Incidental Mutation 'R6734:Mbd1'
ID 528368
Institutional Source Beutler Lab
Gene Symbol Mbd1
Ensembl Gene ENSMUSG00000024561
Gene Name methyl-CpG binding domain protein 1
Synonyms PCM1, Cxxc3
MMRRC Submission 044852-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R6734 (G1)
Quality Score 135.008
Status Validated
Chromosome 18
Chromosomal Location 74400676-74415803 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 74409114 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Histidine at position 399 (R399H)
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
SMART Domains Protein: ENSMUSP00000095137
Gene: ENSMUSG00000024561

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 damaging
Transcript: ENSMUST00000224047
AA Change: R399H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000224159
Predicted Effect probably benign
Transcript: ENSMUST00000224332
Meta Mutation Damage Score 0.1573 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.4%
  • 20x: 95.6%
Validation Efficiency 100% (52/52)
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: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acot11 C T 4: 106,617,327 (GRCm39) G240R probably damaging Het
Ano6 A G 15: 95,847,417 (GRCm39) K554R probably damaging Het
Arhgef10 A T 8: 15,025,053 (GRCm39) I703F probably damaging Het
Bbs1 T C 19: 4,953,924 (GRCm39) S80G probably benign Het
Bhlhe40 TG TGG 6: 108,641,818 (GRCm39) 254 probably null Het
Camk1 C A 6: 113,311,345 (GRCm39) R352L probably benign Het
Cand1 G A 10: 119,047,897 (GRCm39) P531L possibly damaging Het
Cnot2 G A 10: 116,334,058 (GRCm39) P371S possibly damaging Het
Col24a1 C A 3: 145,214,429 (GRCm39) P1384Q probably benign Het
Csmd2 C A 4: 128,357,606 (GRCm39) T1689K probably benign Het
Cyp26a1 T A 19: 37,689,660 (GRCm39) L452H probably damaging Het
Dcpp2 T C 17: 24,119,545 (GRCm39) Y120H probably damaging Het
Dennd6a G T 14: 26,329,774 (GRCm39) R115L possibly damaging Het
Eml2 T A 7: 18,934,432 (GRCm39) V377E probably benign Het
Fam135b T C 15: 71,334,629 (GRCm39) E855G probably benign Het
Fam149a A T 8: 45,834,478 (GRCm39) I107K probably benign Het
Fam227b A T 2: 125,968,896 (GRCm39) Y59* probably null Het
Fbn2 T C 18: 58,169,032 (GRCm39) E2249G probably damaging Het
Flrt1 T C 19: 7,073,524 (GRCm39) D341G possibly damaging Het
Galnt9 G A 5: 110,768,465 (GRCm39) R587H probably damaging Het
Gsdma2 A G 11: 98,540,416 (GRCm39) T112A possibly damaging Het
Klhl24 T C 16: 19,926,279 (GRCm39) V269A probably damaging Het
Lcorl A G 5: 45,890,839 (GRCm39) S505P probably damaging Het
Liph A G 16: 21,802,707 (GRCm39) S121P probably damaging Het
Lrp4 G A 2: 91,316,242 (GRCm39) V787M possibly damaging Het
Lrrd1 A C 5: 3,900,226 (GRCm39) D177A possibly damaging Het
Naa25 C T 5: 121,576,888 (GRCm39) T879M possibly damaging Het
Naa35 T G 13: 59,756,005 (GRCm39) L147R possibly damaging Het
Ninl C A 2: 150,787,003 (GRCm39) probably null Het
Nrap T C 19: 56,333,941 (GRCm39) D972G probably damaging Het
Or9k7 A G 10: 130,046,126 (GRCm39) F291S probably benign Het
Pdzd2 T C 15: 12,592,551 (GRCm39) E31G probably damaging Het
Plec C T 15: 76,078,603 (GRCm39) E41K probably damaging Het
Plxnb1 A T 9: 108,937,988 (GRCm39) K1245* probably null Het
Ppfia1 T C 7: 144,032,790 (GRCm39) T1263A probably damaging Het
Prex2 G A 1: 11,150,283 (GRCm39) V152I probably damaging Het
Prpf40b C T 15: 99,212,784 (GRCm39) R627W probably damaging Het
Prss3l T C 6: 41,422,321 (GRCm39) Y28C probably damaging Het
Prune2 T G 19: 16,981,097 (GRCm39) F85V probably damaging Het
Rrp1b T G 17: 32,274,278 (GRCm39) probably benign Het
Sec62 A G 3: 30,864,609 (GRCm39) T158A probably benign Het
Sema6a G A 18: 47,412,236 (GRCm39) T526I probably benign Het
Shank1 G T 7: 44,003,110 (GRCm39) A1610S probably benign Het
Slc24a4 T C 12: 102,185,259 (GRCm39) V123A probably damaging Het
Stk11ip T C 1: 75,509,013 (GRCm39) V714A probably benign Het
Tas1r3 T C 4: 155,945,257 (GRCm39) T655A probably damaging Het
Tns2 G T 15: 102,011,551 (GRCm39) L10F probably damaging Het
Trmt10c A G 16: 55,854,489 (GRCm39) V382A probably benign Het
Unc45a G C 7: 79,986,746 (GRCm39) T149R probably damaging Het
Zhx3 T G 2: 160,623,640 (GRCm39) I176L probably damaging Het
Zscan12 T A 13: 21,552,966 (GRCm39) C263* probably null 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
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
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'- TGTAGGTAGCTCCTCCATGAG -3'
(R):5'- TGGCAGTACCAGCTAGACTC -3'

Sequencing Primer
(F):5'- AGGATGGCCCTTAGTGACG -3'
(R):5'- TGGCAGTACCAGCTAGACTCATTTAC -3'
Posted On 2018-07-24