Incidental Mutation 'R4464:Mbd4'
ID 330269
Institutional Source Beutler Lab
Gene Symbol Mbd4
Ensembl Gene ENSMUSG00000030322
Gene Name methyl-CpG binding domain protein 4
Synonyms Med1
MMRRC Submission 041722-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.192) question?
Stock # R4464 (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 115826463 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Serine at position 155 (L155S)
Ref Sequence ENSEMBL: ENSMUSP00000125619 (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 benign
Transcript: ENSMUST00000032469
AA Change: L176S

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000032469
Gene: ENSMUSG00000030322
AA Change: L176S

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 damaging
Transcript: ENSMUST00000122816
AA Change: L176S

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000145433
Gene: ENSMUSG00000030322
AA Change: L176S

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 damaging
Transcript: ENSMUST00000147282
AA Change: L155S

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000125619
Gene: ENSMUSG00000030322
AA Change: L155S

DomainStartEndE-ValueType
MBD 45 121 1.25e-29 SMART
low complexity region 157 175 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133830
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: 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
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.8%
Validation Efficiency 97% (35/36)
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: 31 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
0610040J01Rik G T 5: 64,056,182 (GRCm39) probably benign Het
Abcc3 A G 11: 94,249,612 (GRCm39) V1111A probably benign Het
Acot10 G A 15: 20,665,830 (GRCm39) R304* probably null Het
Aldh8a1 C A 10: 21,264,840 (GRCm39) probably benign Het
Alms1 A G 6: 85,597,003 (GRCm39) T1079A possibly damaging Het
Armc3 T C 2: 19,253,470 (GRCm39) Y204H probably damaging Het
Asnsd1 C A 1: 53,391,686 (GRCm39) probably null Het
Atad5 T A 11: 79,991,137 (GRCm39) probably null Het
Cst12 G A 2: 148,631,437 (GRCm39) V53I possibly damaging Het
Cylc2 C G 4: 51,229,651 (GRCm39) T331R unknown Het
Dennd1a A T 2: 38,133,402 (GRCm39) probably benign Het
Gm7535 C A 17: 18,131,924 (GRCm39) probably benign Het
Gpr158 T A 2: 21,831,810 (GRCm39) M970K probably damaging Het
Ifngr1 G A 10: 19,473,265 (GRCm39) V72I possibly damaging Het
Kifap3 C A 1: 163,645,464 (GRCm39) Q269K probably benign Het
Krt86 G A 15: 101,371,795 (GRCm39) D122N probably damaging Het
Lrrcc1 A G 3: 14,622,378 (GRCm39) K694E probably damaging Het
Nalcn T C 14: 123,560,762 (GRCm39) N772D probably benign Het
Or12d17 C T 17: 37,777,742 (GRCm39) S215F probably damaging Het
Prxl2a T A 14: 40,719,832 (GRCm39) K127N probably damaging Het
Psg29 A T 7: 16,944,575 (GRCm39) N362Y possibly damaging Het
Ptpn23 G A 9: 110,215,881 (GRCm39) T1325I probably damaging Het
Rad51ap1 T C 6: 126,911,731 (GRCm39) N52S possibly damaging Het
Rb1 C A 14: 73,436,638 (GRCm39) probably null Het
Slc34a2 T C 5: 53,226,524 (GRCm39) L490P probably damaging Het
Sost G A 11: 101,857,670 (GRCm39) P44S probably damaging Het
St3gal2 A G 8: 111,694,134 (GRCm39) N207D probably benign Het
Stat1 T G 1: 52,176,575 (GRCm39) D257E possibly damaging Het
Tkt A G 14: 30,290,231 (GRCm39) T165A possibly damaging Het
Trim66 A T 7: 109,076,897 (GRCm39) S347R possibly damaging Het
Zfp429 T C 13: 67,538,617 (GRCm39) I276V 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
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
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'- ACTCTAAGAGACTCTTCCTGCAC -3'
(R):5'- TCAGATCAAAACGTTCACTTGC -3'

Sequencing Primer
(F):5'- AAGAGACTCTTCCTGCACTTTTG -3'
(R):5'- CTTCTCAAAAATGGGGAGACTTTTC -3'
Posted On 2015-07-21