Incidental Mutation 'R5925:Satb2'
ID 461763
Institutional Source Beutler Lab
Gene Symbol Satb2
Ensembl Gene ENSMUSG00000038331
Gene Name special AT-rich sequence binding protein 2
Synonyms BAP002
MMRRC Submission 044120-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5925 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 56833140-57017809 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 56836097 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Threonine at position 565 (A565T)
Ref Sequence ENSEMBL: ENSMUSP00000135391 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000042857] [ENSMUST00000114415] [ENSMUST00000177424]
AlphaFold Q8VI24
Predicted Effect probably benign
Transcript: ENSMUST00000042857
AA Change: A624T

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)
SMART Domains Protein: ENSMUSP00000046067
Gene: ENSMUSG00000038331
AA Change: A624T

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: A683T

PolyPhen 2 Score 0.034 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000110057
Gene: ENSMUSG00000038331
AA Change: A683T

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: A565T

PolyPhen 2 Score 0.798 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000135391
Gene: ENSMUSG00000038331
AA Change: A565T

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: 99.8%
  • 3x: 99.4%
  • 10x: 97.4%
  • 20x: 91.8%
Validation Efficiency
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: 43 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9130230L23Rik C T 5: 66,147,735 (GRCm39) W16* probably null Het
Abca8a T C 11: 109,948,049 (GRCm39) D985G probably damaging Het
Afp T A 5: 90,645,147 (GRCm39) C188S probably damaging Het
Ank2 A C 3: 126,726,612 (GRCm39) L894R probably benign Het
Antxr1 A G 6: 87,289,344 (GRCm39) I60T probably damaging Het
Bltp2 T C 11: 78,175,064 (GRCm39) V1733A probably benign Het
Ccdc187 A G 2: 26,183,593 (GRCm39) S136P probably benign Het
Cep95 T C 11: 106,703,227 (GRCm39) S393P probably benign Het
Cyfip2 T C 11: 46,098,263 (GRCm39) Y1053C probably damaging Het
Diaph1 A G 18: 38,024,988 (GRCm39) V491A unknown Het
Dync2i1 A T 12: 116,197,014 (GRCm39) F448I possibly damaging Het
Ehf T C 2: 103,097,338 (GRCm39) probably null Het
Eif2b5 C T 16: 20,326,874 (GRCm39) H99Y probably benign Het
Exosc10 C A 4: 148,657,819 (GRCm39) T655K probably benign Het
Flg A T 3: 93,186,706 (GRCm39) I53F probably damaging Het
Hc T A 2: 34,920,462 (GRCm39) D628V possibly damaging Het
Lmo4 A T 3: 143,900,252 (GRCm39) N83K probably benign Het
Lrp4 A T 2: 91,342,029 (GRCm39) T1881S probably benign Het
Malt1 T A 18: 65,564,439 (GRCm39) L66Q possibly damaging Het
Map3k3 T C 11: 106,040,376 (GRCm39) S314P probably benign Het
Mpzl3 G T 9: 44,973,412 (GRCm39) K50N probably damaging Het
Nbeal2 G T 9: 110,458,948 (GRCm39) Q1992K probably benign Het
Nlrp14 T A 7: 106,785,860 (GRCm39) N645K probably benign Het
Or2g1 T C 17: 38,106,482 (GRCm39) I49T probably benign Het
Or6c76b A G 10: 129,692,744 (GRCm39) D119G probably damaging Het
Pcdha1 T A 18: 37,063,724 (GRCm39) D129E probably damaging Het
Prb1a A G 6: 132,187,475 (GRCm39) L2P unknown Het
Rhbdf1 A G 11: 32,162,906 (GRCm39) Y454H probably benign Het
Sh3pxd2a A T 19: 47,256,051 (GRCm39) L889Q probably damaging Het
Sis T C 3: 72,828,713 (GRCm39) probably null Het
Slc35e2 T C 4: 155,696,084 (GRCm39) V157A probably damaging Het
Slc35f3 T C 8: 127,115,946 (GRCm39) V291A probably benign Het
Snph T C 2: 151,436,151 (GRCm39) D190G probably damaging Het
Tpd52l1 T C 10: 31,208,943 (GRCm39) H170R probably benign Het
Trav18 A G 14: 54,069,152 (GRCm39) T65A probably benign Het
Trip12 G A 1: 84,726,974 (GRCm39) Q9* probably null Het
Ttn C T 2: 76,632,592 (GRCm39) C12408Y probably damaging Het
Ttn T C 2: 76,639,355 (GRCm39) D13806G probably damaging Het
Unc79 G C 12: 103,091,989 (GRCm39) probably null Het
Vmn2r81 T C 10: 79,083,637 (GRCm39) S4P probably damaging Het
Zfp37 G A 4: 62,109,450 (GRCm39) T576I possibly damaging Het
Zfp39 A T 11: 58,782,099 (GRCm39) L221Q possibly damaging Het
Zgrf1 A G 3: 127,366,853 (GRCm39) H744R possibly damaging 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
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
R8009: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'- AGTCCTTGGACCCATCTATTGC -3'
(R):5'- CTCGGTCTCGCACAAAGATC -3'

Sequencing Primer
(F):5'- CTCTGCCTGCGGAGTTCAC -3'
(R):5'- AAAGATCTCTTTGGAAGCCCTGG -3'
Posted On 2017-02-28