Mutagenetix > Incidental Mutation

Incidental Mutation 'R7363:Mbd1'

571505

Institutional Source

Beutler Lab

Gene Symbol

Mbd1

Ensembl Gene

ENSMUSG00000024561

Gene Name

methyl-CpG binding domain protein 1

Synonyms

PCM1, Cxxc3

MMRRC Submission

045448-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7363 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

74400676-74415803 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 74406357 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Alanine at position 63 (D63A)

Ref Sequence

ENSEMBL: ENSMUSP00000095137 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000097530
AA Change: D63A

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000095137
Gene: ENSMUSG00000024561
AA Change: D63A

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 damaging
Transcript: ENSMUST00000224047
AA Change: D63A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

Predicted Effect

probably benign
Transcript: ENSMUST00000224332

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930568D16Rik	T	A	2: 35,244,782 (GRCm39)	N190I	probably damaging	Het
Ablim1	G	T	19: 57,204,173 (GRCm39)	L73I	probably benign	Het
Adamts4	A	T	1: 171,086,608 (GRCm39)	Q800L	probably benign	Het
Atm	A	T	9: 53,376,598 (GRCm39)	I2014N	probably damaging	Het
Atp2a1	A	G	7: 126,062,061 (GRCm39)	C12R	possibly damaging	Het
B3galnt1	A	T	3: 69,483,157 (GRCm39)	Y35N	probably damaging	Het
Bnc2	A	T	4: 84,210,308 (GRCm39)	M687K	probably benign	Het
Cacna2d4	A	G	6: 119,320,939 (GRCm39)	Y917C	probably damaging	Het
Cemip2	T	C	19: 21,833,575 (GRCm39)	F1338L	probably benign	Het
Ces2e	A	G	8: 105,659,632 (GRCm39)		probably null	Het
Cldn23	A	G	8: 36,292,659 (GRCm39)		probably null	Het
Cntn5	G	T	9: 10,172,021 (GRCm39)	S54R	probably benign	Het
Cyria	T	A	12: 12,390,665 (GRCm39)		probably null	Het
Dido1	G	T	2: 180,304,310 (GRCm39)	S1198*	probably null	Het
Dnah12	A	G	14: 26,445,766 (GRCm39)	M776V	probably benign	Het
Dnah14	A	G	1: 181,518,089 (GRCm39)		probably null	Het
Dnttip1	GGGCCGGC	GGGC	2: 164,599,605 (GRCm39)		probably null	Het
Dusp28	A	T	1: 92,834,861 (GRCm39)	T29S	probably benign	Het
Erich1	A	T	8: 14,083,688 (GRCm39)	S127R	probably benign	Het
Fam151a	T	A	4: 106,602,681 (GRCm39)	L200H	probably damaging	Het
Fbxw8	A	T	5: 118,263,057 (GRCm39)	H207Q	probably damaging	Het
Fgf22	A	G	10: 79,592,676 (GRCm39)	E116G	probably benign	Het
Gapvd1	C	A	2: 34,602,207 (GRCm39)	V647F	probably benign	Het
Garin4	A	T	1: 190,895,910 (GRCm39)	S244R	probably damaging	Het
Gja4	T	A	4: 127,206,487 (GRCm39)	Y92F	probably damaging	Het
Gtf3c2	G	A	5: 31,327,600 (GRCm39)	R288W	probably damaging	Het
Hira	G	T	16: 18,716,532 (GRCm39)	R99L	possibly damaging	Het
Ighv16-1	C	T	12: 114,032,721 (GRCm39)	G27D	probably damaging	Het
Igkv1-133	C	T	6: 67,702,395 (GRCm39)	P38S	probably benign	Het
Igkv4-59	T	C	6: 69,415,396 (GRCm39)	Y53C	probably damaging	Het
Il23a	T	C	10: 128,133,020 (GRCm39)	E113G	probably damaging	Het
Kcnip1	A	G	11: 33,584,589 (GRCm39)	V188A	probably benign	Het
L3mbtl3	T	C	10: 26,216,850 (GRCm39)	K155E	unknown	Het
Lancl2	T	G	6: 57,699,664 (GRCm39)	C169G	probably benign	Het
Lrrc26	A	G	2: 25,180,581 (GRCm39)	D194G	probably benign	Het
Lrrfip1	C	T	1: 91,050,842 (GRCm39)	A545V	probably benign	Het
Lrtm1	T	C	14: 28,743,850 (GRCm39)	F106S	probably damaging	Het
Lypd2	A	T	15: 74,604,848 (GRCm39)	M49K	probably damaging	Het
Mdn1	T	C	4: 32,691,729 (GRCm39)	F990L	probably damaging	Het
Mtfr1l	T	C	4: 134,256,577 (GRCm39)	E196G	probably benign	Het
Myh10	A	G	11: 68,705,874 (GRCm39)	T2007A	probably benign	Het
Nckap1	G	A	2: 80,370,512 (GRCm39)	R393C	probably damaging	Het
Nup205	C	T	6: 35,209,508 (GRCm39)	T1605M	probably benign	Het
Or1e33	T	C	11: 73,738,741 (GRCm39)	D70G	probably damaging	Het
Or5j3	GTACTTTTT	GT	2: 86,128,338 (GRCm39)		probably null	Het
Pgap2	T	A	7: 101,875,467 (GRCm39)		probably null	Het
Pitrm1	A	G	13: 6,619,387 (GRCm39)	S741G	probably benign	Het
Plcd4	A	T	1: 74,590,231 (GRCm39)	S155C	probably null	Het
Poc5	A	T	13: 96,540,925 (GRCm39)	T365S	possibly damaging	Het
Ppp2r5c	G	A	12: 110,489,041 (GRCm39)	A71T	probably benign	Het
Prdm6	T	A	18: 53,598,199 (GRCm39)	I187N	possibly damaging	Het
Pxk	A	G	14: 8,152,118 (GRCm38)	Q478R	probably benign	Het
Rgl1	T	C	1: 152,394,914 (GRCm39)	Y718C	probably damaging	Het
Ring1	G	T	17: 34,243,336 (GRCm39)	T2K	possibly damaging	Het
Sdk1	A	G	5: 142,173,897 (GRCm39)	S2022G	probably benign	Het
Sec61a1	C	A	6: 88,492,533 (GRCm39)	V32F	probably benign	Het
Sv2b	G	A	7: 74,797,402 (GRCm39)	P331S	probably damaging	Het
Syne1	T	C	10: 5,090,970 (GRCm39)	S795G	possibly damaging	Het
Tmod2	T	C	9: 75,484,023 (GRCm39)	E309G	probably damaging	Het
Tpp2	T	G	1: 44,024,582 (GRCm39)	S987A	probably benign	Het
Trim75	G	C	8: 65,435,539 (GRCm39)	H304D	probably damaging	Het
Trp53bp2	G	T	1: 182,272,231 (GRCm39)	D447Y	probably damaging	Het
Ube3a	A	G	7: 58,936,751 (GRCm39)	K697E	probably benign	Het
Vmn2r13	T	A	5: 109,339,909 (GRCm39)	H22L	probably benign	Het
Vmn2r4	G	A	3: 64,314,432 (GRCm39)	S183F	probably damaging	Het
Vwa8	T	C	14: 79,256,147 (GRCm39)	Y721H	probably benign	Het
Wbp1l	C	T	19: 46,642,569 (GRCm39)	P190L	possibly damaging	Het
Zcchc4	A	T	5: 52,942,510 (GRCm39)	Q105L	possibly damaging	Het
Zfp236	T	C	18: 82,639,456 (GRCm39)	R1264G	probably damaging	Het
Zfpm2	T	A	15: 40,616,413 (GRCm39)	N54K	probably damaging	Het
Zkscan3	C	T	13: 21,571,992 (GRCm39)	G547S	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
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)
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'- ACAGACTCCAGACTGCTTGC -3'
(R):5'- GCAGTAGGGGCCTTATATTCC -3'

Sequencing Primer
(F):5'- CCGCATCTCACCAGATCTGTGAG -3'
(R):5'- GGCCTTATATTCCCCCTGTGGAG -3'

Posted On

2019-09-13