Incidental Mutation 'R7611:Mbd3'
ID 588612
Institutional Source Beutler Lab
Gene Symbol Mbd3
Ensembl Gene ENSMUSG00000035478
Gene Name methyl-CpG binding domain protein 3
Synonyms
MMRRC Submission 045715-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7611 (G1)
Quality Score 225.009
Status Not validated
Chromosome 10
Chromosomal Location 80228373-80235365 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 80231352 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 63 (D63G)
Ref Sequence ENSEMBL: ENSMUSP00000089948 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000092295] [ENSMUST00000105347] [ENSMUST00000105348] [ENSMUST00000105349]
AlphaFold Q9Z2D8
Predicted Effect probably damaging
Transcript: ENSMUST00000092295
AA Change: D63G

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000089948
Gene: ENSMUSG00000035478
AA Change: D63G

DomainStartEndE-ValueType
MBD 3 76 8.9e-35 SMART
Pfam:MBDa 79 148 8.2e-32 PFAM
Pfam:MBD_C 152 243 4.7e-37 PFAM
low complexity region 268 283 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000105347
AA Change: D39G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000100984
Gene: ENSMUSG00000035478
AA Change: D39G

DomainStartEndE-ValueType
Pfam:MBD 12 48 4.4e-8 PFAM
Pfam:MBD_C 126 219 9.8e-39 PFAM
low complexity region 244 259 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000105348
AA Change: D31G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000100985
Gene: ENSMUSG00000035478
AA Change: D31G

DomainStartEndE-ValueType
MBD 1 44 4.8e-6 SMART
Pfam:MBD_C 146 239 1.7e-35 PFAM
low complexity region 264 279 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000105349
AA Change: D31G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000100986
Gene: ENSMUSG00000035478
AA Change: D31G

DomainStartEndE-ValueType
Pfam:MBD 4 40 4.7e-8 PFAM
Pfam:MBD_C 118 211 1.1e-38 PFAM
low complexity region 236 251 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000142997
SMART Domains Protein: ENSMUSP00000120675
Gene: ENSMUSG00000035478

DomainStartEndE-ValueType
Pfam:MBDa 1 48 2.4e-25 PFAM
Pfam:MBD_C 52 143 1.3e-37 PFAM
low complexity region 168 183 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.0%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a member of the MBD family of nuclear proteins that contain a methyl-CpG binding domain (MBD). The encoded protein is a component of the nucleosome remodeling and histone deacetylation (NuRD) complex. Deletion of this gene causes embryonic lethality in mice. Embryonic stem cells lacking the encoded protein are severely compromised in their ability to differentiate and fail to commit to developmental lineages in the absence of leukemia inhibitory factor. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]
PHENOTYPE: Mice homozygous for disruptions in this gene experience deficiencies as embryos around implantation and die before birth. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acta2 G A 19: 34,229,931 (GRCm39) T8I probably benign Het
Adcy8 C T 15: 64,792,882 (GRCm39) G25S probably benign Het
Ahnak2 G T 12: 112,751,749 (GRCm39) D35E Het
Birc6 T C 17: 74,969,713 (GRCm39) M4261T probably damaging Het
Caln1 T G 5: 130,534,918 (GRCm39) F45V probably damaging Het
Camta2 A T 11: 70,572,372 (GRCm39) I313N possibly damaging Het
Capns1 T A 7: 29,889,539 (GRCm39) E220V probably damaging Het
Carmil1 C A 13: 24,197,315 (GRCm39) V1374L probably benign Het
Casp2 T G 6: 42,250,972 (GRCm39) L290R possibly damaging Het
Cdkn2b C A 4: 89,228,980 (GRCm39) V19L probably benign Het
Ces1c T C 8: 93,851,139 (GRCm39) N162D probably benign Het
Cfap96 A G 8: 46,423,488 (GRCm39) Y75H probably damaging Het
Chd9 T C 8: 91,763,017 (GRCm39) S2281P probably damaging Het
Chst13 T C 6: 90,285,999 (GRCm39) D321G probably damaging Het
Ckap2l G T 2: 129,127,600 (GRCm39) P193T possibly damaging Het
Clca4b T A 3: 144,627,757 (GRCm39) T405S probably benign Het
Cmah T C 13: 24,619,630 (GRCm39) V265A probably benign Het
Cyp3a11 A T 5: 145,797,191 (GRCm39) M396K probably benign Het
Ddr2 A T 1: 169,825,727 (GRCm39) M291K possibly damaging Het
Ddx43 T A 9: 78,309,635 (GRCm39) I145N probably benign Het
Ephb2 T A 4: 136,388,212 (GRCm39) probably null Het
Fgfr1 A T 8: 26,048,221 (GRCm39) K106* probably null Het
Gpr6 A G 10: 40,946,875 (GRCm39) F236L probably benign Het
Grin2c A G 11: 115,143,511 (GRCm39) S750P probably damaging Het
Hecw2 A G 1: 53,952,459 (GRCm39) S925P probably damaging Het
Hivep3 CGG CG 4: 119,955,108 (GRCm39) 1141 probably null Het
Hmg20b T A 10: 81,185,432 (GRCm39) probably benign Het
Kcnk10 T A 12: 98,484,899 (GRCm39) Y79F probably damaging Het
Lrrc30 A T 17: 67,939,424 (GRCm39) F52Y probably damaging Het
Lrriq1 T C 10: 103,036,432 (GRCm39) K907R possibly damaging Het
Mettl21a C T 1: 64,654,266 (GRCm39) A84T probably benign Het
Mmp19 A G 10: 128,634,857 (GRCm39) D491G probably benign Het
Mug1 A T 6: 121,852,387 (GRCm39) probably null Het
Myh1 A T 11: 67,101,243 (GRCm39) H673L possibly damaging Het
Nlrc5 T C 8: 95,239,276 (GRCm39) probably null Het
Nme9 T A 9: 99,352,843 (GRCm39) S264R probably benign Het
Nup153 T C 13: 46,840,798 (GRCm39) T937A probably benign Het
Obsl1 T C 1: 75,482,024 (GRCm39) E282G probably damaging Het
Or1o3 A G 17: 37,573,745 (GRCm39) V270A probably benign Het
Or2w2 A G 13: 21,758,488 (GRCm39) V46A probably benign Het
Or4l15 C A 14: 50,198,368 (GRCm39) A54S probably benign Het
Or5an10 T A 19: 12,276,242 (GRCm39) M85L probably damaging Het
Or5b99 T A 19: 12,976,431 (GRCm39) I27N possibly damaging Het
Or5m5 T A 2: 85,814,407 (GRCm39) C74* probably null Het
Or8k30 T A 2: 86,339,397 (GRCm39) I198K possibly damaging Het
Pcdhga12 T C 18: 37,901,478 (GRCm39) F770S possibly damaging Het
Pfkp T A 13: 6,655,119 (GRCm39) probably null Het
Prr29 C G 11: 106,267,158 (GRCm39) H58D probably damaging Het
Ptprz1 T A 6: 23,001,219 (GRCm39) M1103K probably benign Het
Rigi T C 4: 40,225,651 (GRCm39) E250G probably damaging Het
Rsph4a C T 10: 33,781,473 (GRCm39) P108S probably benign Het
Setd1b A C 5: 123,290,657 (GRCm39) M875L unknown Het
Slc15a2 A G 16: 36,576,673 (GRCm39) S485P probably benign Het
Smoc1 A G 12: 81,226,444 (GRCm39) D423G probably damaging Het
Spast T A 17: 74,676,198 (GRCm39) V337D probably damaging Het
Spesp1 T C 9: 62,179,987 (GRCm39) K307R possibly damaging Het
Sulf1 A G 1: 12,906,467 (GRCm39) E503G probably benign Het
Susd6 T C 12: 80,921,341 (GRCm39) Y313H probably damaging Het
Them4 A T 3: 94,238,865 (GRCm39) D224V possibly damaging Het
Tpsg1 G T 17: 25,592,184 (GRCm39) G86V probably damaging Het
Tspear A T 10: 77,717,049 (GRCm39) T575S probably benign Het
Usp21 A T 1: 171,113,142 (GRCm39) H211Q probably benign Het
Vmn1r189 T C 13: 22,286,322 (GRCm39) S172G probably benign Het
Vmn2r114 T C 17: 23,515,944 (GRCm39) S516G probably damaging Het
Vmn2r28 T A 7: 5,484,255 (GRCm39) R648S probably benign Het
Vmn2r6 C A 3: 64,472,563 (GRCm39) V53F probably damaging Het
Vmn2r76 A G 7: 85,879,388 (GRCm39) I304T probably benign Het
Vmn2r88 A C 14: 51,651,454 (GRCm39) Y256S Het
Zfhx4 A T 3: 5,468,831 (GRCm39) K3021N probably damaging Het
Zfp647 T C 15: 76,795,988 (GRCm39) H224R probably damaging Het
Zfp865 A G 7: 5,034,130 (GRCm39) E705G probably damaging Het
Other mutations in Mbd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00158:Mbd3 APN 10 80,229,717 (GRCm39) splice site probably benign
IGL01573:Mbd3 APN 10 80,229,095 (GRCm39) missense probably benign 0.03
IGL03080:Mbd3 APN 10 80,229,085 (GRCm39) missense probably damaging 1.00
R1489:Mbd3 UTSW 10 80,229,740 (GRCm39) missense probably damaging 1.00
R1500:Mbd3 UTSW 10 80,230,420 (GRCm39) missense possibly damaging 0.90
R4454:Mbd3 UTSW 10 80,229,817 (GRCm39) missense probably damaging 1.00
R4921:Mbd3 UTSW 10 80,231,410 (GRCm39) missense probably damaging 1.00
R7659:Mbd3 UTSW 10 80,231,019 (GRCm39) missense probably damaging 1.00
X0063:Mbd3 UTSW 10 80,231,287 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- CTTAGCCAGAGCCTGAATGG -3'
(R):5'- GCCTTCCTAATGACCTGGTG -3'

Sequencing Primer
(F):5'- ATCAGGCACGGAGATCTCC -3'
(R):5'- CTTCCTAATGACCTGGTGAAAACAG -3'
Posted On 2019-10-24