Incidental Mutation 'R8009:Satb2'
ID 616779
Institutional Source Beutler Lab
Gene Symbol Satb2
Ensembl Gene ENSMUSG00000038331
Gene Name special AT-rich sequence binding protein 2
Synonyms BAP002
MMRRC Submission 046049-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8009 (G1)
Quality Score 225.009
Status Validated
Chromosome 1
Chromosomal Location 56833140-57017809 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 56910917 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 243 (S243P)
Ref Sequence ENSEMBL: ENSMUSP00000110057 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000042857] [ENSMUST00000114415] [ENSMUST00000177424]
AlphaFold Q8VI24
Predicted Effect probably benign
Transcript: ENSMUST00000042857
AA Change: S184P

PolyPhen 2 Score 0.162 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000046067
Gene: ENSMUSG00000038331
AA Change: S184P

DomainStartEndE-ValueType
PDB:3TUO|D 45 98 8e-19 PDB
PDB:3NZL|A 106 174 4e-35 PDB
low complexity region 235 251 N/A INTRINSIC
CUT 292 378 1.3e-36 SMART
low complexity region 381 399 N/A INTRINSIC
CUT 415 501 3.58e-39 SMART
low complexity region 510 524 N/A INTRINSIC
low complexity region 533 551 N/A INTRINSIC
HOX 555 618 1.06e-7 SMART
low complexity region 629 650 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000114415
AA Change: S243P

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000110057
Gene: ENSMUSG00000038331
AA Change: S243P

DomainStartEndE-ValueType
Pfam:ULD 58 156 1.7e-39 PFAM
Pfam:CUTL 162 233 3.9e-46 PFAM
low complexity region 294 310 N/A INTRINSIC
CUT 351 437 1.3e-36 SMART
low complexity region 440 458 N/A INTRINSIC
CUT 474 560 3.58e-39 SMART
low complexity region 569 583 N/A INTRINSIC
low complexity region 592 610 N/A INTRINSIC
HOX 614 677 1.06e-7 SMART
low complexity region 688 709 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000177424
AA Change: S125P

PolyPhen 2 Score 0.691 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000135391
Gene: ENSMUSG00000038331
AA Change: S125P

DomainStartEndE-ValueType
PDB:3TUO|D 57 115 6e-23 PDB
low complexity region 176 192 N/A INTRINSIC
CUT 233 319 1.3e-36 SMART
low complexity region 322 340 N/A INTRINSIC
CUT 356 442 3.58e-39 SMART
low complexity region 451 465 N/A INTRINSIC
low complexity region 474 492 N/A INTRINSIC
HOX 496 559 1.06e-7 SMART
low complexity region 570 591 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency 100% (54/54)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a DNA binding protein that specifically binds nuclear matrix attachment regions. The encoded protein is involved in transcription regulation and chromatin remodeling. Defects in this gene are associated with isolated cleft palate and mental retardation. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Feb 2010]
PHENOTYPE: Homozygous inactivation of this gene causes complete perinatal lethality and craniofacial anomalies, such as cleft palate, micrognathia, microcephaly, decreased tongue size, absent incisors and nasal capsule hypoplasia, and leads to short limbs and defects in osteoblast differentiation and function. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb1b T A 5: 8,878,870 (GRCm39) N751K possibly damaging Het
Akap13 G A 7: 75,380,213 (GRCm39) R462H probably damaging Het
Baz1a A T 12: 54,941,816 (GRCm39) Y1466* probably null Het
Ccng1 G A 11: 40,642,096 (GRCm39) H229Y probably benign Het
Cenpn C A 8: 117,663,976 (GRCm39) T256N probably benign Het
Ciart A G 3: 95,788,629 (GRCm39) V70A possibly damaging Het
Clcc1 A G 3: 108,568,774 (GRCm39) N36S probably damaging Het
Dmrt1 T A 19: 25,523,245 (GRCm39) S199T possibly damaging Het
Dmrt3 T C 19: 25,588,272 (GRCm39) V37A possibly damaging Het
Dock1 T A 7: 134,346,786 (GRCm39) D239E possibly damaging Het
Dyrk3 A G 1: 131,063,995 (GRCm39) probably null Het
Esyt1 T C 10: 128,347,354 (GRCm39) E1057G probably benign Het
Fsip2 A G 2: 82,818,793 (GRCm39) E4842G possibly damaging Het
Gadd45b G A 10: 80,766,984 (GRCm39) V90I probably benign Het
Gfi1 T A 5: 107,871,667 (GRCm39) H79L probably damaging Het
Golm2 T C 2: 121,737,242 (GRCm39) V261A probably benign Het
Idh2 T C 7: 79,748,001 (GRCm39) H233R probably benign Het
Itsn2 G A 12: 4,714,553 (GRCm39) A950T probably benign Het
Kcna5 A G 6: 126,510,517 (GRCm39) L537P probably benign Het
Krtap5-4 C T 7: 141,857,671 (GRCm39) Q114* probably null Het
Loxl3 T C 6: 83,027,790 (GRCm39) F734S possibly damaging Het
Lpcat1 C T 13: 73,659,498 (GRCm39) T420I probably damaging Het
Lrch3 A T 16: 32,826,083 (GRCm39) D720V possibly damaging Het
Lrrk1 T C 7: 65,915,222 (GRCm39) D1622G possibly damaging Het
Meioc G C 11: 102,567,569 (GRCm39) A788P probably damaging Het
Mmp1a A T 9: 7,467,236 (GRCm39) T271S possibly damaging Het
Nrp2 C T 1: 62,784,567 (GRCm39) R239C probably damaging Het
Ntrk3 T A 7: 78,103,076 (GRCm39) D408V probably benign Het
Odf1 A G 15: 38,226,840 (GRCm39) I247V unknown Het
Or14j5 A T 17: 38,161,693 (GRCm39) D70V probably damaging Het
Or8k39 A G 2: 86,563,848 (GRCm39) L36P probably damaging Het
Pcsk1 T C 13: 75,274,958 (GRCm39) S516P probably benign Het
Phactr3 A C 2: 177,974,737 (GRCm39) R523S probably damaging Het
Pikfyve A G 1: 65,294,293 (GRCm39) D1411G probably damaging Het
Ppcs A T 4: 119,276,262 (GRCm39) S281T probably benign Het
Prkcg A G 7: 3,362,708 (GRCm39) D294G probably benign Het
Psg28 T A 7: 18,156,922 (GRCm39) I438L probably damaging Het
Pspc1 G A 14: 57,009,304 (GRCm39) Q177* probably null Het
Rbm33 G A 5: 28,599,606 (GRCm39) G185R Het
Rps6ka5 T C 12: 100,544,048 (GRCm39) E350G probably damaging Het
Serinc5 T C 13: 92,797,699 (GRCm39) probably null Het
Sgce T C 6: 4,691,636 (GRCm39) D313G probably damaging Het
Sntg1 C T 1: 8,433,794 (GRCm39) V486I probably damaging Het
Stxbp5 A G 10: 9,692,046 (GRCm39) V366A probably damaging Het
Tep1 A G 14: 51,061,687 (GRCm39) S2610P possibly damaging Het
Tlr3 G A 8: 45,853,819 (GRCm39) T167M not run Het
Tmem200a A G 10: 25,869,904 (GRCm39) S122P probably damaging Het
Tmprss15 C T 16: 78,887,751 (GRCm39) V19M probably damaging Het
Tnks2 T A 19: 36,829,901 (GRCm39) M194K probably benign Het
Trav14d-3-dv8 A C 14: 53,316,224 (GRCm39) Q28P probably damaging Het
Trpm5 T C 7: 142,634,106 (GRCm39) E700G probably benign Het
Ubqln3 T A 7: 103,791,797 (GRCm39) I98L probably benign Het
Uso1 A T 5: 92,314,439 (GRCm39) E115D probably benign Het
Vmn1r28 T C 6: 58,242,178 (GRCm39) V7A probably benign Het
Other mutations in Satb2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00742:Satb2 APN 1 56,870,700 (GRCm39) missense possibly damaging 0.56
IGL02008:Satb2 APN 1 56,835,952 (GRCm39) missense possibly damaging 0.70
IGL02209:Satb2 APN 1 56,910,677 (GRCm39) missense probably damaging 1.00
IGL02956:Satb2 APN 1 56,987,334 (GRCm39) missense probably damaging 0.99
IGL03214:Satb2 APN 1 56,884,739 (GRCm39) missense probably damaging 1.00
IGL03272:Satb2 APN 1 56,884,802 (GRCm39) missense probably damaging 1.00
IGL03356:Satb2 APN 1 56,930,333 (GRCm39) missense probably damaging 1.00
Optimism UTSW 1 56,884,880 (GRCm39) nonsense probably null
prophecy UTSW 1 56,884,778 (GRCm39) missense probably damaging 1.00
R0990:Satb2 UTSW 1 56,889,343 (GRCm39) missense probably damaging 0.96
R1534:Satb2 UTSW 1 56,987,392 (GRCm39) nonsense probably null
R1711:Satb2 UTSW 1 56,889,448 (GRCm39) missense probably damaging 0.99
R1952:Satb2 UTSW 1 56,938,229 (GRCm39) missense probably damaging 1.00
R2404:Satb2 UTSW 1 56,987,267 (GRCm39) missense probably damaging 1.00
R3792:Satb2 UTSW 1 56,884,779 (GRCm39) missense probably damaging 1.00
R3870:Satb2 UTSW 1 56,930,379 (GRCm39) missense probably damaging 1.00
R3871:Satb2 UTSW 1 56,930,379 (GRCm39) missense probably damaging 1.00
R4333:Satb2 UTSW 1 56,884,745 (GRCm39) missense probably damaging 1.00
R4621:Satb2 UTSW 1 56,884,778 (GRCm39) missense probably damaging 1.00
R4962:Satb2 UTSW 1 56,930,327 (GRCm39) missense probably benign 0.25
R5296:Satb2 UTSW 1 56,836,066 (GRCm39) missense probably damaging 0.99
R5314:Satb2 UTSW 1 56,870,686 (GRCm39) missense probably damaging 0.99
R5407:Satb2 UTSW 1 56,987,309 (GRCm39) missense probably damaging 1.00
R5925:Satb2 UTSW 1 56,836,097 (GRCm39) missense possibly damaging 0.80
R6355:Satb2 UTSW 1 56,987,356 (GRCm39) missense probably damaging 1.00
R6634:Satb2 UTSW 1 56,884,880 (GRCm39) nonsense probably null
R6645:Satb2 UTSW 1 56,836,166 (GRCm39) missense possibly damaging 0.51
R7578:Satb2 UTSW 1 56,910,943 (GRCm39) missense probably benign 0.01
R7694:Satb2 UTSW 1 56,910,683 (GRCm39) missense probably benign
R7811:Satb2 UTSW 1 56,884,880 (GRCm39) missense probably benign 0.19
R7961:Satb2 UTSW 1 56,910,917 (GRCm39) missense probably benign 0.01
R8023:Satb2 UTSW 1 56,930,390 (GRCm39) missense probably damaging 1.00
R8094:Satb2 UTSW 1 56,870,623 (GRCm39) missense possibly damaging 0.95
R8745:Satb2 UTSW 1 57,008,796 (GRCm39) missense unknown
R8960:Satb2 UTSW 1 56,910,470 (GRCm39) critical splice donor site probably null
R9382:Satb2 UTSW 1 56,870,797 (GRCm39) critical splice acceptor site probably null
Predicted Primers PCR Primer
(F):5'- ACAAGCTGAGGACTGAGCTG -3'
(R):5'- TGACAGCTTAACCCTTTACCATAAG -3'

Sequencing Primer
(F):5'- AGGACTGAGCTGCGGTG -3'
(R):5'- CCCTTTACCATAAGGATAACTGACTC -3'
Posted On 2020-01-23