Mutagenetix > Incidental Mutation

Incidental Mutation 'R8032:Mbd4'

618014

Institutional Source

Beutler Lab

Gene Symbol

Mbd4

Ensembl Gene

ENSMUSG00000030322

Gene Name

methyl-CpG binding domain protein 4

Synonyms

Med1

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.187) question?

Stock #

R8032 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

115817658-115830332 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 115821594 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 474 (S474P)

Ref Sequence

ENSEMBL: ENSMUSP00000032469 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032469] [ENSMUST00000122816] [ENSMUST00000147282] [ENSMUST00000203643]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000032469
AA Change: S474P

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000032469
Gene: ENSMUSG00000030322
AA Change: S474P

Domain	Start	End	E-Value	Type
MBD	66	142	1.25e-29	SMART
low complexity region	178	196	N/A	INTRINSIC
PDB:1NGN\|A	400	554	1e-111	PDB
SCOP:d1keaa_	405	545	1e-23	SMART
Blast:ENDO3c	439	514	2e-6	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000122816

SMART Domains

Protein: ENSMUSP00000145433
Gene: ENSMUSG00000030322

Domain	Start	End	E-Value	Type
MBD	66	142	7.6e-32	SMART
low complexity region	178	196	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000147282

SMART Domains

Protein: ENSMUSP00000125619
Gene: ENSMUSG00000030322

Domain	Start	End	E-Value	Type
MBD	45	121	1.25e-29	SMART
low complexity region	157	175	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000203643
AA Change: S95P

PolyPhen 2 Score 0.886 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000144930
Gene: ENSMUSG00000030322
AA Change: S95P

Domain	Start	End	E-Value	Type
Pfam:HhH-GPD	56	168	2.7e-5	PFAM

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

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 an MBD domain at the N-terminus that functions both in binding to methylated DNA and in protein interactions and a C-terminal mismatch-specific glycosylase domain that is involved in DNA repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2013]
PHENOTYPE: Mice homozygous for a null allele have an increased rate of DNA mutation, specifically at CpGs. [provided by MGI curators]

Allele List at MGI

All alleles(8) : Targeted(6) Gene trapped(2)

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actrt2	T	A	4: 154,751,955 (GRCm39)	E60D	probably benign	Het
Adamts12	T	C	15: 11,259,189 (GRCm39)		probably null	Het
Ak9	T	A	10: 41,300,616 (GRCm39)	C1609S	unknown	Het
Aox1	A	T	1: 58,389,442 (GRCm39)	Y1147F	probably benign	Het
Atf7ip	T	C	6: 136,542,110 (GRCm39)	F615L	probably benign	Het
BC005624	A	G	2: 30,865,901 (GRCm39)		probably null	Het
BC024063	T	A	10: 81,943,738 (GRCm39)	M33K	probably benign	Het
Bmpr2	T	A	1: 59,906,502 (GRCm39)	S532T	probably benign	Het
Cast	G	A	13: 74,883,360 (GRCm39)	Q292*	probably null	Het
Ccdc7a	G	T	8: 129,551,864 (GRCm39)	H1249N	unknown	Het
Cd177	C	T	7: 24,455,594 (GRCm39)	W309*	probably null	Het
Col15a1	T	C	4: 47,288,108 (GRCm39)	I4T	unknown	Het
Cyp2c39	A	G	19: 39,499,426 (GRCm39)	I38V	probably benign	Het
Dmpk	A	G	7: 18,821,978 (GRCm39)	D312G	possibly damaging	Het
Dnah1	T	C	14: 30,993,505 (GRCm39)	D2892G	probably damaging	Het
Dnah10	G	A	5: 124,823,676 (GRCm39)	D566N	probably damaging	Het
Dsc2	C	T	18: 20,165,331 (GRCm39)	G881R	possibly damaging	Het
Exd2	T	A	12: 80,536,427 (GRCm39)	D352E	probably benign	Het
Fgf8	A	T	19: 45,725,676 (GRCm39)	L187Q	probably damaging	Het
Frrs1	A	G	3: 116,672,009 (GRCm39)	I36V	probably benign	Het
Gga2	A	T	7: 121,620,210 (GRCm39)		probably null	Het
Gigyf2	C	G	1: 87,334,735 (GRCm39)	H249D	unknown	Het
Gli2	A	T	1: 118,763,900 (GRCm39)	M1417K	probably damaging	Het
Gm10801	C	CGTA	2: 98,494,152 (GRCm39)		probably null	Het
Gm49380	A	T	9: 44,023,000 (GRCm39)	I416N	probably damaging	Het
Gpr137	T	C	19: 6,919,480 (GRCm39)	T16A	unknown	Het
Grid1	T	A	14: 35,045,316 (GRCm39)	D386E	probably benign	Het
Grm3	A	G	5: 9,562,272 (GRCm39)	V526A	probably benign	Het
Havcr2	A	T	11: 46,370,118 (GRCm39)	I231F	probably damaging	Het
Icam5	C	A	9: 20,944,514 (GRCm39)	R72S	probably benign	Het
Ighv9-2	T	A	12: 114,072,764 (GRCm39)	I70L	possibly damaging	Het
Inpp5e	C	T	2: 26,286,865 (GRCm39)	S119N		Het
Kash5	CGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTC	CGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTCAGGCTC	7: 44,837,608 (GRCm39)		probably benign	Het
Kash5	TCAGGC	TCAGGCACAGGC	7: 44,837,630 (GRCm39)		probably benign	Het
Kxd1	T	A	8: 70,966,791 (GRCm39)	D110V	possibly damaging	Het
Meaf6	C	A	4: 124,996,795 (GRCm39)	H168Q	unknown	Het
Nek2	T	C	1: 191,558,457 (GRCm39)	L254S	probably damaging	Het
Nhej1	T	C	1: 75,007,959 (GRCm39)	D104G	probably benign	Het
Nmnat3	A	G	9: 98,292,271 (GRCm39)	E172G	probably benign	Het
Npm3	A	T	19: 45,736,682 (GRCm39)	D152E	probably benign	Het
Nsd1	A	T	13: 55,458,196 (GRCm39)	K2103M	probably damaging	Het
Ntrk3	C	T	7: 78,005,807 (GRCm39)	R518H	probably damaging	Het
Nup210	T	A	6: 91,051,331 (GRCm39)	T351S	probably benign	Het
Or10h5	T	A	17: 33,434,924 (GRCm39)	R131S	possibly damaging	Het
Or9g19	A	G	2: 85,600,210 (GRCm39)	I22V	probably benign	Het
Otof	T	A	5: 30,619,142 (GRCm39)	M1L	probably benign	Het
Pacs2	T	A	12: 113,025,278 (GRCm39)	Y477N	probably damaging	Het
Panx3	A	G	9: 37,572,966 (GRCm39)	Y195H	probably damaging	Het
Pcsk5	T	C	19: 17,692,151 (GRCm39)	R178G	probably damaging	Het
Pde7a	A	G	3: 19,314,429 (GRCm39)	S56P	possibly damaging	Het
Prcp	T	G	7: 92,577,906 (GRCm39)	C392G	probably damaging	Het
Prkdc	A	G	16: 15,597,315 (GRCm39)	K2825R	probably benign	Het
Ptpn12	T	C	5: 21,203,041 (GRCm39)	H579R	probably benign	Het
Rbl1	A	T	2: 157,029,918 (GRCm39)	Y468*	probably null	Het
Rbmxl2	A	G	7: 106,809,429 (GRCm39)	Y238C	probably damaging	Het
Scgb2b20	A	T	7: 33,065,724 (GRCm39)	M1K	probably null	Het
Slc25a18	G	A	6: 120,769,452 (GRCm39)	G237D	probably damaging	Het
Slc9a3	G	A	13: 74,305,763 (GRCm39)	G260D	probably damaging	Het
Sorcs1	A	T	19: 50,463,846 (GRCm39)	S201R	probably benign	Het
Strip1	A	C	3: 107,525,394 (GRCm39)	D547E	probably damaging	Het
Thsd7a	C	T	6: 12,555,287 (GRCm39)	C199Y		Het
Top1mt	A	G	15: 75,540,572 (GRCm39)	V233A	probably damaging	Het
Tpp2	C	G	1: 44,014,628 (GRCm39)	P656A	possibly damaging	Het
Ttc1	A	T	11: 43,628,806 (GRCm39)	L193Q	probably damaging	Het
Ttll4	T	A	1: 74,735,632 (GRCm39)	D1013E	possibly damaging	Het
Unc5a	T	C	13: 55,144,299 (GRCm39)	V208A	possibly damaging	Het
Vmn1r185	C	A	7: 26,310,558 (GRCm39)	V316F	probably benign	Het
Vmn2r112	T	A	17: 22,822,375 (GRCm39)	V351E	probably benign	Het
Wdfy4	T	A	14: 32,751,043 (GRCm39)	K2391*	probably null	Het
Zfhx3	T	C	8: 109,677,854 (GRCm39)	V2968A	possibly damaging	Het
Zfp551	G	A	7: 12,152,487 (GRCm39)	A82V	possibly damaging	Het

Other mutations in Mbd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01516:Mbd4	APN	6	115,826,491 (GRCm39)	missense	probably damaging	0.99
IGL01545:Mbd4	APN	6	115,827,758 (GRCm39)	missense	probably damaging	1.00
IGL01657:Mbd4	APN	6	115,826,598 (GRCm39)	missense	probably damaging	0.99
IGL02406:Mbd4	APN	6	115,825,986 (GRCm39)	missense	possibly damaging	0.96
E0370:Mbd4	UTSW	6	115,826,116 (GRCm39)	missense	possibly damaging	0.91
R0025:Mbd4	UTSW	6	115,821,529 (GRCm39)	critical splice donor site	probably null
R0025:Mbd4	UTSW	6	115,821,529 (GRCm39)	critical splice donor site	probably null
R0538:Mbd4	UTSW	6	115,826,443 (GRCm39)	missense	probably damaging	0.99
R2085:Mbd4	UTSW	6	115,825,918 (GRCm39)	missense	probably benign	0.01
R4405:Mbd4	UTSW	6	115,826,076 (GRCm39)	missense	possibly damaging	0.92
R4464:Mbd4	UTSW	6	115,826,463 (GRCm39)	missense	probably damaging	0.99
R4780:Mbd4	UTSW	6	115,826,345 (GRCm39)	missense	probably benign
R4782:Mbd4	UTSW	6	115,822,283 (GRCm39)	missense	possibly damaging	0.49
R4799:Mbd4	UTSW	6	115,822,283 (GRCm39)	missense	probably benign	0.26
R4814:Mbd4	UTSW	6	115,826,260 (GRCm39)	missense	possibly damaging	0.85
R4860:Mbd4	UTSW	6	115,825,887 (GRCm39)	missense	possibly damaging	0.51
R4860:Mbd4	UTSW	6	115,825,887 (GRCm39)	missense	possibly damaging	0.51
R4976:Mbd4	UTSW	6	115,827,685 (GRCm39)	missense	possibly damaging	0.95
R5126:Mbd4	UTSW	6	115,825,929 (GRCm39)	splice site	probably null
R5202:Mbd4	UTSW	6	115,826,363 (GRCm39)	missense	probably damaging	0.96
R5485:Mbd4	UTSW	6	115,827,679 (GRCm39)	missense	probably benign	0.21
R6179:Mbd4	UTSW	6	115,822,386 (GRCm39)	missense	probably benign	0.00
R6661:Mbd4	UTSW	6	115,826,116 (GRCm39)	nonsense	probably null
R7008:Mbd4	UTSW	6	115,827,685 (GRCm39)	missense	possibly damaging	0.95
R7244:Mbd4	UTSW	6	115,821,564 (GRCm39)	missense	probably benign	0.00
R7723:Mbd4	UTSW	6	115,822,324 (GRCm39)	missense	possibly damaging	0.47
R7755:Mbd4	UTSW	6	115,821,546 (GRCm39)	missense	probably damaging	0.99
R7837:Mbd4	UTSW	6	115,826,500 (GRCm39)	missense	probably benign	0.20
R9707:Mbd4	UTSW	6	115,826,559 (GRCm39)	missense	probably benign	0.04

Predicted Primers

PCR Primer
(F):5'- GCTACTCAGTGTTGGGCAAAG -3'
(R):5'- ACGGCCTGAAGTTTATAGATGC -3'

Sequencing Primer
(F):5'- CAAGCGGCCTGTTTTAAATGTC -3'
(R):5'- CGGCCTGAAGTTTATAGATGCAAAAC -3'

Posted On

2020-01-23