Incidental Mutation 'R4109:Satb1'
ID 317223
Institutional Source Beutler Lab
Gene Symbol Satb1
Ensembl Gene ENSMUSG00000023927
Gene Name special AT-rich sequence binding protein 1
Synonyms 2610306G12Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4109 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 52043215-52140318 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 52111378 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 160 (V160A)
Ref Sequence ENSEMBL: ENSMUSP00000134957 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000124222] [ENSMUST00000129205] [ENSMUST00000129667] [ENSMUST00000133574] [ENSMUST00000140979] [ENSMUST00000152830] [ENSMUST00000176669] [ENSMUST00000144331] [ENSMUST00000169480] [ENSMUST00000148559]
AlphaFold Q60611
Predicted Effect probably benign
Transcript: ENSMUST00000124222
Predicted Effect probably benign
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: V160A

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000116020
Gene: ENSMUSG00000023927
AA Change: V160A

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: V160A

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000120536
Gene: ENSMUSG00000023927
AA Change: V160A

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 damaging
Transcript: ENSMUST00000140979
AA Change: V160A

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000118839
Gene: ENSMUSG00000023927
AA Change: V160A

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: ENSMUST00000152830
AA Change: V160A

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000119842
Gene: ENSMUSG00000023927
AA Change: V160A

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: V160A

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000134957
Gene: ENSMUSG00000023927
AA Change: V160A

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: V160A

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000116006
Gene: ENSMUSG00000023927
AA Change: V160A

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: ENSMUST00000169480
AA Change: V160A

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000128841
Gene: ENSMUSG00000023927
AA Change: V160A

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
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.5%
  • 20x: 96.1%
Validation Efficiency
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: 28 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2010315B03Rik A T 9: 124,057,733 (GRCm39) D59E probably benign Het
Acads T C 5: 115,248,913 (GRCm39) *302W probably null Het
Aldh1l1 A G 6: 90,539,626 (GRCm39) E185G probably benign Het
Arhgap20 A G 9: 51,727,985 (GRCm39) H66R possibly damaging Het
Arhgap31 A G 16: 38,422,788 (GRCm39) S1093P probably damaging Het
Atg2a A G 19: 6,308,404 (GRCm39) T1646A possibly damaging Het
Cd200r1 C G 16: 44,610,447 (GRCm39) T185S possibly damaging Het
Cnbd2 T C 2: 156,177,318 (GRCm39) V92A probably damaging Het
Col1a2 A T 6: 4,510,705 (GRCm39) R52* probably null Het
Eml5 T C 12: 98,807,807 (GRCm39) probably null Het
Ifi206 T G 1: 173,308,554 (GRCm39) T481P probably benign Het
Nfya G T 17: 48,699,912 (GRCm39) Y37* probably null Het
Nos1ap A T 1: 170,146,237 (GRCm39) M439K probably benign Het
Paxbp1 T A 16: 90,813,786 (GRCm39) T864S probably benign Het
Ryr3 C G 2: 112,506,218 (GRCm39) R3443P probably damaging Het
Scn3a A G 2: 65,325,379 (GRCm39) I1046T probably benign Het
Setd1b TCCACCACCACCACCACCACCACCA TCCACCACCACCACCACCACCA 5: 123,290,137 (GRCm39) probably benign Het
Slc19a3 A T 1: 83,000,678 (GRCm39) F113Y probably damaging Het
Slc1a7 T C 4: 107,825,858 (GRCm39) V39A probably benign Het
Spire1 T C 18: 67,630,287 (GRCm39) Q338R probably damaging Het
Supt16 T C 14: 52,400,188 (GRCm39) E985G probably damaging Het
Tmprss11f T C 5: 86,677,795 (GRCm39) K325E possibly damaging Het
Tpo G A 12: 30,142,585 (GRCm39) P713L probably damaging Het
Trav13-2 A C 14: 53,872,698 (GRCm39) H58P probably benign Het
Trbv13-2 A T 6: 41,098,578 (GRCm39) Y51F probably benign Het
Ttn G C 2: 76,581,215 (GRCm39) A23226G probably damaging Het
Ttn C T 2: 76,608,809 (GRCm39) V15990I probably benign Het
Zan G A 5: 137,456,881 (GRCm39) T1285I unknown 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
R1436:Satb1 UTSW 17 52,111,391 (GRCm39) splice site probably null
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
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'- ATCTTTTGATAGCACGCAGGG -3'
(R):5'- GAAGTAACACTATTGGCTGTGG -3'

Sequencing Primer
(F):5'- GGGGGAGGAAGTAAATTTTAAAGTC -3'
(R):5'- AACACTATTGGCTGTGGTGGGG -3'
Posted On 2015-05-15