Mutagenetix > Incidental Mutation

Incidental Mutation 'R1575:Mbd1'

171137

Institutional Source

Beutler Lab

Gene Symbol

Mbd1

Ensembl Gene

ENSMUSG00000024561

Gene Name

methyl-CpG binding domain protein 1

Synonyms

PCM1, Cxxc3

MMRRC Submission

039613-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1575 (G1)

Quality Score

195

Status

Validated

Chromosome

Chromosomal Location

74400676-74415803 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to A at 74408490 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

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

SMART Domains

Protein: ENSMUSP00000095137
Gene: ENSMUSG00000024561

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224159

Predicted Effect

probably null
Transcript: ENSMUST00000224332

Meta Mutation Damage Score

0.9596

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 96.0%
20x: 91.5%

Validation Efficiency

100% (72/72)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrl2	T	A	3: 148,558,398 (GRCm39)	T437S	probably benign	Het
Akna	A	G	4: 63,297,570 (GRCm39)	F828S	probably benign	Het
Alg9	G	T	9: 50,686,802 (GRCm39)	A40S	possibly damaging	Het
Alox8	T	A	11: 69,076,067 (GRCm39)	H628L	possibly damaging	Het
Aox3	T	C	1: 58,191,713 (GRCm39)	W422R	probably benign	Het
Atp13a4	T	C	16: 29,228,528 (GRCm39)	D984G	probably benign	Het
Bcam	T	C	7: 19,494,307 (GRCm39)	E363G	possibly damaging	Het
Cadps2	C	A	6: 23,429,217 (GRCm39)	V519F	probably damaging	Het
Calca	A	G	7: 114,234,396 (GRCm39)	Y18H	probably damaging	Het
Cd70	A	G	17: 57,453,364 (GRCm39)	I100T	probably damaging	Het
Cdk4	T	A	10: 126,900,520 (GRCm39)	H95Q	probably damaging	Het
Chchd1	T	A	14: 20,753,410 (GRCm39)	N11K	probably damaging	Het
Cma2	T	A	14: 56,210,272 (GRCm39)	N52K	probably damaging	Het
Cyp3a16	A	G	5: 145,373,267 (GRCm39)	V500A	probably benign	Het
Dicer1	A	G	12: 104,688,228 (GRCm39)		probably null	Het
Dnajc13	A	G	9: 104,034,037 (GRCm39)	S2206P	probably benign	Het
Dtl	T	C	1: 191,293,658 (GRCm39)		probably null	Het
Fam186b	T	C	15: 99,184,852 (GRCm39)	T24A	probably benign	Het
Fbxw21	A	G	9: 108,990,984 (GRCm39)	V25A	probably benign	Het
Gins1	T	C	2: 150,754,758 (GRCm39)	S45P	probably benign	Het
Gtpbp2	T	A	17: 46,476,869 (GRCm39)	V349D	probably damaging	Het
Hyal5	G	T	6: 24,876,792 (GRCm39)	D222Y	probably damaging	Het
Itgal	A	G	7: 126,900,060 (GRCm39)		probably null	Het
Klk14	A	G	7: 43,343,377 (GRCm39)		probably null	Het
Lama1	T	A	17: 68,117,404 (GRCm39)	L2518Q	possibly damaging	Het
Lrrc2	G	A	9: 110,808,555 (GRCm39)	G264D	probably benign	Het
Ltbp4	A	G	7: 27,022,245 (GRCm39)	S893P	probably damaging	Het
Mast4	G	A	13: 102,875,771 (GRCm39)	P1107L	probably damaging	Het
Naip2	A	T	13: 100,291,529 (GRCm39)	D1136E	probably benign	Het
Naip2	G	A	13: 100,291,537 (GRCm39)		probably benign	Het
Ncan	G	A	8: 70,562,848 (GRCm39)	T470I	probably benign	Het
Npy1r	A	T	8: 67,156,813 (GRCm39)	I78F	probably damaging	Het
Or10q1b	A	T	19: 13,682,889 (GRCm39)	M233L	probably benign	Het
Or8b52	G	A	9: 38,576,573 (GRCm39)	T189M	probably damaging	Het
Palb2	A	T	7: 121,710,061 (GRCm39)		probably null	Het
Pax3	T	C	1: 78,080,121 (GRCm39)	T422A	probably benign	Het
Pebp1	A	T	5: 117,424,229 (GRCm39)	D72E	possibly damaging	Het
Pnliprp1	A	T	19: 58,728,901 (GRCm39)	T363S	probably benign	Het
Rbm44	G	A	1: 91,084,565 (GRCm39)		probably null	Het
Rbm47	T	A	5: 66,182,358 (GRCm39)	Y425F	probably benign	Het
Robo3	G	T	9: 37,340,957 (GRCm39)	A83E	probably damaging	Het
Rrm1	A	G	7: 102,105,721 (GRCm39)	Y279C	probably damaging	Het
Rslcan18	A	T	13: 67,256,121 (GRCm39)		probably benign	Het
Scara5	C	A	14: 65,968,314 (GRCm39)	Q196K	probably benign	Het
Setd1b	C	T	5: 123,301,210 (GRCm39)		probably benign	Het
Siah1a	A	G	8: 87,451,869 (GRCm39)	F205S	probably damaging	Het
Smr2	AT	ATT	5: 88,256,683 (GRCm39)		probably null	Het
Ssu72	A	G	4: 155,815,814 (GRCm39)	D86G	probably benign	Het
St7	G	T	6: 17,886,110 (GRCm39)	K357N	probably damaging	Het
Sv2b	G	A	7: 74,797,425 (GRCm39)	T323I	probably damaging	Het
Syt1	T	C	10: 108,340,361 (GRCm39)	N319S	probably benign	Het
Tanc1	T	A	2: 59,621,995 (GRCm39)	F371L	probably damaging	Het
Tcf20	C	A	15: 82,739,693 (GRCm39)	G586V	probably benign	Het
Tg	T	C	15: 66,601,534 (GRCm39)		probably null	Het
Tyk2	A	T	9: 21,026,758 (GRCm39)	N620K	probably benign	Het
Ube2j1	T	A	4: 33,045,116 (GRCm39)	S130T	probably benign	Het
Ubr2	G	T	17: 47,243,418 (GRCm39)	P1696H	probably damaging	Het
Ubr5	A	T	15: 38,041,085 (GRCm39)	D266E	probably damaging	Het
Vipr2	A	G	12: 116,107,892 (GRCm39)	T426A	probably benign	Het
Vmn2r104	A	T	17: 20,262,477 (GRCm39)	W218R	probably damaging	Het
Vmn2r83	T	A	10: 79,314,956 (GRCm39)	N401K	probably damaging	Het
Vwf	A	G	6: 125,632,214 (GRCm39)	E82G	unknown	Het
Vwf	T	A	6: 125,640,534 (GRCm39)	Y2323*	probably null	Het
Wdr76	T	G	2: 121,359,402 (GRCm39)	V329G	probably damaging	Het
Zan	A	G	5: 137,460,214 (GRCm39)	C1226R	unknown	Het
Zbtb16	G	T	9: 48,743,572 (GRCm39)	Q247K	probably damaging	Het
Zfp541	T	C	7: 15,812,640 (GRCm39)	V431A	possibly 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
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

PCR Primer
(F):5'- TGCACACTGCCTGACCACTCAATG -3'
(R):5'- AGCCGTGCTGGCTTACTCTATCTG -3'

Sequencing Primer
(F):5'- CGTGATTCTAGTAAGAGAGGCTC -3'
(R):5'- AGGGTCACTGTTCAGCCATC -3'

Posted On

2014-04-13