Incidental Mutation 'R4651:Stag1'
ID 351297
Institutional Source Beutler Lab
Gene Symbol Stag1
Ensembl Gene ENSMUSG00000037286
Gene Name STAG1 cohesin complex component
Synonyms SA-1, Scc3
MMRRC Submission 041911-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4651 (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: 97.3%
  • 20x: 95.3%
Validation Efficiency 97% (98/101)
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: 91 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
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
Ahnak2 T G 12: 112,741,271 (GRCm39) S128R possibly damaging Het
Ankrd26 T C 6: 118,492,787 (GRCm39) D1319G probably benign Het
Ankrd35 T C 3: 96,591,343 (GRCm39) V543A probably benign Het
Ano10 A T 9: 122,090,181 (GRCm39) Y377* probably null 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
Atp5f1c A G 2: 10,068,287 (GRCm39) F180S probably damaging Het
Btnl4 A G 17: 34,691,602 (GRCm39) S296P probably benign Het
Cast A G 13: 74,894,133 (GRCm39) S171P probably benign Het
Catsperb G A 12: 101,507,771 (GRCm39) A513T probably benign Het
Ccnf C A 17: 24,450,760 (GRCm39) R406L probably damaging Het
Ceacam12 A G 7: 17,801,359 (GRCm39) T113A probably damaging Het
Cipc T C 12: 87,008,864 (GRCm39) V241A probably benign Het
Col12a1 A T 9: 79,520,228 (GRCm39) D2815E probably damaging Het
Cpox G T 16: 58,491,050 (GRCm39) R87L possibly damaging 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
Cyp3a25 T C 5: 145,931,701 (GRCm39) T136A probably benign Het
Dhx58 T A 11: 100,592,185 (GRCm39) N288Y probably damaging Het
Dnah10 T C 5: 124,806,207 (GRCm39) Y127H probably benign Het
Dnd1 G A 18: 36,898,114 (GRCm39) probably benign Het
Ehmt2 C A 17: 35,132,790 (GRCm39) N1171K probably damaging Het
Fanci T A 7: 79,085,004 (GRCm39) M838K possibly damaging Het
Flot1 T C 17: 36,143,436 (GRCm39) probably benign Het
Gad2 A T 2: 22,558,374 (GRCm39) D364V probably damaging Het
Gm10375 C A 14: 43,844,326 (GRCm39) probably null Het
Gm9996 T A 10: 29,019,754 (GRCm39) probably benign Het
Gnat3 T A 5: 18,220,568 (GRCm39) L247H probably damaging Het
Ip6k3 C T 17: 27,364,265 (GRCm39) C261Y probably damaging Het
Irgc C A 7: 24,132,238 (GRCm39) R193L probably damaging Het
Kalrn G T 16: 33,996,761 (GRCm39) P1477Q probably damaging Het
Kyat1 G T 2: 30,084,076 (GRCm39) H15N probably benign Het
Lamc1 T G 1: 153,104,523 (GRCm39) S59R probably damaging Het
Llgl1 A G 11: 60,599,477 (GRCm39) D486G possibly damaging Het
Lrrc9 T C 12: 72,524,160 (GRCm39) W790R probably damaging Het
Lsm2 T A 17: 35,204,571 (GRCm39) probably benign 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
Mettl25b T C 3: 87,834,979 (GRCm39) H107R probably benign Het
Mettl3 T A 14: 52,532,549 (GRCm39) I545F probably damaging Het
Naa20 CTCTAGA C 2: 145,753,752 (GRCm39) probably benign Het
Ncapg2 T A 12: 116,389,407 (GRCm39) N342K probably damaging Het
Ndufaf6 T A 4: 11,062,070 (GRCm39) Y187F probably damaging Het
Nomo1 T A 7: 45,717,866 (GRCm39) I799N 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
Or6n2 A G 1: 173,897,394 (GRCm39) I177V possibly damaging Het
Or7g30 T A 9: 19,352,591 (GRCm39) C127* probably null Het
Pgm3 T A 9: 86,440,523 (GRCm39) R389S probably benign Het
Pkd2l2 A T 18: 34,542,889 (GRCm39) R20* probably null Het
Pkhd1 T A 1: 20,451,747 (GRCm39) I2183F probably damaging Het
Ppp4r3a T A 12: 101,049,170 (GRCm39) probably benign Het
Prpf38b G A 3: 108,811,408 (GRCm39) probably benign Het
Prpf4b A T 13: 35,083,954 (GRCm39) M908L probably benign 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
Ptprk T C 10: 28,139,686 (GRCm39) I137T probably damaging Het
Sdr42e1 T C 8: 118,390,360 (GRCm39) T94A probably benign Het
Setd2 A G 9: 110,423,200 (GRCm39) D2085G possibly damaging Het
Sgce T C 6: 4,689,560 (GRCm39) probably benign Het
Shisa3 A G 5: 67,765,992 (GRCm39) D81G probably damaging 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
Slc5a3 T A 16: 91,874,090 (GRCm39) V49E probably benign Het
Slc9c1 A T 16: 45,367,756 (GRCm39) *163L probably null Het
Smyd3 A G 1: 178,871,306 (GRCm39) Y358H probably benign 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
Syne2 A G 12: 76,036,013 (GRCm39) T3767A probably damaging Het
Sytl2 C A 7: 90,024,633 (GRCm39) P207Q 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
Trim38 A T 13: 23,966,952 (GRCm39) D133V probably damaging Het
Ttn A G 2: 76,576,979 (GRCm39) V24638A possibly damaging Het
Ttn A G 2: 76,701,213 (GRCm39) probably benign Het
Tyro3 G C 2: 119,647,349 (GRCm39) G826A probably benign Het
Ube2b A G 11: 51,886,199 (GRCm39) probably null Het
Ubxn4 T A 1: 128,202,587 (GRCm39) W410R probably benign Het
Unc45a T C 7: 79,982,777 (GRCm39) K383E possibly damaging Het
Usp7 A C 16: 8,516,278 (GRCm39) probably benign Het
Vmn1r193 C T 13: 22,403,695 (GRCm39) G99D probably damaging Het
Vrk2 T C 11: 26,439,803 (GRCm39) D256G probably damaging Het
Wdr81 A G 11: 75,342,066 (GRCm39) V1067A probably damaging Het
Wiz C T 17: 32,576,655 (GRCm39) R624Q 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
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'- ACTGAGATTAGTCTATTCCTGTCAG -3'
(R):5'- TGTCACCCTTACTCAATGGTG -3'

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