Incidental Mutation 'R0538:Mbd4'
ID 49572
Institutional Source Beutler Lab
Gene Symbol Mbd4
Ensembl Gene ENSMUSG00000030322
Gene Name methyl-CpG binding domain protein 4
Synonyms Med1
MMRRC Submission 038730-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.192) question?
Stock # R0538 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 115817658-115830332 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 115826443 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 183 (S183P)
Ref Sequence ENSEMBL: ENSMUSP00000032469 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032469] [ENSMUST00000038234] [ENSMUST00000112923] [ENSMUST00000112925] [ENSMUST00000122816] [ENSMUST00000147282] [ENSMUST00000203643] [ENSMUST00000141305]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000032469
AA Change: S183P

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000032469
Gene: ENSMUSG00000030322
AA Change: S183P

DomainStartEndE-ValueType
MBD 66 142 1.25e-29 SMART
low complexity region 178 196 N/A INTRINSIC
PDB:1NGN|A 400 554 1e-111 PDB
SCOP:d1keaa_ 405 545 1e-23 SMART
Blast:ENDO3c 439 514 2e-6 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000038234
SMART Domains Protein: ENSMUSP00000045468
Gene: ENSMUSG00000030323

DomainStartEndE-ValueType
WD40 1 39 7.1e1 SMART
WD40 42 81 7.16e-10 SMART
WD40 83 120 1.54e0 SMART
WD40 122 160 1.43e0 SMART
WD40 162 208 2.29e1 SMART
WD40 210 249 1.91e1 SMART
WD40 251 290 3.45e-3 SMART
WD40 448 483 1.43e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112923
SMART Domains Protein: ENSMUSP00000108545
Gene: ENSMUSG00000030323

DomainStartEndE-ValueType
WD40 1 39 7.1e1 SMART
WD40 42 81 7.16e-10 SMART
WD40 83 120 1.54e0 SMART
WD40 122 160 1.43e0 SMART
Blast:WD40 163 267 3e-46 BLAST
WD40 269 308 1.91e1 SMART
WD40 310 349 3.45e-3 SMART
WD40 507 542 1.43e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112925
SMART Domains Protein: ENSMUSP00000108547
Gene: ENSMUSG00000030323

DomainStartEndE-ValueType
WD40 1 39 7.1e1 SMART
WD40 42 81 7.16e-10 SMART
WD40 83 120 1.54e0 SMART
WD40 122 160 1.43e0 SMART
WD40 162 208 2.29e1 SMART
WD40 210 249 1.91e1 SMART
WD40 251 290 3.45e-3 SMART
WD40 448 483 1.43e1 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000122816
AA Change: S183P

PolyPhen 2 Score 0.930 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000145433
Gene: ENSMUSG00000030322
AA Change: S183P

DomainStartEndE-ValueType
MBD 66 142 7.6e-32 SMART
low complexity region 178 196 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125889
Predicted Effect possibly damaging
Transcript: ENSMUST00000147282
AA Change: S162P

PolyPhen 2 Score 0.930 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000125619
Gene: ENSMUSG00000030322
AA Change: S162P

DomainStartEndE-ValueType
MBD 45 121 1.25e-29 SMART
low complexity region 157 175 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000203243
Predicted Effect probably benign
Transcript: ENSMUST00000203643
SMART Domains Protein: ENSMUSP00000144930
Gene: ENSMUSG00000030322

DomainStartEndE-ValueType
Pfam:HhH-GPD 56 168 2.7e-5 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133830
Predicted Effect probably benign
Transcript: ENSMUST00000141305
SMART Domains Protein: ENSMUSP00000138535
Gene: ENSMUSG00000030323

DomainStartEndE-ValueType
WD40 1 39 7.1e1 SMART
WD40 42 81 7.16e-10 SMART
WD40 83 120 1.54e0 SMART
low complexity region 124 134 N/A INTRINSIC
low complexity region 162 176 N/A INTRINSIC
Meta Mutation Damage Score 0.0755 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.3%
  • 20x: 92.7%
Validation Efficiency 98% (126/129)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcription from methylated gene promoters. This protein contains an MBD domain at the N-terminus that functions both in binding to methylated DNA and in protein interactions and a C-terminal mismatch-specific glycosylase domain that is involved in DNA repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]
PHENOTYPE: Mice homozygous for a null allele have an increased rate of DNA mutation, specifically at CpGs. [provided by MGI curators]
Allele List at MGI

All alleles(8) : Targeted(6) Gene trapped(2)

Other mutations in this stock
Total: 129 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930578I07Rik A T 14: 67,175,823 (GRCm39) H6L unknown Het
Abca13 G A 11: 9,217,622 (GRCm39) probably null Het
Acad12 C T 5: 121,745,511 (GRCm39) R260Q possibly damaging Het
Actn1 G A 12: 80,306,874 (GRCm39) probably benign Het
Acvrl1 A G 15: 101,034,030 (GRCm39) T182A probably damaging Het
Adam23 T C 1: 63,607,003 (GRCm39) probably benign Het
Adamtsl1 A T 4: 86,261,358 (GRCm39) T1190S probably benign Het
Adh6b A T 3: 138,063,411 (GRCm39) Y330F probably benign Het
Ak7 A G 12: 105,732,876 (GRCm39) E540G probably damaging Het
Akr1c19 T A 13: 4,287,099 (GRCm39) L106Q probably damaging Het
Ankrd12 A T 17: 66,356,847 (GRCm39) S57T probably damaging Het
Aoc3 G A 11: 101,222,964 (GRCm39) R400Q possibly damaging Het
Arel1 A T 12: 84,988,611 (GRCm39) I46N probably damaging Het
Armc5 A G 7: 127,843,463 (GRCm39) D752G probably damaging Het
Atp11b T C 3: 35,891,163 (GRCm39) V812A probably damaging Het
Axin1 A G 17: 26,403,215 (GRCm39) H131R possibly damaging Het
Bpifb3 A G 2: 153,765,789 (GRCm39) E184G probably benign Het
Cacna2d2 T C 9: 107,401,582 (GRCm39) probably benign Het
Catsperd T C 17: 56,969,828 (GRCm39) F641L probably benign Het
Ccdc83 A C 7: 89,877,591 (GRCm39) L284V probably damaging Het
Ccn2 T A 10: 24,472,364 (GRCm39) C136S probably damaging Het
Ccnt2 T A 1: 127,730,902 (GRCm39) V593E probably damaging Het
Cd53 T A 3: 106,669,444 (GRCm39) I185F probably benign Het
Cep350 A T 1: 155,724,366 (GRCm39) D3077E possibly damaging Het
Ces1h C A 8: 94,083,628 (GRCm39) probably null Het
Chrna3 T A 9: 54,923,290 (GRCm39) T173S probably benign Het
Clca4b T C 3: 144,627,717 (GRCm39) D418G probably benign Het
Col11a2 T C 17: 34,270,302 (GRCm39) probably benign Het
Coq2 T A 5: 100,815,889 (GRCm39) I97F possibly damaging Het
Cr2 A G 1: 194,842,667 (GRCm39) probably benign Het
D2hgdh A G 1: 93,754,099 (GRCm39) Y24C probably damaging Het
D630045J12Rik G A 6: 38,168,628 (GRCm39) R974C probably damaging Het
Dach1 A G 14: 98,140,715 (GRCm39) V429A possibly damaging Het
Ddr1 G A 17: 35,995,899 (GRCm39) T660I probably damaging Het
Dlg1 A C 16: 31,615,682 (GRCm39) probably null Het
Dmbt1 T C 7: 130,651,631 (GRCm39) probably benign Het
Dmxl2 A T 9: 54,301,120 (GRCm39) D2330E probably benign Het
Dnai4 T C 4: 102,953,815 (GRCm39) N128S possibly damaging Het
Doc2a A G 7: 126,447,983 (GRCm39) T5A probably benign Het
Dock2 G A 11: 34,595,545 (GRCm39) probably benign Het
Dok4 T A 8: 95,591,866 (GRCm39) Y290F probably damaging Het
Dop1a A G 9: 86,367,550 (GRCm39) D11G probably damaging Het
E230025N22Rik T C 18: 36,821,987 (GRCm39) H235R probably benign Het
Ear6 A G 14: 52,091,909 (GRCm39) D152G probably damaging Het
Ecscr T A 18: 35,846,689 (GRCm39) probably benign Het
Eml6 A T 11: 29,710,010 (GRCm39) probably benign Het
Epha4 T A 1: 77,365,178 (GRCm39) Q607L probably damaging Het
Exoc4 A G 6: 33,948,998 (GRCm39) N947S probably benign Het
Flg A G 3: 93,186,767 (GRCm39) E73G probably damaging Het
Fndc1 C T 17: 8,003,173 (GRCm39) probably benign Het
Gad1-ps T C 10: 99,280,854 (GRCm39) noncoding transcript Het
Gata6 A G 18: 11,064,771 (GRCm39) T528A probably benign Het
Gjd4 T C 18: 9,280,244 (GRCm39) E278G probably benign Het
Gm20091 T A 10: 96,244,864 (GRCm39) noncoding transcript Het
Gnb3 G A 6: 124,812,659 (GRCm39) Q266* probably null Het
Grm3 A G 5: 9,562,446 (GRCm39) V468A possibly damaging Het
Igf1r C T 7: 67,857,574 (GRCm39) R1085C probably damaging Het
Igsf10 T C 3: 59,227,527 (GRCm39) T2049A probably damaging Het
Jak3 A T 8: 72,138,126 (GRCm39) D859V probably benign Het
Kcnb2 G T 1: 15,783,108 (GRCm39) probably benign Het
Kcnh3 G A 15: 99,138,839 (GRCm39) G858D probably benign Het
Kif1a C A 1: 92,971,360 (GRCm39) R1006L probably damaging Het
Klhl23 C T 2: 69,654,757 (GRCm39) A209V probably benign Het
Mapk13 T C 17: 28,994,229 (GRCm39) Y104H probably damaging Het
Mga T C 2: 119,750,187 (GRCm39) probably null Het
Mipol1 G A 12: 57,461,197 (GRCm39) probably null Het
Mmp14 A G 14: 54,676,166 (GRCm39) T299A possibly damaging Het
Mmrn1 A G 6: 60,953,453 (GRCm39) E578G probably benign Het
Mov10l1 G A 15: 88,879,063 (GRCm39) C193Y possibly damaging Het
Mppe1 A G 18: 67,370,548 (GRCm39) C50R probably damaging Het
Msantd1 C A 5: 35,075,069 (GRCm39) R44S probably damaging Het
Myt1l T C 12: 29,892,570 (GRCm39) V69A possibly damaging Het
Nav1 A T 1: 135,392,430 (GRCm39) probably benign Het
Ncan A G 8: 70,561,252 (GRCm39) S572P possibly damaging Het
Nck2 T C 1: 43,608,304 (GRCm39) probably benign Het
Nemf A T 12: 69,403,088 (GRCm39) D31E probably damaging Het
Nlrp12 T C 7: 3,297,892 (GRCm39) D93G possibly damaging Het
Nsmaf A T 4: 6,419,930 (GRCm39) probably null Het
Nup98 T C 7: 101,835,892 (GRCm39) T184A probably damaging Het
Oog2 C A 4: 143,922,654 (GRCm39) Y306* probably null Het
Or13a18 A T 7: 140,190,297 (GRCm39) N73Y probably damaging Het
Or6ae1 A T 7: 139,742,144 (GRCm39) S240T probably damaging Het
Or6b2b A T 1: 92,419,055 (GRCm39) C141S possibly damaging Het
Osmr A G 15: 6,871,419 (GRCm39) probably benign Het
P2rx6 A G 16: 17,386,162 (GRCm39) N275S probably benign Het
Pbxip1 G T 3: 89,354,926 (GRCm39) G482W possibly damaging Het
Pcsk4 T G 10: 80,161,168 (GRCm39) I249L probably damaging Het
Pou4f2 C T 8: 79,162,291 (GRCm39) G104E probably damaging Het
Pramel28 T A 4: 143,691,653 (GRCm39) T357S possibly damaging Het
Prkdc G T 16: 15,651,652 (GRCm39) R3763L probably damaging Het
Ptpre A T 7: 135,265,044 (GRCm39) I207F probably damaging Het
Rapgef3 A T 15: 97,655,698 (GRCm39) probably benign Het
Rasgrp1 T G 2: 117,115,428 (GRCm39) K685T probably benign Het
Rnf148 C T 6: 23,654,237 (GRCm39) R253Q probably damaging Het
Rock1 T C 18: 10,132,227 (GRCm39) I241V possibly damaging Het
Rp1l1 T G 14: 64,259,541 (GRCm39) V61G probably damaging Het
Scin A C 12: 40,131,770 (GRCm39) S255A probably damaging Het
Scn8a A T 15: 100,933,505 (GRCm39) K1570* probably null Het
Sec14l4 A C 11: 3,990,018 (GRCm39) M106L probably benign Het
Sec63 G A 10: 42,674,795 (GRCm39) R226H probably benign Het
Septin2 T A 1: 93,429,345 (GRCm39) N271K probably damaging Het
Serac1 G T 17: 6,099,101 (GRCm39) probably benign Het
Shc2 T A 10: 79,465,974 (GRCm39) probably benign Het
Sipa1l1 T A 12: 82,471,873 (GRCm39) D1284E probably benign Het
Slc11a2 A G 15: 100,306,097 (GRCm39) L105P probably damaging Het
Slc1a3 T A 15: 8,680,406 (GRCm39) T151S probably benign Het
Smarca2 G T 19: 26,668,762 (GRCm39) K920N probably damaging Het
Sugp2 G A 8: 70,711,598 (GRCm39) E964K probably damaging Het
Tas2r122 A C 6: 132,688,778 (GRCm39) N38K probably benign Het
Tecpr1 G A 5: 144,143,092 (GRCm39) R730C probably damaging Het
Tent2 A T 13: 93,312,123 (GRCm39) probably benign Het
Themis3 G T 17: 66,900,265 (GRCm39) N34K possibly damaging Het
Traf3ip1 A G 1: 91,427,341 (GRCm39) T104A unknown Het
Trappc11 A G 8: 47,956,447 (GRCm39) V843A probably benign Het
Trmt61a T A 12: 111,645,361 (GRCm39) L99Q probably damaging Het
Trp53tg5 T A 2: 164,313,401 (GRCm39) K91N probably damaging Het
Ufsp2 T C 8: 46,445,187 (GRCm39) S339P probably damaging Het
Usp20 T A 2: 30,894,462 (GRCm39) V126E probably damaging Het
Vmn1r75 T A 7: 11,614,797 (GRCm39) N176K probably damaging Het
Vmn2r24 A G 6: 123,793,012 (GRCm39) S780G probably benign Het
Vmn2r89 A G 14: 51,695,048 (GRCm39) probably null Het
Vps13d A T 4: 144,771,665 (GRCm39) S4038T probably damaging Het
Vwa7 A G 17: 35,241,627 (GRCm39) T421A probably damaging Het
Wdr95 C A 5: 149,504,271 (GRCm39) L332I probably damaging Het
Wrn T A 8: 33,826,119 (GRCm39) K181I probably damaging Het
Zc3h6 T A 2: 128,859,143 (GRCm39) I1058N possibly damaging Het
Zfp423 T A 8: 88,508,713 (GRCm39) I544F probably damaging Het
Zfp446 T A 7: 12,713,516 (GRCm39) S161T possibly damaging Het
Zmym6 T A 4: 127,017,162 (GRCm39) M889K probably benign Het
Other mutations in Mbd4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01516:Mbd4 APN 6 115,826,491 (GRCm39) missense probably damaging 0.99
IGL01545:Mbd4 APN 6 115,827,758 (GRCm39) missense probably damaging 1.00
IGL01657:Mbd4 APN 6 115,826,598 (GRCm39) missense probably damaging 0.99
IGL02406:Mbd4 APN 6 115,825,986 (GRCm39) missense possibly damaging 0.96
E0370:Mbd4 UTSW 6 115,826,116 (GRCm39) missense possibly damaging 0.91
R0025:Mbd4 UTSW 6 115,821,529 (GRCm39) critical splice donor site probably null
R0025:Mbd4 UTSW 6 115,821,529 (GRCm39) critical splice donor site probably null
R2085:Mbd4 UTSW 6 115,825,918 (GRCm39) missense probably benign 0.01
R4405:Mbd4 UTSW 6 115,826,076 (GRCm39) missense possibly damaging 0.92
R4464:Mbd4 UTSW 6 115,826,463 (GRCm39) missense probably damaging 0.99
R4780:Mbd4 UTSW 6 115,826,345 (GRCm39) missense probably benign
R4782:Mbd4 UTSW 6 115,822,283 (GRCm39) missense possibly damaging 0.49
R4799:Mbd4 UTSW 6 115,822,283 (GRCm39) missense probably benign 0.26
R4814:Mbd4 UTSW 6 115,826,260 (GRCm39) missense possibly damaging 0.85
R4860:Mbd4 UTSW 6 115,825,887 (GRCm39) missense possibly damaging 0.51
R4860:Mbd4 UTSW 6 115,825,887 (GRCm39) missense possibly damaging 0.51
R4976:Mbd4 UTSW 6 115,827,685 (GRCm39) missense possibly damaging 0.95
R5126:Mbd4 UTSW 6 115,825,929 (GRCm39) splice site probably null
R5202:Mbd4 UTSW 6 115,826,363 (GRCm39) missense probably damaging 0.96
R5485:Mbd4 UTSW 6 115,827,679 (GRCm39) missense probably benign 0.21
R6179:Mbd4 UTSW 6 115,822,386 (GRCm39) missense probably benign 0.00
R6661:Mbd4 UTSW 6 115,826,116 (GRCm39) nonsense probably null
R7008:Mbd4 UTSW 6 115,827,685 (GRCm39) missense possibly damaging 0.95
R7244:Mbd4 UTSW 6 115,821,564 (GRCm39) missense probably benign 0.00
R7723:Mbd4 UTSW 6 115,822,324 (GRCm39) missense possibly damaging 0.47
R7755:Mbd4 UTSW 6 115,821,546 (GRCm39) missense probably damaging 0.99
R7837:Mbd4 UTSW 6 115,826,500 (GRCm39) missense probably benign 0.20
R8032:Mbd4 UTSW 6 115,821,594 (GRCm39) missense probably damaging 1.00
R9707:Mbd4 UTSW 6 115,826,559 (GRCm39) missense probably benign 0.04
Predicted Primers PCR Primer
(F):5'- AGCTGGGCATTTCAGAGCCATC -3'
(R):5'- ACTGCCGAAAGGGAGCATCAATC -3'

Sequencing Primer
(F):5'- GAGTAGACTCTAAGAGACTCTTCCTG -3'
(R):5'- GGAGCATCAATCCCGGTTATAAAC -3'
Posted On 2013-06-12