Incidental Mutation 'R4924:Stag1'
ID 378874
Institutional Source Beutler Lab
Gene Symbol Stag1
Ensembl Gene ENSMUSG00000037286
Gene Name STAG1 cohesin complex component
Synonyms SA-1, Scc3
MMRRC Submission 042526-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4924 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 100479762-100840597 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 100678808 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Leucine at position 243 (H243L)
Ref Sequence ENSEMBL: ENSMUSP00000116322 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000041418] [ENSMUST00000123302] [ENSMUST00000129269] [ENSMUST00000138405] [ENSMUST00000146312] [ENSMUST00000155108]
AlphaFold Q9D3E6
Predicted Effect probably benign
Transcript: ENSMUST00000041418
AA Change: H243L

PolyPhen 2 Score 0.025 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000040724
Gene: ENSMUSG00000037286
AA Change: H243L

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: H243L

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000117879
Gene: ENSMUSG00000037286
AA Change: H243L

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: H243L

PolyPhen 2 Score 0.025 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000116205
Gene: ENSMUSG00000037286
AA Change: H243L

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 possibly damaging
Transcript: ENSMUST00000138405
AA Change: H243L

PolyPhen 2 Score 0.665 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000116322
Gene: ENSMUSG00000037286
AA Change: H243L

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: H185L
SMART Domains Protein: ENSMUSP00000116597
Gene: ENSMUSG00000037286
AA Change: H185L

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
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.2%
  • 10x: 96.0%
  • 20x: 91.6%
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: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aatk G A 11: 119,902,351 (GRCm39) H625Y probably damaging Het
Adamts4 C T 1: 171,086,643 (GRCm39) R812W probably damaging Het
Ajuba A C 14: 54,809,056 (GRCm39) probably null Het
Aox1 T A 1: 58,344,503 (GRCm39) V532D probably damaging Het
Arpc1b G A 5: 145,063,625 (GRCm39) S295N probably benign Het
Baiap2 A G 11: 119,887,850 (GRCm39) S335G probably damaging Het
Brap T G 5: 121,803,318 (GRCm39) N155K probably damaging Het
Btn1a1 A G 13: 23,648,396 (GRCm39) probably benign Het
Ccl12 G A 11: 81,993,475 (GRCm39) V38I probably benign Het
Cemip T C 7: 83,602,146 (GRCm39) Y881C probably damaging Het
Cep128 T C 12: 90,989,174 (GRCm39) silent Het
Chd5 A C 4: 152,450,886 (GRCm39) D670A possibly damaging Het
Cmip T C 8: 117,983,994 (GRCm39) Y52H probably benign Het
Dmtn A G 14: 70,855,399 (GRCm39) I30T probably benign Het
Dscaml1 T A 9: 45,656,487 (GRCm39) M1609K probably damaging Het
Edar C A 10: 58,465,197 (GRCm39) E55D probably damaging Het
Ehmt1 A T 2: 24,729,734 (GRCm39) I601N probably damaging Het
Fam120a A T 13: 49,055,572 (GRCm39) N705K probably benign Het
Gm21718 G T 14: 51,550,292 (GRCm39) noncoding transcript Het
Gnaz A G 10: 74,827,545 (GRCm39) D99G probably benign Het
Helz G A 11: 107,493,165 (GRCm39) G196D probably damaging Het
Hif1a T C 12: 73,986,331 (GRCm39) S341P probably damaging Het
Hivep1 G T 13: 42,311,792 (GRCm39) S1344I probably benign Het
Hspa1l T A 17: 35,196,832 (GRCm39) Y290* probably null Het
Ift81 A G 5: 122,732,679 (GRCm39) L285S possibly damaging Het
Inpp4b T A 8: 82,849,253 (GRCm39) N891K probably damaging Het
Irx6 C T 8: 93,404,981 (GRCm39) T283M probably benign Het
Kdm5b A G 1: 134,559,089 (GRCm39) K1538E probably benign Het
Kif13a A G 13: 47,083,075 (GRCm39) V8A probably damaging Het
Krtap15-1 T A 16: 88,626,036 (GRCm39) N34K probably damaging Het
Lama2 T G 10: 27,245,137 (GRCm39) I215L probably damaging Het
Ldlrad3 C T 2: 101,900,328 (GRCm39) R58H possibly damaging Het
Lvrn C T 18: 47,027,792 (GRCm39) P869L probably damaging Het
Myo1d A G 11: 80,565,504 (GRCm39) F411S probably damaging Het
Myo5b T A 18: 74,828,455 (GRCm39) H702Q probably benign Het
Nat8f4 G T 6: 85,878,401 (GRCm39) Q41K probably benign Het
Nckap5 C A 1: 125,954,765 (GRCm39) E596* probably null Het
Nek10 T A 14: 14,846,594 (GRCm38) probably null Het
Notch3 T C 17: 32,363,705 (GRCm39) Y1145C probably damaging Het
Nr4a2 A T 2: 57,002,035 (GRCm39) H76Q probably benign Het
Nup98 T C 7: 101,784,185 (GRCm39) Q1049R probably damaging Het
Or4k48 A T 2: 111,476,121 (GRCm39) S74T possibly damaging Het
Or5k1b T A 16: 58,580,982 (GRCm39) R186* probably null Het
Or8k33 A T 2: 86,383,853 (GRCm39) F205Y probably damaging Het
Pepd T C 7: 34,720,409 (GRCm39) Y231H probably benign Het
Plagl1 G T 10: 13,003,301 (GRCm39) A190S possibly damaging Het
Plat T A 8: 23,268,269 (GRCm39) I345N probably damaging Het
Pnmt A G 11: 98,278,286 (GRCm39) E120G probably damaging Het
Prkrip1 C A 5: 136,227,797 (GRCm39) probably null Het
Pygm G A 19: 6,443,754 (GRCm39) A572T probably damaging Het
Rbm4b T C 19: 4,807,400 (GRCm39) F39L probably damaging Het
Rpe65 A G 3: 159,328,268 (GRCm39) H388R probably benign Het
Scn4a G T 11: 106,210,914 (GRCm39) A1701E possibly damaging Het
Sdk2 C A 11: 113,748,584 (GRCm39) W616L probably damaging Het
Serpina3m T A 12: 104,357,729 (GRCm39) S218T probably benign Het
Siglece C T 7: 43,309,297 (GRCm39) R87H probably damaging Het
Sim1 C A 10: 50,785,998 (GRCm39) L284M probably damaging Het
Smok3c G T 5: 138,063,844 (GRCm39) E444* probably null Het
Snx4 T C 16: 33,115,100 (GRCm39) V427A probably benign Het
Srp68 A T 11: 116,151,684 (GRCm39) V304E probably damaging Het
Stx6 T C 1: 155,049,737 (GRCm39) V14A probably damaging Het
Sv2b T A 7: 74,786,169 (GRCm39) Y417F probably benign Het
Tas2r103 A G 6: 133,013,161 (GRCm39) Y302H probably benign Het
Thop1 T C 10: 80,916,028 (GRCm39) S404P probably benign Het
Trp53bp1 G T 2: 121,051,701 (GRCm39) C988* probably null Het
Tsbp1 C T 17: 34,678,951 (GRCm39) P221L probably damaging Het
Ube3c A G 5: 29,836,269 (GRCm39) E630G possibly damaging Het
Usf3 T C 16: 44,037,718 (GRCm39) S733P probably benign Het
Vmn1r195 A G 13: 22,463,189 (GRCm39) T220A probably benign Het
Vmn1r201 A T 13: 22,658,882 (GRCm39) H32L probably benign Het
Wnt2 A G 6: 18,023,239 (GRCm39) C137R probably damaging Het
Ythdc2 T C 18: 44,980,871 (GRCm39) S489P probably damaging Het
Zfp248 A G 6: 118,406,033 (GRCm39) C418R probably damaging Het
Zfp946 T G 17: 22,674,502 (GRCm39) F419V probably damaging Het
Zfp994 C T 17: 22,419,738 (GRCm39) E404K probably damaging Het
Zfpm1 T C 8: 123,061,347 (GRCm39) V304A possibly 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
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
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'- GCAACTGAGATTAGTCTATTCCTGTC -3'
(R):5'- GACCCGTATGAATTTTCTATTGTCC -3'

Sequencing Primer
(F):5'- AGATTAGTCTATTCCTGTCAGTTACC -3'
(R):5'- AACTTTCTGTGCAGCCAAGG -3'
Posted On 2016-04-15