Mutagenetix > Incidental Mutation

Incidental Mutation 'R5860:Mbd1'

453877

Institutional Source

Beutler Lab

Gene Symbol

Mbd1

Ensembl Gene

ENSMUSG00000024561

Gene Name

methyl-CpG binding domain protein 1

Synonyms

PCM1, Cxxc3

MMRRC Submission

044072-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5860 (G1)

Quality Score

207

Status

Validated

Chromosome

Chromosomal Location

74400676-74415803 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

C to A at 74409768 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Stop codon at position 339 (C339*)

Ref Sequence

ENSEMBL: ENSMUSP00000153085 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000097530] [ENSMUST00000224047] [ENSMUST00000224332]

AlphaFold

no structure available at present

Predicted Effect

probably null
Transcript: ENSMUST00000097530
AA Change: C449*

SMART Domains

Protein: ENSMUSP00000095137
Gene: ENSMUSG00000024561
AA Change: C449*

Domain	Start	End	E-Value	Type
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 null
Transcript: ENSMUST00000224047
AA Change: C505*

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224159

Predicted Effect

probably null
Transcript: ENSMUST00000224332
AA Change: C339*

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.9%
3x: 99.4%
10x: 97.1%
20x: 90.8%

Validation Efficiency

97% (75/77)

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930568A12Rik	A	G	1: 34,524,661 (GRCm39)		noncoding transcript	Het
A2ml1	T	C	6: 128,518,024 (GRCm39)	T1421A	probably benign	Het
Actr8	T	A	14: 29,708,242 (GRCm39)	Y150*	probably null	Het
Adamts1	A	G	16: 85,595,432 (GRCm39)	C249R	probably damaging	Het
Adgre1	T	A	17: 57,752,034 (GRCm39)	I594N	probably damaging	Het
Atf6	A	T	1: 170,669,344 (GRCm39)	L119H	probably damaging	Het
Atf6	G	A	1: 170,669,345 (GRCm39)	L119F	possibly damaging	Het
B3gat2	G	A	1: 23,854,400 (GRCm39)	W33*	probably null	Het
Bach2	A	G	4: 32,580,268 (GRCm39)	D831G	probably damaging	Het
Ccnk	A	T	12: 108,153,466 (GRCm39)	I76F	probably damaging	Het
Cdyl	A	C	13: 36,042,066 (GRCm39)	K368T	possibly damaging	Het
Chi3l1	A	G	1: 134,112,909 (GRCm39)	T114A	probably benign	Het
Cnppd1	A	G	1: 75,113,131 (GRCm39)	V379A	probably benign	Het
Col11a2	C	A	17: 34,283,159 (GRCm39)		probably benign	Het
Creb3l1	T	C	2: 91,854,399 (GRCm39)	S18G	probably benign	Het
Crybg3	A	C	16: 59,385,632 (GRCm39)	D197E	probably damaging	Het
Cryga	T	C	1: 65,142,527 (GRCm39)		probably benign	Het
Cthrc1	T	C	15: 38,950,080 (GRCm39)	C146R	probably damaging	Het
Cyp2c39	A	T	19: 39,525,270 (GRCm39)	D191V	probably damaging	Het
Dchs1	C	T	7: 105,421,242 (GRCm39)	A393T	probably damaging	Het
Dhx30	G	A	9: 109,913,645 (GRCm39)	T1126I	probably damaging	Het
Dock2	C	T	11: 34,206,562 (GRCm39)	G1345R	probably damaging	Het
Dsc1	T	C	18: 20,228,081 (GRCm39)	E425G	probably damaging	Het
Dynlt2b	A	G	16: 32,247,614 (GRCm39)	Y143C	probably damaging	Het
Exosc8	C	T	3: 54,642,463 (GRCm39)		probably benign	Het
Fat1	C	T	8: 45,504,166 (GRCm39)	A4553V	probably benign	Het
Flnb	T	A	14: 7,931,135 (GRCm38)	L2119Q	probably damaging	Het
Fnbp4	T	A	2: 90,587,826 (GRCm39)	D401E	probably benign	Het
Glyctk	T	C	9: 106,032,906 (GRCm39)	E369G	possibly damaging	Het
Gm14149	C	A	2: 151,066,225 (GRCm39)		noncoding transcript	Het
Golga4	T	C	9: 118,387,174 (GRCm39)	L1432P	probably damaging	Het
Gtpbp4	A	T	13: 9,023,196 (GRCm39)	S623T	probably benign	Het
Insc	A	C	7: 114,390,383 (GRCm39)	S85R	probably damaging	Het
Lgr4	G	A	2: 109,821,496 (GRCm39)	R126H	probably damaging	Het
M1ap	T	A	6: 82,980,795 (GRCm39)	L227Q	probably damaging	Het
Marchf7	T	C	2: 60,067,187 (GRCm39)	I569T	probably damaging	Het
Moxd2	T	A	6: 40,857,341 (GRCm39)	Y473F	probably damaging	Het
Mrgpra6	T	C	7: 46,839,099 (GRCm39)	H2R	probably benign	Het
Mtus1	T	G	8: 41,529,303 (GRCm39)	L742F	probably damaging	Het
Nek11	A	G	9: 105,270,160 (GRCm39)	Y21H	probably benign	Het
Notch4	G	T	17: 34,801,392 (GRCm39)	C1080F	probably damaging	Het
Nsd3	C	A	8: 26,156,107 (GRCm39)	P558Q	probably damaging	Het
Oas1e	A	T	5: 120,930,015 (GRCm39)	S168T	probably benign	Het
Ogfr	T	C	2: 180,234,285 (GRCm39)	S119P	probably damaging	Het
Or2y15	A	G	11: 49,350,563 (GRCm39)	D19G	probably damaging	Het
Or8g20	T	A	9: 39,395,767 (GRCm39)	M261L	probably benign	Het
Pde4dip	A	G	3: 97,631,504 (GRCm39)	I1135T	possibly damaging	Het
Prex1	G	A	2: 166,486,604 (GRCm39)		probably benign	Het
Ptprf	T	C	4: 118,068,486 (GRCm39)		probably benign	Het
Rapsn	T	C	2: 90,875,859 (GRCm39)	V359A	probably damaging	Het
Ric1	A	G	19: 29,577,245 (GRCm39)	S1050G	possibly damaging	Het
Rnft2	A	G	5: 118,366,868 (GRCm39)	I290T	possibly damaging	Het
Senp7	C	A	16: 55,975,722 (GRCm39)	A476E	possibly damaging	Het
Serpinh1	G	A	7: 98,995,571 (GRCm39)	S337L	probably damaging	Het
Slc5a12	C	A	2: 110,427,969 (GRCm39)	A8D	probably benign	Het
Smg5	T	A	3: 88,250,214 (GRCm39)	C109S	probably damaging	Het
Speer4b	T	C	5: 27,705,226 (GRCm39)	H49R	possibly damaging	Het
Tas2r109	T	C	6: 132,957,664 (GRCm39)	I89V	probably benign	Het
Tet1	A	G	10: 62,648,399 (GRCm39)		probably null	Het
Tmed6	G	T	8: 107,790,786 (GRCm39)	T87K	probably damaging	Het
Tpgs1	G	A	10: 79,505,545 (GRCm39)	G101D	probably damaging	Het
Trim13	T	G	14: 61,842,188 (GRCm39)	S68R	probably damaging	Het
Vwf	A	G	6: 125,620,053 (GRCm39)	N1577S		Het
Vwf	G	T	6: 125,656,228 (GRCm39)		probably benign	Het
Xpr1	T	C	1: 155,207,868 (GRCm39)		probably benign	Het
Ylpm1	C	T	12: 85,087,660 (GRCm39)	P1148L	probably damaging	Het
Zftraf1	A	T	15: 76,532,391 (GRCm39)	I239N	probably damaging	Het
Zftraf1	T	C	15: 76,540,615 (GRCm39)	Y101C	probably damaging	Het
Zscan29	G	T	2: 120,994,518 (GRCm39)	T489N	probably damaging	Het

Other mutations in Mbd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- CTGAGCTCTCCCTTAAAGGC -3'
(R):5'- CCCAAACCTTGCTAGGGAAG -3'

Sequencing Primer
(F):5'- CCCTTAAAGGCCCCTTGG -3'
(R):5'- AAGGTCGTGACTGCTGTCCAC -3'

Posted On

2017-02-10