Incidental Mutation 'R1290:Mbd1'
ID 150775
Institutional Source Beutler Lab
Gene Symbol Mbd1
Ensembl Gene ENSMUSG00000024561
Gene Name methyl-CpG binding domain protein 1
Synonyms PCM1, Cxxc3
MMRRC Submission 039356-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1290 (G1)
Quality Score 225
Status Not validated
Chromosome 18
Chromosomal Location 74400676-74415803 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 74402557 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 20 (S20P)
Ref Sequence ENSEMBL: ENSMUSP00000153428 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000097530] [ENSMUST00000224047] [ENSMUST00000224332]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000097530
AA Change: S20P

PolyPhen 2 Score 0.028 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000095137
Gene: ENSMUSG00000024561
AA Change: S20P

DomainStartEndE-ValueType
MBD 3 76 3.94e-27 SMART
low complexity region 82 97 N/A INTRINSIC
low complexity region 123 153 N/A INTRINSIC
Pfam:zf-CXXC 194 241 1.9e-13 PFAM
Pfam:zf-CXXC 243 288 1.2e-13 PFAM
low complexity region 358 368 N/A INTRINSIC
low complexity region 513 527 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000224047
AA Change: S20P

PolyPhen 2 Score 0.593 (Sensitivity: 0.87; Specificity: 0.91)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224159
Predicted Effect probably benign
Transcript: ENSMUST00000224332
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224907
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.8%
Validation Efficiency
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 multiple domains: MBD at the N-terminus that functions both in binding to methylated DNA and in protein interactions; several CXXC-type zinc finger domains that mediate binding to non-methylated CpG dinucleotides; transcriptional repression domain (TRD) at the C-terminus that is involved in transcription repression and in protein interactions. Numerous alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Feb 2011]
PHENOTYPE: Homozygous null exhibited defects in adult hippocampal neurogenesis and function. Spatial learning was also impaired in mutant mice. [provided by MGI curators]
Allele List at MGI

All alleles(3) : Targeted(2) Gene trapped(1)

Other mutations in this stock
Total: 24 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Arfrp1 C T 2: 181,006,397 (GRCm39) probably null Het
Borcs5 A G 6: 134,621,331 (GRCm39) D34G possibly damaging Het
Dync1h1 G A 12: 110,602,943 (GRCm39) E2195K probably benign Het
Efl1 T C 7: 82,320,936 (GRCm39) V123A probably damaging Het
Exd2 T A 12: 80,531,100 (GRCm39) L99Q probably benign Het
Fnip2 T C 3: 79,373,000 (GRCm39) D1026G probably damaging Het
Gprin3 A G 6: 59,331,449 (GRCm39) F286S possibly damaging Het
Gramd1b A G 9: 40,228,117 (GRCm39) probably null Het
Ints1 A T 5: 139,757,165 (GRCm39) L417* probably null Het
Iqgap2 A T 13: 95,805,021 (GRCm39) V845E probably damaging Het
Kcnh3 G A 15: 99,125,001 (GRCm39) probably null Het
Mef2c A T 13: 83,810,478 (GRCm39) T375S probably benign Het
Mmp16 A T 4: 18,051,725 (GRCm39) N238I probably damaging Het
Neurod2 A T 11: 98,218,114 (GRCm39) V350E possibly damaging Het
P3h2 C T 16: 25,805,953 (GRCm39) E297K probably damaging Het
Pcdhb1 A G 18: 37,398,283 (GRCm39) H78R possibly damaging Het
Slc22a14 A C 9: 119,007,518 (GRCm39) L297R probably damaging Het
Slc22a8 G A 19: 8,587,275 (GRCm39) G445D probably damaging Het
Spink5 A G 18: 44,140,778 (GRCm39) D659G probably damaging Het
St6gal1 A G 16: 23,140,411 (GRCm39) Q194R probably benign Het
Tas2r104 A T 6: 131,661,808 (GRCm39) C300* probably null Het
Ttc6 G A 12: 57,707,199 (GRCm39) S702N probably benign Het
Wnk4 C G 11: 101,167,166 (GRCm39) probably benign Het
Zfyve28 A T 5: 34,356,145 (GRCm39) D785E probably benign Het
Other mutations in Mbd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00902:Mbd1 APN 18 74,408,310 (GRCm39) missense possibly damaging 0.72
IGL01551:Mbd1 APN 18 74,402,614 (GRCm39) unclassified probably benign
IGL02213:Mbd1 APN 18 74,408,453 (GRCm39) missense probably damaging 1.00
IGL02562:Mbd1 APN 18 74,409,993 (GRCm39) missense probably benign 0.00
IGL02596:Mbd1 APN 18 74,409,868 (GRCm39) splice site probably benign
IGL02944:Mbd1 APN 18 74,410,481 (GRCm39) missense probably damaging 1.00
IGL02973:Mbd1 APN 18 74,408,498 (GRCm39) splice site probably benign
IGL03200:Mbd1 APN 18 74,409,502 (GRCm39) missense probably benign 0.02
IGL03247:Mbd1 APN 18 74,407,825 (GRCm39) nonsense probably null
IGL03340:Mbd1 APN 18 74,407,553 (GRCm39) missense probably benign 0.00
Shortbread UTSW 18 74,407,128 (GRCm39) critical splice donor site probably null
FR4737:Mbd1 UTSW 18 74,406,644 (GRCm39) small deletion probably benign
P0016:Mbd1 UTSW 18 74,407,609 (GRCm39) nonsense probably null
R0385:Mbd1 UTSW 18 74,406,312 (GRCm39) frame shift probably null
R0630:Mbd1 UTSW 18 74,409,798 (GRCm39) splice site probably benign
R0717:Mbd1 UTSW 18 74,406,668 (GRCm39) missense possibly damaging 0.89
R1084:Mbd1 UTSW 18 74,402,603 (GRCm39) missense probably damaging 1.00
R1575:Mbd1 UTSW 18 74,408,490 (GRCm39) critical splice donor site probably null
R2065:Mbd1 UTSW 18 74,409,955 (GRCm39) missense probably damaging 1.00
R2192:Mbd1 UTSW 18 74,410,449 (GRCm39) missense probably damaging 0.99
R2308:Mbd1 UTSW 18 74,409,548 (GRCm39) missense probably benign 0.42
R2697:Mbd1 UTSW 18 74,406,688 (GRCm39) missense possibly damaging 0.95
R3407:Mbd1 UTSW 18 74,410,438 (GRCm39) missense possibly damaging 0.94
R4348:Mbd1 UTSW 18 74,407,487 (GRCm39) missense probably damaging 1.00
R4664:Mbd1 UTSW 18 74,402,597 (GRCm39) missense possibly damaging 0.86
R5460:Mbd1 UTSW 18 74,402,581 (GRCm39) missense probably benign 0.03
R5860:Mbd1 UTSW 18 74,409,768 (GRCm39) nonsense probably null
R6431:Mbd1 UTSW 18 74,406,762 (GRCm39) splice site probably null
R6734:Mbd1 UTSW 18 74,409,114 (GRCm39) missense probably damaging 1.00
R6861:Mbd1 UTSW 18 74,406,645 (GRCm39)
R7363:Mbd1 UTSW 18 74,406,357 (GRCm39) missense probably damaging 0.97
R7543:Mbd1 UTSW 18 74,407,520 (GRCm39) missense probably damaging 0.97
R7657:Mbd1 UTSW 18 74,407,804 (GRCm39) missense probably damaging 0.99
R7871:Mbd1 UTSW 18 74,407,128 (GRCm39) critical splice donor site probably null
R8960:Mbd1 UTSW 18 74,406,890 (GRCm39) critical splice donor site probably null
R9161:Mbd1 UTSW 18 74,407,792 (GRCm39) missense probably benign 0.01
R9774:Mbd1 UTSW 18 74,408,274 (GRCm39) missense probably benign
RF005:Mbd1 UTSW 18 74,406,644 (GRCm39) small deletion probably benign
RF011:Mbd1 UTSW 18 74,406,681 (GRCm39) small deletion probably benign
RF024:Mbd1 UTSW 18 74,406,681 (GRCm39) small deletion probably benign
RF024:Mbd1 UTSW 18 74,406,644 (GRCm39) small deletion probably benign
RF058:Mbd1 UTSW 18 74,406,680 (GRCm39) frame shift probably null
Z1177:Mbd1 UTSW 18 74,410,010 (GRCm39) missense probably null 0.72
Predicted Primers
Posted On 2014-01-29