Incidental Mutation 'R5460:Mbd1'
ID 432994
Institutional Source Beutler Lab
Gene Symbol Mbd1
Ensembl Gene ENSMUSG00000024561
Gene Name methyl-CpG binding domain protein 1
Synonyms PCM1, Cxxc3
MMRRC Submission 042849-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5460 (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 74402581 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 28 (F28L)
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: F28L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000095137
Gene: ENSMUSG00000024561
AA Change: F28L

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 probably benign
Transcript: ENSMUST00000224047
AA Change: F28L

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224159
Predicted Effect probably benign
Transcript: ENSMUST00000224332
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224907
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 96.0%
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: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actbl2 T A 13: 111,392,238 (GRCm39) M191K probably benign Het
Actn1 T C 12: 80,230,342 (GRCm39) N304S probably benign Het
Acyp2 C T 11: 30,456,354 (GRCm39) E98K possibly damaging Het
Adamtsl2 T A 2: 26,985,410 (GRCm39) probably null Het
Adgrv1 T C 13: 81,572,377 (GRCm39) E4928G possibly damaging Het
Alms1 T A 6: 85,673,713 (GRCm39) C3103S probably benign Het
Appl2 T A 10: 83,438,696 (GRCm39) I578F probably benign Het
Atp10b T C 11: 43,121,282 (GRCm39) S982P probably benign Het
Brd10 G T 19: 29,732,250 (GRCm39) P254Q probably damaging Het
Capn7 T C 14: 31,090,160 (GRCm39) probably null Het
Cd200r3 A G 16: 44,778,093 (GRCm39) T166A possibly damaging Het
Dctn6 C T 8: 34,572,135 (GRCm39) probably null Het
Duxf4 G A 10: 58,071,717 (GRCm39) H166Y possibly damaging Het
Fam114a1 T A 5: 65,185,776 (GRCm39) F366I probably damaging Het
Fam98b A T 2: 117,089,737 (GRCm39) S85C probably damaging Het
Fat3 T A 9: 15,830,463 (GRCm39) N4344Y probably damaging Het
Fhl3 T G 4: 124,599,796 (GRCm39) C92W probably damaging Het
Flrt1 T C 19: 7,073,105 (GRCm39) T481A probably damaging Het
Gng2 G T 14: 19,941,426 (GRCm39) N5K probably benign Het
Iqcm A T 8: 76,441,417 (GRCm39) D230V probably benign Het
Limk2 T C 11: 3,302,332 (GRCm39) I176V probably benign Het
Lrrk2 T A 15: 91,698,847 (GRCm39) probably null Het
Maml1 T C 11: 50,157,180 (GRCm39) T332A probably benign Het
Matcap2 T C 9: 22,351,216 (GRCm39) F453L probably benign Het
Morf4l1 G A 9: 89,977,183 (GRCm39) T246I probably benign Het
Mtres1 T C 10: 43,408,861 (GRCm39) K94R probably benign Het
Naa12 C T 18: 80,255,138 (GRCm39) A144V probably damaging Het
Ndufaf1 T G 2: 119,490,958 (GRCm39) D34A probably benign Het
Or4a77 T A 2: 89,487,414 (GRCm39) I124F probably damaging Het
Or4c114 C T 2: 88,905,208 (GRCm39) V76I probably benign Het
Patl1 C T 19: 11,913,082 (GRCm39) R542C possibly damaging Het
Pcdha2 T C 18: 37,072,474 (GRCm39) V35A probably damaging Het
Phf11b G A 14: 59,568,713 (GRCm39) P67S probably benign Het
Plxnd1 T C 6: 115,934,609 (GRCm39) I1775V probably damaging Het
Ryr1 T A 7: 28,771,386 (GRCm39) T2552S probably damaging Het
Scai A T 2: 38,973,585 (GRCm39) L52H probably damaging Het
Scai G C 2: 38,973,586 (GRCm39) L52V probably damaging Het
Stag1 A T 9: 100,838,506 (GRCm39) probably null Het
Tgs1 A G 4: 3,586,170 (GRCm39) K349R probably benign Het
Tpbgl T C 7: 99,274,961 (GRCm39) I299V probably benign Het
Ttc3 A G 16: 94,258,241 (GRCm39) T1325A probably benign Het
Ubxn11 A T 4: 133,852,396 (GRCm39) E210D probably damaging Het
Unc13c T C 9: 73,453,271 (GRCm39) I1840V probably benign Het
Zfp74 A T 7: 29,635,316 (GRCm39) F131I 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
R1290:Mbd1 UTSW 18 74,402,557 (GRCm39) missense possibly damaging 0.59
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
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 PCR Primer
(F):5'- AGGGAGAAACAGGTTGCTTTTG -3'
(R):5'- GCACCGTGAATATTGACTTTGAC -3'

Sequencing Primer
(F):5'- GTGGCCTGGAAATACTTTGCCAC -3'
(R):5'- CTTGTAATAAGGACTATGTGC -3'
Posted On 2016-10-06