Mutagenetix > Incidental Mutation

Incidental Mutation 'R7657:Mbd1'

591308

Institutional Source

Beutler Lab

Gene Symbol

Mbd1

Ensembl Gene

ENSMUSG00000024561

Gene Name

methyl-CpG binding domain protein 1

Synonyms

PCM1, Cxxc3

MMRRC Submission

045733-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7657 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

74400676-74415803 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 74407804 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Arginine at position 277 (L277R)

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: L277R

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000095137
Gene: ENSMUSG00000024561
AA Change: L277R

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: L277R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

Predicted Effect

probably damaging
Transcript: ENSMUST00000224332
AA Change: L167R

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

Meta Mutation Damage Score

0.1973

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (80/80)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310033P09Rik	A	G	11: 59,099,337 (GRCm39)	E28G	possibly damaging	Het
Acot6	G	A	12: 84,153,304 (GRCm39)	G182D	possibly damaging	Het
Actl9	A	G	17: 33,652,014 (GRCm39)	T25A	probably benign	Het
Adam26b	G	A	8: 43,974,579 (GRCm39)	T141I	possibly damaging	Het
Agl	T	C	3: 116,572,812 (GRCm39)	H148R		Het
Angptl1	A	G	1: 156,684,790 (GRCm39)	I320V	probably benign	Het
Arhgef10	C	T	8: 15,029,893 (GRCm39)	R932C	probably damaging	Het
Atp13a2	A	G	4: 140,719,815 (GRCm39)	E91G	possibly damaging	Het
Bptf	T	A	11: 106,965,555 (GRCm39)	E1213V	probably damaging	Het
C530025M09Rik	A	G	2: 149,672,541 (GRCm39)	V198A	unknown	Het
Casd1	A	T	6: 4,619,773 (GRCm39)	I173F	probably benign	Het
Ccng2	C	G	5: 93,421,202 (GRCm39)	S237R	probably benign	Het
Col1a2	A	T	6: 4,527,152 (GRCm39)	K627M	probably null	Het
Ctcfl	G	A	2: 172,955,449 (GRCm39)	T271I	possibly damaging	Het
Dctn2	T	C	10: 127,102,383 (GRCm39)	Y6H	probably damaging	Het
Denr	T	C	5: 124,046,263 (GRCm39)	V31A	probably damaging	Het
Entpd7	T	C	19: 43,713,906 (GRCm39)	F422L	possibly damaging	Het
Fastkd5	G	C	2: 130,458,176 (GRCm39)	P138R	probably benign	Het
Fmn1	G	T	2: 113,355,538 (GRCm39)	A758S	unknown	Het
Fmo2	A	G	1: 162,716,413 (GRCm39)	V58A	probably damaging	Het
Fmo6	A	G	1: 162,750,285 (GRCm39)	I257T	probably benign	Het
Foxn1	T	C	11: 78,256,790 (GRCm39)	T302A	probably benign	Het
Ganab	C	T	19: 8,884,721 (GRCm39)	L175F	probably damaging	Het
Gga1	A	T	15: 78,773,327 (GRCm39)		probably null	Het
Gjd3	G	T	11: 98,873,586 (GRCm39)	S86*	probably null	Het
Gm1330	A	G	2: 148,841,154 (GRCm39)		probably null	Het
Gm18596	A	C	10: 77,577,947 (GRCm39)	S176A	unknown	Het
Gnl2	A	G	4: 124,923,951 (GRCm39)	S10G	probably benign	Het
Gpsm2	G	A	3: 108,608,061 (GRCm39)	A239V	probably damaging	Het
Grik2	T	C	10: 49,659,247 (GRCm39)	R37G	probably benign	Het
Grm3	A	G	5: 9,561,452 (GRCm39)		probably null	Het
Gtpbp3	T	C	8: 71,943,765 (GRCm39)	L216P	probably benign	Het
Hhla1	T	C	15: 65,837,308 (GRCm39)	T99A	probably damaging	Het
Igtp	A	T	11: 58,097,654 (GRCm39)	Q275L	probably benign	Het
Itga6	G	A	2: 71,676,595 (GRCm39)	A993T	probably benign	Het
Jakmip3	T	A	7: 138,620,903 (GRCm39)	I234N	probably damaging	Het
Kcnh7	A	G	2: 62,566,379 (GRCm39)	F851L	probably damaging	Het
Krr1	A	G	10: 111,811,504 (GRCm39)	Y66C	probably damaging	Het
Krt33a	T	A	11: 99,906,693 (GRCm39)	Q94L	probably benign	Het
Mat1a	A	T	14: 40,844,476 (GRCm39)	K369*	probably null	Het
Mmp21	C	T	7: 133,280,562 (GRCm39)	G136D	probably benign	Het
Mroh3	A	G	1: 136,109,532 (GRCm39)	Y892H	possibly damaging	Het
Ncbp3	G	A	11: 72,964,193 (GRCm39)	R381Q	probably damaging	Het
Nlrp2	T	A	7: 5,322,167 (GRCm39)	I827L	probably benign	Het
Nrip1	T	A	16: 76,091,587 (GRCm39)		probably null	Het
Or2ak4	A	T	11: 58,648,755 (GRCm39)	D88V	probably benign	Het
Or4f6	A	G	2: 111,839,093 (GRCm39)	V146A	probably benign	Het
Or5w13	C	T	2: 87,523,336 (GRCm39)	V297I	probably damaging	Het
Oxt	C	T	2: 130,418,710 (GRCm39)	P107L	possibly damaging	Het
Pcdhga2	G	A	18: 37,803,481 (GRCm39)	V442M	probably damaging	Het
Phtf1	T	G	3: 103,876,429 (GRCm39)	S10A	probably benign	Het
Plb1	A	C	5: 32,487,211 (GRCm39)	N902T	probably damaging	Het
Plppr3	T	C	10: 79,702,272 (GRCm39)	I267V	probably benign	Het
Pms2	C	A	5: 143,856,357 (GRCm39)	H278Q	possibly damaging	Het
Pmvk	T	A	3: 89,376,158 (GRCm39)	S154T	possibly damaging	Het
Polr3b	T	A	10: 84,491,855 (GRCm39)	M338K	probably damaging	Het
Ppp1r21	T	A	17: 88,863,110 (GRCm39)	I283N	probably damaging	Het
Ptprj	A	T	2: 90,282,501 (GRCm39)		probably null	Het
Rft1	T	A	14: 30,388,724 (GRCm39)	L216H	probably damaging	Het
Rpl3	G	A	15: 79,965,258 (GRCm39)	P174S	probably benign	Het
Rtl1	T	C	12: 109,561,818 (GRCm39)	D7G	possibly damaging	Het
Slc13a2	A	G	11: 78,289,223 (GRCm39)	V496A	probably damaging	Het
Slc14a1	A	G	18: 78,156,879 (GRCm39)		probably null	Het
Slc8a3	T	C	12: 81,361,158 (GRCm39)	R554G	probably damaging	Het
Spata31d1b	T	C	13: 59,863,577 (GRCm39)	S242P	possibly damaging	Het
Spocd1	G	A	4: 129,823,535 (GRCm39)	V111I		Het
Stxbp5l	G	A	16: 37,030,534 (GRCm39)	A479V	probably null	Het
Tasor2	A	G	13: 3,623,777 (GRCm39)	S2058P	probably damaging	Het
Tmem238	C	G	7: 4,792,226 (GRCm39)	G106R	probably damaging	Het
Trak1	T	G	9: 121,301,652 (GRCm39)	Y803D	probably damaging	Het
Trim5	T	C	7: 103,925,884 (GRCm39)	S226G	possibly damaging	Het
Trim6	T	A	7: 103,881,068 (GRCm39)	D282E	possibly damaging	Het
Ube2e2	A	G	14: 18,586,997 (GRCm38)	V121A	probably benign	Het
Ufd1	T	G	16: 18,636,713 (GRCm39)	M77R	probably benign	Het
Unc13c	C	T	9: 73,441,185 (GRCm39)		probably null	Het
Wfs1	A	G	5: 37,125,578 (GRCm39)	S438P	probably benign	Het
Zbtb6	A	C	2: 37,319,087 (GRCm39)	D280E	probably benign	Het
Zfp595	G	A	13: 67,465,817 (GRCm39)	L152F	probably damaging	Het
Zfpm2	A	G	15: 40,966,671 (GRCm39)	E1052G	possibly damaging	Het
Zmym5	A	G	14: 57,041,653 (GRCm39)	V150A	probably benign	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)
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
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'- AAGGTGAGCCCAGTCACAAG -3'
(R):5'- ACATCCTTGAGAGTGGCCTC -3'

Sequencing Primer
(F):5'- CGGCTGACTCCAGACAT -3'
(R):5'- CTTGAGAGTGGCCTCGGAAG -3'

Posted On

2019-11-12