Incidental Mutation 'R1436:Satb1'
ID 160669
Institutional Source Beutler Lab
Gene Symbol Satb1
Ensembl Gene ENSMUSG00000023927
Gene Name special AT-rich sequence binding protein 1
Synonyms 2610306G12Rik
MMRRC Submission 039491-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1436 (G1)
Quality Score 225
Status Validated
Chromosome 17
Chromosomal Location 52043215-52140318 bp(-) (GRCm39)
Type of Mutation splice site (3 bp from exon)
DNA Base Change (assembly) T to G at 52111391 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000123409 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000124222] [ENSMUST00000129205] [ENSMUST00000129205] [ENSMUST00000129205] [ENSMUST00000129667] [ENSMUST00000133574] [ENSMUST00000140979] [ENSMUST00000169480] [ENSMUST00000144331] [ENSMUST00000152830] [ENSMUST00000176669] [ENSMUST00000148559]
AlphaFold Q60611
Predicted Effect probably benign
Transcript: ENSMUST00000124222
Predicted Effect probably null
Transcript: ENSMUST00000129205
SMART Domains Protein: ENSMUSP00000123409
Gene: ENSMUSG00000023927

DomainStartEndE-ValueType
PDB:3TUO|D 71 154 2e-58 PDB
Predicted Effect probably null
Transcript: ENSMUST00000129205
SMART Domains Protein: ENSMUSP00000123409
Gene: ENSMUSG00000023927

DomainStartEndE-ValueType
PDB:3TUO|D 71 154 2e-58 PDB
Predicted Effect probably null
Transcript: ENSMUST00000129205
SMART Domains Protein: ENSMUSP00000123409
Gene: ENSMUSG00000023927

DomainStartEndE-ValueType
PDB:3TUO|D 71 154 2e-58 PDB
Predicted Effect probably damaging
Transcript: ENSMUST00000129667
AA Change: M156L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000116020
Gene: ENSMUSG00000023927
AA Change: M156L

DomainStartEndE-ValueType
PDB:3TUO|D 71 171 5e-66 PDB
PDB:3NZL|A 179 250 5e-45 PDB
Blast:CUT 245 327 9e-48 BLAST
CUT 362 448 1.08e-38 SMART
CUT 485 571 4.41e-39 SMART
low complexity region 593 619 N/A INTRINSIC
HOX 644 707 6.73e-10 SMART
low complexity region 720 730 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000133574
AA Change: M156L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000120536
Gene: ENSMUSG00000023927
AA Change: M156L

DomainStartEndE-ValueType
PDB:3TUO|D 71 171 5e-66 PDB
PDB:3NZL|A 179 250 5e-45 PDB
Blast:CUT 245 327 9e-48 BLAST
CUT 362 448 1.08e-38 SMART
CUT 485 571 4.41e-39 SMART
low complexity region 593 620 N/A INTRINSIC
HOX 645 708 6.73e-10 SMART
low complexity region 721 731 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140727
Predicted Effect probably benign
Transcript: ENSMUST00000140979
AA Change: M156L

PolyPhen 2 Score 0.177 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000118839
Gene: ENSMUSG00000023927
AA Change: M156L

DomainStartEndE-ValueType
Pfam:ULD 72 170 3.2e-40 PFAM
Pfam:CUTL 176 247 1.6e-46 PFAM
CUT 362 448 1.08e-38 SMART
CUT 485 571 4.41e-39 SMART
low complexity region 616 661 N/A INTRINSIC
HOX 676 739 6.73e-10 SMART
low complexity region 752 762 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000169480
AA Change: M156L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000128841
Gene: ENSMUSG00000023927
AA Change: M156L

DomainStartEndE-ValueType
PDB:3TUO|D 71 171 5e-66 PDB
PDB:3NZL|A 179 250 5e-45 PDB
Blast:CUT 245 327 9e-48 BLAST
CUT 362 448 1.08e-38 SMART
CUT 485 571 4.41e-39 SMART
low complexity region 593 620 N/A INTRINSIC
HOX 645 708 6.73e-10 SMART
low complexity region 721 731 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000144331
AA Change: M156L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000116006
Gene: ENSMUSG00000023927
AA Change: M156L

DomainStartEndE-ValueType
PDB:3TUO|D 71 171 5e-66 PDB
PDB:3NZL|A 179 250 5e-45 PDB
Blast:CUT 245 327 9e-48 BLAST
CUT 362 448 1.08e-38 SMART
CUT 485 571 4.41e-39 SMART
low complexity region 593 620 N/A INTRINSIC
HOX 645 708 6.73e-10 SMART
low complexity region 721 731 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000152830
AA Change: M156L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000119842
Gene: ENSMUSG00000023927
AA Change: M156L

DomainStartEndE-ValueType
PDB:3TUO|D 71 171 5e-66 PDB
PDB:3NZL|A 179 250 5e-45 PDB
Blast:CUT 245 327 9e-48 BLAST
CUT 362 448 1.08e-38 SMART
CUT 485 571 4.41e-39 SMART
low complexity region 593 620 N/A INTRINSIC
HOX 645 708 6.73e-10 SMART
low complexity region 721 731 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000176669
AA Change: M156L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000134957
Gene: ENSMUSG00000023927
AA Change: M156L

DomainStartEndE-ValueType
PDB:3TUO|D 71 171 5e-66 PDB
PDB:3NZL|A 179 250 5e-45 PDB
Blast:CUT 245 327 9e-48 BLAST
CUT 362 448 1.08e-38 SMART
CUT 485 571 4.41e-39 SMART
low complexity region 593 620 N/A INTRINSIC
HOX 645 708 6.73e-10 SMART
low complexity region 721 731 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146414
Predicted Effect probably benign
Transcript: ENSMUST00000148559
Meta Mutation Damage Score 0.1279 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.8%
  • 10x: 94.6%
  • 20x: 86.8%
Validation Efficiency 94% (65/69)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a matrix protein which binds nuclear matrix and scaffold-associating DNAs through a unique nuclear architecture. The protein recruits chromatin-remodeling factors in order to regulate chromatin structure and gene expression. [provided by RefSeq, Apr 2016]
PHENOTYPE: Homozygous mice for a targeted null mutation exhibit reduced size of the lymphoid organs, abnormal T cell development, general growth retardation and die by 3-4 weeks of age. Mice homozegous for a different targeted allele exhibit postnatal growth retardation and postnatal lethality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2m T C 6: 121,621,172 (GRCm39) F292S probably benign Het
Aadacl2fm3 A T 3: 59,772,760 (GRCm39) D88V probably damaging Het
Abca13 T C 11: 9,242,646 (GRCm39) V1503A probably damaging Het
AI661453 C T 17: 47,777,627 (GRCm39) probably benign Het
Ano2 T C 6: 125,844,134 (GRCm39) probably null Het
Areg G T 5: 91,287,664 (GRCm39) probably benign Het
Atg16l2 A G 7: 100,940,757 (GRCm39) V453A probably damaging Het
BC034090 A G 1: 155,101,662 (GRCm39) S563P probably benign Het
Bhmt-ps1 A G 4: 26,369,591 (GRCm39) noncoding transcript Het
Birc6 C A 17: 74,959,700 (GRCm39) P3855Q probably damaging Het
Cd151 A T 7: 141,049,197 (GRCm39) K8M probably damaging Het
Cd163 T C 6: 124,304,890 (GRCm39) V1089A possibly damaging Het
Chd3 A T 11: 69,248,400 (GRCm39) probably null Het
Cnot6l T A 5: 96,281,971 (GRCm39) E9V probably damaging Het
Col22a1 A G 15: 71,794,806 (GRCm39) probably benign Het
Cyp2c68 A G 19: 39,729,484 (GRCm39) M1T probably null Het
Dbp T C 7: 45,357,879 (GRCm39) V149A probably damaging Het
Dnah10 T C 5: 124,839,285 (GRCm39) V1241A probably benign Het
Galnt10 T C 11: 57,662,295 (GRCm39) S314P probably damaging Het
Glce C T 9: 61,977,292 (GRCm39) probably null Het
Gm5093 C G 17: 46,750,680 (GRCm39) D116H probably damaging Het
Golim4 A G 3: 75,785,951 (GRCm39) probably null Het
Helz2 A T 2: 180,877,317 (GRCm39) I1107N probably damaging Het
Hoxc9 T C 15: 102,890,304 (GRCm39) S74P probably benign Het
Ikbkb T A 8: 23,163,419 (GRCm39) N297I probably benign Het
Il20ra T A 10: 19,625,000 (GRCm39) I93N probably damaging Het
Itch C A 2: 155,034,065 (GRCm39) N412K probably damaging Het
Kcna5 T A 6: 126,511,724 (GRCm39) T135S probably damaging Het
Lncpint G A 6: 31,157,974 (GRCm39) noncoding transcript Het
Lrrc39 A T 3: 116,373,293 (GRCm39) probably null Het
Mad2l1 T A 6: 66,516,797 (GRCm39) V163E possibly damaging Het
Moxd1 C T 10: 24,120,256 (GRCm39) T128M probably damaging Het
Mpeg1 C T 19: 12,439,823 (GRCm39) S427F probably damaging Het
Nckap5 T C 1: 125,953,798 (GRCm39) Y854C possibly damaging Het
Ncln C T 10: 81,325,727 (GRCm39) E373K probably damaging Het
Neurod4 T C 10: 130,106,540 (GRCm39) T245A possibly damaging Het
Nsun5 T C 5: 135,399,067 (GRCm39) L39P probably damaging Het
Or2ad1 G T 13: 21,327,162 (GRCm39) Q22K probably benign Het
Or4c105 A T 2: 88,648,336 (GRCm39) T274S possibly damaging Het
Or4f7 A G 2: 111,644,906 (GRCm39) L55S probably damaging Het
Pde8b T C 13: 95,162,678 (GRCm39) T815A probably benign Het
Pofut2 C T 10: 77,104,398 (GRCm39) R392W probably damaging Het
Ppip5k2 G A 1: 97,639,507 (GRCm39) T1186I probably benign Het
Rhot2 A C 17: 26,060,374 (GRCm39) S277R probably benign Het
Sec31b T C 19: 44,524,634 (GRCm39) I88V probably damaging Het
Selenon T A 4: 134,267,997 (GRCm39) E483V probably damaging Het
Serpinc1 A G 1: 160,820,981 (GRCm39) T22A possibly damaging Het
Sf3a2 G A 10: 80,640,040 (GRCm39) probably benign Het
Sf3b1 A G 1: 55,040,580 (GRCm39) Y561H possibly damaging Het
Smarcc1 T A 9: 109,947,708 (GRCm39) probably benign Het
Stard3nl C T 13: 19,556,819 (GRCm39) R107Q probably damaging Het
Syce1 C T 7: 140,357,593 (GRCm39) R324H possibly damaging Het
Tnk1 G T 11: 69,743,119 (GRCm39) probably benign Het
Trim46 A G 3: 89,150,968 (GRCm39) F198L probably damaging Het
Trip4 A T 9: 65,788,233 (GRCm39) W71R probably damaging Het
Ubox5 A C 2: 130,439,213 (GRCm39) probably benign Het
Ust G A 10: 8,183,202 (GRCm39) T167M probably damaging Het
Zbtb2 T C 10: 4,318,697 (GRCm39) Q443R probably benign Het
Zfp407 A G 18: 84,361,196 (GRCm39) probably benign Het
Other mutations in Satb1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01128:Satb1 APN 17 52,112,317 (GRCm39) missense probably damaging 1.00
IGL01658:Satb1 APN 17 52,082,279 (GRCm39) missense probably benign 0.33
IGL02070:Satb1 APN 17 52,047,095 (GRCm39) missense probably damaging 0.98
IGL02212:Satb1 APN 17 52,082,319 (GRCm39) missense possibly damaging 0.82
IGL02971:Satb1 APN 17 52,049,717 (GRCm39) missense possibly damaging 0.62
R0049:Satb1 UTSW 17 52,047,374 (GRCm39) missense probably benign 0.28
R0056:Satb1 UTSW 17 52,047,231 (GRCm39) missense probably damaging 1.00
R0060:Satb1 UTSW 17 52,047,231 (GRCm39) missense probably damaging 1.00
R0067:Satb1 UTSW 17 52,111,364 (GRCm39) missense probably damaging 1.00
R0067:Satb1 UTSW 17 52,111,364 (GRCm39) missense probably damaging 1.00
R0113:Satb1 UTSW 17 52,089,726 (GRCm39) nonsense probably null
R0347:Satb1 UTSW 17 52,046,934 (GRCm39) nonsense probably null
R0667:Satb1 UTSW 17 52,089,889 (GRCm39) missense probably damaging 1.00
R1595:Satb1 UTSW 17 52,089,729 (GRCm39) missense possibly damaging 0.82
R1686:Satb1 UTSW 17 52,047,027 (GRCm39) missense probably benign 0.08
R1921:Satb1 UTSW 17 52,049,143 (GRCm39) nonsense probably null
R1952:Satb1 UTSW 17 52,047,173 (GRCm39) missense probably damaging 1.00
R2012:Satb1 UTSW 17 52,089,816 (GRCm39) nonsense probably null
R2156:Satb1 UTSW 17 52,047,438 (GRCm39) missense probably benign 0.02
R2180:Satb1 UTSW 17 52,110,524 (GRCm39) missense probably damaging 0.96
R2959:Satb1 UTSW 17 52,082,331 (GRCm39) missense possibly damaging 0.91
R3107:Satb1 UTSW 17 52,089,810 (GRCm39) missense possibly damaging 0.95
R3108:Satb1 UTSW 17 52,089,810 (GRCm39) missense possibly damaging 0.95
R3814:Satb1 UTSW 17 52,089,935 (GRCm39) missense probably damaging 0.98
R4109:Satb1 UTSW 17 52,111,378 (GRCm39) missense probably damaging 0.99
R4727:Satb1 UTSW 17 52,111,375 (GRCm39) missense probably damaging 1.00
R5209:Satb1 UTSW 17 52,116,235 (GRCm39) missense probably benign 0.26
R5652:Satb1 UTSW 17 52,049,823 (GRCm39) missense probably damaging 1.00
R5815:Satb1 UTSW 17 52,089,981 (GRCm39) missense possibly damaging 0.92
R6141:Satb1 UTSW 17 52,082,404 (GRCm39) missense possibly damaging 0.93
R6370:Satb1 UTSW 17 52,089,825 (GRCm39) missense possibly damaging 0.94
R7371:Satb1 UTSW 17 52,090,008 (GRCm39) nonsense probably null
R7409:Satb1 UTSW 17 52,116,217 (GRCm39) missense possibly damaging 0.90
R7471:Satb1 UTSW 17 52,090,029 (GRCm39) missense probably damaging 0.96
R7568:Satb1 UTSW 17 52,089,752 (GRCm39) missense possibly damaging 0.88
R7626:Satb1 UTSW 17 52,074,995 (GRCm39) missense probably benign 0.25
R7749:Satb1 UTSW 17 52,074,961 (GRCm39) missense possibly damaging 0.70
R7863:Satb1 UTSW 17 52,112,350 (GRCm39) missense possibly damaging 0.91
R8339:Satb1 UTSW 17 52,089,977 (GRCm39) missense probably damaging 0.97
R8429:Satb1 UTSW 17 52,074,978 (GRCm39) missense probably damaging 1.00
R8987:Satb1 UTSW 17 52,112,381 (GRCm39) missense probably damaging 1.00
R9160:Satb1 UTSW 17 52,047,053 (GRCm39) missense probably benign
R9251:Satb1 UTSW 17 52,112,293 (GRCm39) missense probably damaging 1.00
R9656:Satb1 UTSW 17 52,112,264 (GRCm39) missense possibly damaging 0.95
Z1088:Satb1 UTSW 17 52,089,980 (GRCm39) missense probably damaging 0.98
Z1088:Satb1 UTSW 17 52,089,967 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- TGGCAAAAGCGAATAAGGCATTCTTTC -3'
(R):5'- AGGCTGTGAATATCTTCATTGACCTGC -3'

Sequencing Primer
(F):5'- TGTACACAGATGGCACTGTTC -3'
(R):5'- CAGAAGTAACACTATTGGCTGTG -3'
Posted On 2014-03-14