Incidental Mutation 'R1500:Mbd3'
ID169191
Institutional Source Beutler Lab
Gene Symbol Mbd3
Ensembl Gene ENSMUSG00000035478
Gene Namemethyl-CpG binding domain protein 3
Synonyms
MMRRC Submission 039551-MU
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #R1500 (G1)
Quality Score117
Status Validated
Chromosome10
Chromosomal Location80392539-80399550 bp(-) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 80394586 bp
ZygosityHeterozygous
Amino Acid Change Aspartic acid to Glycine at position 160 (D160G)
Ref Sequence ENSEMBL: ENSMUSP00000089948 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000092295] [ENSMUST00000105347] [ENSMUST00000105348] [ENSMUST00000105349]
Predicted Effect possibly damaging
Transcript: ENSMUST00000092295
AA Change: D160G

PolyPhen 2 Score 0.897 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000089948
Gene: ENSMUSG00000035478
AA Change: D160G

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 possibly damaging
Transcript: ENSMUST00000105347
AA Change: D136G

PolyPhen 2 Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000100984
Gene: ENSMUSG00000035478
AA Change: D136G

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 possibly damaging
Transcript: ENSMUST00000105348
AA Change: D156G

PolyPhen 2 Score 0.672 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000100985
Gene: ENSMUSG00000035478
AA Change: D156G

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 possibly damaging
Transcript: ENSMUST00000105349
AA Change: D128G

PolyPhen 2 Score 0.648 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000100986
Gene: ENSMUSG00000035478
AA Change: D128G

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 noncoding transcript
Transcript: ENSMUST00000125618
Predicted Effect unknown
Transcript: ENSMUST00000142997
AA Change: D59G
SMART Domains Protein: ENSMUSP00000120675
Gene: ENSMUSG00000035478
AA Change: D59G

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
Meta Mutation Damage Score 0.332 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.8%
  • 10x: 94.7%
  • 20x: 87.1%
Validation Efficiency 95% (81/85)
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: 81 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610507B11Rik C A 11: 78,284,132 Q1698K possibly damaging Het
A230050P20Rik AGAGGAGGAGGAGGAGGAGGAGGAGGA AGAGGAGGAGGAGGAGGAGGAGGA 9: 20,873,717 probably benign Het
Abcg1 A G 17: 31,111,279 D518G probably benign Het
Acaca T A 11: 84,293,984 D96E probably benign Het
Actbl2 G A 13: 111,255,320 R63Q probably damaging Het
Adamts6 T A 13: 104,312,881 H266Q probably damaging Het
Aff4 T C 11: 53,372,378 V75A probably benign Het
Ank2 A G 3: 126,932,982 S888P probably benign Het
Ano7 T C 1: 93,397,328 F534S probably damaging Het
Arhgef6 T C X: 57,338,562 M5V probably benign Het
Bcam T A 7: 19,758,964 D484V possibly damaging Het
Ccdc88a T C 11: 29,482,713 Y1240H probably benign Het
Cfh T C 1: 140,100,876 Y500C probably damaging Het
Chd1l G A 3: 97,582,805 A478V probably benign Het
Dnah1 T C 14: 31,316,758 D122G probably benign Het
Dnah11 A T 12: 118,012,829 probably null Het
Dnah17 T C 11: 118,101,053 K1230E probably benign Het
Dync1h1 G A 12: 110,636,509 E2195K probably benign Het
E330020D12Rik A T 1: 153,408,379 noncoding transcript Het
Ece2 T C 16: 20,644,242 L639P probably damaging Het
Epha3 A T 16: 63,595,662 V658E probably benign Het
Erbb2 C T 11: 98,428,978 T632I probably damaging Het
Erc2 A G 14: 28,271,660 T883A probably damaging Het
Extl2 T C 3: 116,027,140 V198A probably benign Het
Fktn G T 4: 53,735,065 M234I probably benign Het
Ggt7 A G 2: 155,499,046 S400P probably benign Het
Gldc A C 19: 30,113,825 V790G possibly damaging Het
Gm14496 A C 2: 181,991,233 Q3P probably benign Het
H2-D1 G A 17: 35,263,588 E95K probably benign Het
Ikzf3 T C 11: 98,518,695 E14G probably benign Het
Jag1 A T 2: 137,115,638 N51K possibly damaging Het
Khdrbs3 A G 15: 68,928,786 D14G possibly damaging Het
Krt84 A G 15: 101,530,224 V276A probably damaging Het
Lamb1 T C 12: 31,298,949 I660T possibly damaging Het
Lcmt2 A T 2: 121,140,007 S198R probably benign Het
Lcn6 G A 2: 25,677,119 R44H probably benign Het
Lrfn5 A T 12: 61,839,741 H105L probably damaging Het
Lrit1 G A 14: 37,062,134 R473K probably benign Het
March1 A G 8: 66,468,390 T495A probably damaging Het
Marveld3 T G 8: 109,948,542 probably null Het
Mrc2 T G 11: 105,347,725 C1233G probably damaging Het
Ms4a13 T G 19: 11,183,861 T105P probably damaging Het
Mtbp T C 15: 55,617,555 Y306H probably damaging Het
Muc3a T C 5: 137,210,501 probably benign Het
Myo1g T A 11: 6,520,811 Y15F probably benign Het
Nae1 A T 8: 104,523,584 Y226N probably benign Het
Nlrp9a A G 7: 26,567,891 S715G probably benign Het
Olfr1193 T A 2: 88,677,875 S7T possibly damaging Het
Olfr338 A T 2: 36,377,621 M282L probably benign Het
Olfr699 T C 7: 106,790,821 Y60C probably damaging Het
Olfr844 A T 9: 19,319,316 S267C probably damaging Het
Olfr972 G T 9: 39,873,411 M45I probably benign Het
Pex5l T C 3: 33,014,980 T123A probably damaging Het
Pip5kl1 A T 2: 32,576,679 N62I probably benign Het
Pkhd1l1 T C 15: 44,545,494 V2459A probably damaging Het
Prb1 T A 6: 132,207,476 Q398L unknown Het
Prkab2 T C 3: 97,663,947 L165S probably damaging Het
Prl3d2 C G 13: 27,121,706 probably benign Het
Ptdss1 G A 13: 66,995,408 G435D probably benign Het
Qrfpr A G 3: 36,182,580 L224P probably damaging Het
Rasl2-9 C T 7: 5,125,442 W163* probably null Het
Rgs5 A G 1: 169,690,414 probably null Het
Rnf19b T C 4: 129,078,961 L255P probably damaging Het
Rp9 A C 9: 22,457,455 N69K probably damaging Het
Sh3bp4 G T 1: 89,145,488 S686I probably damaging Het
Spp2 C A 1: 88,412,293 Q5K possibly damaging Het
Svep1 C T 4: 58,070,239 G2516R probably damaging Het
Syncrip A C 9: 88,479,896 S55R probably damaging Het
Tacc3 T C 5: 33,661,308 L29P probably damaging Het
Tex15 A G 8: 33,575,092 T1517A probably damaging Het
Tmem140 A G 6: 34,872,725 M59V probably benign Het
Ttn G T 2: 76,745,528 A25007E probably damaging Het
Ubr2 T C 17: 46,986,689 T253A possibly damaging Het
Unc80 C T 1: 66,521,581 H823Y possibly damaging Het
Usp38 A G 8: 80,995,770 L374P probably damaging Het
Vmn1r42 T A 6: 89,845,501 I29L probably benign Het
Vmn2r94 C T 17: 18,256,980 V390M probably benign Het
Vmp1 A G 11: 86,661,200 Y113H possibly damaging Het
Wdr20 T C 12: 110,794,030 M450T probably benign Het
Ylpm1 T C 12: 85,014,996 V557A unknown Het
Zpld1 T C 16: 55,233,572 N286D probably damaging Het
Other mutations in Mbd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00158:Mbd3 APN 10 80393883 splice site probably benign
IGL01573:Mbd3 APN 10 80393261 missense probably benign 0.03
IGL03080:Mbd3 APN 10 80393251 missense probably damaging 1.00
R1489:Mbd3 UTSW 10 80393906 missense probably damaging 1.00
R4454:Mbd3 UTSW 10 80393983 missense probably damaging 1.00
R4921:Mbd3 UTSW 10 80395576 missense probably damaging 1.00
X0063:Mbd3 UTSW 10 80395453 missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- TCGTCAGCCAGAAGATAAGGAGCC -3'
(R):5'- CTCTGAGGAAGGAGAGTCATGAATTGC -3'

Sequencing Primer
(F):5'- gctcacaactccctgtaagtc -3'
(R):5'- AACAAAGCACTGCTTCTTCTGTG -3'
Posted On2014-04-13