16: 11,185,588 (GRCm39) M57K probably benign Het
Svep1 C A 4: 58,097,292 (GRCm39) C1417F possibly damaging Het
Tbc1d23 T C 16: 57,009,714 (GRCm39) I392V probably benign Het
Tchh T C 3: 93,354,106 (GRCm39) L1182P unknown Het
Tle3 T A 9: 61,301,915 (GRCm39) V108E probably damaging Het
Tmem144 T C 3: 79,732,707 (GRCm39) probably null Het
Tpr T G 1: 150,295,658 (GRCm39) L894V possibly damaging Het
Trappc9 A T 15: 72,871,874 (GRCm39) V472E probably damaging Het
Trim38 T C 13: 23,975,081 (GRCm39) V340A probably damaging Het
Ttn A T 2: 76,641,587 (GRCm39) L5176Q possibly damaging Het
Vmn1r12 T A 6: 57,136,494 (GRCm39) I197N possibly damaging Het
Vmn1r26 T C 6: 57,986,111 (GRCm39) Y26C possibly damaging Het
Vwa3a A G 7: 120,358,177 (GRCm39) I83V probably null Het
Xirp1 C T 9: 119,847,657 (GRCm39) E409K probably benign Het
Zc3h14 T G 12: 98,730,181 (GRCm39) I46R probably damaging Het
Zfp976 A G 7: 42,263,265 (GRCm39) C191R probably damaging 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
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'- TCTAGGTGCTAACAGCCAAAGAAAG -3'
(R):5'- AAGCATCCAGGTGCTGAAGG -3'

Sequencing Primer
(F):5'- GGAAAACTCAAATTGATGATAGGAAC -3'
(R):5'- CATCAGTTGTTGACTAACCTA -3'
Posted On 2014-08-25