Incidental Mutation 'R6661:Mbd4'
ID 526842
Institutional Source Beutler Lab
Gene Symbol Mbd4
Ensembl Gene ENSMUSG00000030322
Gene Name methyl-CpG binding domain protein 4
Synonyms Med1
MMRRC Submission 044781-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.192) question?
Stock # R6661 (G1)
Quality Score 225.009
Status Validated
Chromosome 6
Chromosomal Location 115817658-115830332 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) C to A at 115826116 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Stop codon at position 271 (E271*)
Ref Sequence ENSEMBL: ENSMUSP00000125619 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032469] [ENSMUST00000038234] [ENSMUST00000112923] [ENSMUST00000112925] [ENSMUST00000122816] [ENSMUST00000147282] [ENSMUST00000141305] [ENSMUST00000203643]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000032469
AA Change: E292*
SMART Domains Protein: ENSMUSP00000032469
Gene: ENSMUSG00000030322
AA Change: E292*

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 probably null
Transcript: ENSMUST00000122816
AA Change: E292*
SMART Domains Protein: ENSMUSP00000145433
Gene: ENSMUSG00000030322
AA Change: E292*

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 probably null
Transcript: ENSMUST00000147282
AA Change: E271*
SMART Domains Protein: ENSMUSP00000125619
Gene: ENSMUSG00000030322
AA Change: E271*

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: 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
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
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.8%
  • 20x: 93.8%
Validation Efficiency 93% (38/41)
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: 41 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Amy2a1 T C 3: 113,325,363 (GRCm39) Y77C probably damaging Het
Ankrd9 C A 12: 110,944,202 (GRCm39) probably benign Het
Arhgap28 C A 17: 68,152,746 (GRCm39) W675L probably damaging Het
Arhgap44 A G 11: 64,900,834 (GRCm39) S595P probably damaging Het
Brd10 A T 19: 29,700,864 (GRCm39) H741Q possibly damaging Het
Cacna1d C A 14: 29,811,832 (GRCm39) D1273Y probably damaging Het
Ccr4 T C 9: 114,325,031 (GRCm39) probably benign Het
Celsr1 A G 15: 85,803,135 (GRCm39) V2468A probably damaging Het
Chd2 T C 7: 73,140,230 (GRCm39) E666G possibly damaging Het
Ctnnd1 C A 2: 84,439,986 (GRCm39) V775L probably damaging Het
Cux2 C A 5: 122,007,360 (GRCm39) R767L probably benign Het
Decr2 A G 17: 26,302,561 (GRCm39) L217S possibly damaging Het
Dennd4c T A 4: 86,717,626 (GRCm39) M541K possibly damaging Het
Dnah7a T C 1: 53,662,609 (GRCm39) R651G probably benign Het
Fbrsl1 A T 5: 110,525,963 (GRCm39) F80I probably damaging Het
Fmnl2 C A 2: 52,998,297 (GRCm39) P554Q probably damaging Het
Gapvd1 C T 2: 34,618,450 (GRCm39) D308N probably damaging Het
Gatb A G 3: 85,559,726 (GRCm39) probably null Het
Jcad G A 18: 4,675,256 (GRCm39) G1006D probably damaging Het
Krt1c A G 15: 101,724,398 (GRCm39) Y289H probably damaging Het
Lrrc52 A G 1: 167,293,922 (GRCm39) F121S probably damaging Het
Lrrc63 G A 14: 75,362,633 (GRCm39) T299I unknown Het
Magi1 T C 6: 93,920,289 (GRCm39) N109S probably benign Het
Meis2 T A 2: 115,694,751 (GRCm39) D457V probably damaging Het
Mroh8 A G 2: 157,067,547 (GRCm39) V604A probably benign Het
Nedd4 T A 9: 72,593,377 (GRCm39) V150E probably damaging Het
Nes A G 3: 87,884,243 (GRCm39) E790G probably damaging Het
Or8h8 T C 2: 86,753,492 (GRCm39) N128S probably benign Het
Pik3c2a T C 7: 115,967,993 (GRCm39) I834V possibly damaging Het
Plxnb1 T C 9: 108,933,367 (GRCm39) C666R possibly damaging Het
Prg2 T C 2: 84,813,620 (GRCm39) probably null Het
Selenbp2 A G 3: 94,609,821 (GRCm39) D257G probably damaging Het
Slf1 T C 13: 77,191,964 (GRCm39) R957G probably damaging Het
Smim10l1 T A 6: 133,082,513 (GRCm39) M46K possibly damaging Het
Sptbn5 T C 2: 119,902,856 (GRCm39) Y50C possibly damaging Het
Tcea1 A G 1: 4,928,652 (GRCm39) probably benign Het
Tex14 A G 11: 87,385,842 (GRCm39) E234G probably damaging Het
Tmbim4 T C 10: 120,060,556 (GRCm39) V181A probably benign Het
Trappc9 A G 15: 72,461,993 (GRCm39) S1091P possibly damaging Het
Txnrd3 T A 6: 89,631,134 (GRCm39) C143* probably null Het
Ushbp1 C T 8: 71,843,305 (GRCm39) C314Y unknown 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
R0538:Mbd4 UTSW 6 115,826,443 (GRCm39) missense probably damaging 0.99
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
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'- GCCATCCTGTAAAACACCAGTATG -3'
(R):5'- GTGACTGTTTTGAAAGGAACTGC -3'

Sequencing Primer
(F):5'- TCCTGTAAAACACCAGTATGCAAATG -3'
(R):5'- GACTGTTTTGAAAGGAACTGCAAGTC -3'
Posted On 2018-07-23