Mutagenetix > Incidental Mutation

Incidental Mutation 'R4814:Mbd4'

369636

Institutional Source

Beutler Lab

Gene Symbol

Mbd4

Ensembl Gene

ENSMUSG00000030322

Gene Name

methyl-CpG binding domain protein 4

Synonyms

Med1

MMRRC Submission

042432-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.192) question?

Stock #

R4814 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

115817658-115830332 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 115826260 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 223 (S223T)

Ref Sequence

ENSEMBL: ENSMUSP00000125619 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000032469] [ENSMUST00000038234] [ENSMUST00000112923] [ENSMUST00000112925] [ENSMUST00000122816] [ENSMUST00000147282] [ENSMUST00000203643] [ENSMUST00000141305]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000032469
AA Change: S244T

PolyPhen 2 Score 0.633 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000032469
Gene: ENSMUSG00000030322
AA Change: S244T

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: ENSMUST00000038234

SMART Domains

Protein: ENSMUSP00000045468
Gene: ENSMUSG00000030323

Domain	Start	End	E-Value	Type
WD40	1	39	7.1e1	SMART
WD40	42	81	7.16e-10	SMART
WD40	83	120	1.54e0	SMART
WD40	122	160	1.43e0	SMART
WD40	162	208	2.29e1	SMART
WD40	210	249	1.91e1	SMART
WD40	251	290	3.45e-3	SMART
WD40	448	483	1.43e1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112923

SMART Domains

Protein: ENSMUSP00000108545
Gene: ENSMUSG00000030323

Domain	Start	End	E-Value	Type
WD40	1	39	7.1e1	SMART
WD40	42	81	7.16e-10	SMART
WD40	83	120	1.54e0	SMART
WD40	122	160	1.43e0	SMART
Blast:WD40	163	267	3e-46	BLAST
WD40	269	308	1.91e1	SMART
WD40	310	349	3.45e-3	SMART
WD40	507	542	1.43e1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112925

SMART Domains

Protein: ENSMUSP00000108547
Gene: ENSMUSG00000030323

Domain	Start	End	E-Value	Type
WD40	1	39	7.1e1	SMART
WD40	42	81	7.16e-10	SMART
WD40	83	120	1.54e0	SMART
WD40	122	160	1.43e0	SMART
WD40	162	208	2.29e1	SMART
WD40	210	249	1.91e1	SMART
WD40	251	290	3.45e-3	SMART
WD40	448	483	1.43e1	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000122816
AA Change: S244T

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000145433
Gene: ENSMUSG00000030322
AA Change: S244T

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125889

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133830

Predicted Effect

possibly damaging
Transcript: ENSMUST00000147282
AA Change: S223T

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000125619
Gene: ENSMUSG00000030322
AA Change: S223T

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000203243

Predicted Effect

probably benign
Transcript: ENSMUST00000203643

SMART Domains

Protein: ENSMUSP00000144930
Gene: ENSMUSG00000030322

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

Predicted Effect

probably benign
Transcript: ENSMUST00000141305

SMART Domains

Protein: ENSMUSP00000138535
Gene: ENSMUSG00000030323

Domain	Start	End	E-Value	Type
WD40	1	39	7.1e1	SMART
WD40	42	81	7.16e-10	SMART
WD40	83	120	1.54e0	SMART
low complexity region	124	134	N/A	INTRINSIC
low complexity region	162	176	N/A	INTRINSIC

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.7%
20x: 93.7%

Validation Efficiency

100% (79/79)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abi3bp	T	G	16: 56,471,116 (GRCm39)	V587G	probably benign	Het
Abtb2	A	G	2: 103,547,632 (GRCm39)	D1002G	probably benign	Het
Acap2	A	G	16: 30,926,944 (GRCm39)	S524P	probably benign	Het
Acsm1	A	T	7: 119,254,687 (GRCm39)	I385L	probably benign	Het
Adra1a	C	G	14: 66,875,481 (GRCm39)	A152G	probably benign	Het
Agbl4	A	T	4: 111,513,565 (GRCm39)	Y437F	possibly damaging	Het
Amt	A	G	9: 108,176,979 (GRCm39)	T196A	probably benign	Het
Apobr	G	A	7: 126,185,859 (GRCm39)	V457M	probably benign	Het
Birc6	A	G	17: 74,956,667 (GRCm39)	K3563E	probably damaging	Het
Cdadc1	AGACGGA	AGA	14: 59,806,440 (GRCm39)		probably null	Het
Chrna9	T	C	5: 66,134,492 (GRCm39)	W448R	probably damaging	Het
Cyp4a31	A	T	4: 115,427,466 (GRCm39)	D224V	probably damaging	Het
Ddx10	C	A	9: 53,115,405 (GRCm39)	R643L	possibly damaging	Het
Dip2c	A	G	13: 9,586,896 (GRCm39)	H200R	probably benign	Het
Dnah8	A	T	17: 30,986,898 (GRCm39)	R3182S	probably damaging	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Het
Egfr	T	C	11: 16,819,354 (GRCm39)	C295R	probably damaging	Het
Garem1	A	T	18: 21,281,173 (GRCm39)	N394K	probably damaging	Het
Gcat	T	C	15: 78,915,322 (GRCm39)		probably null	Het
Gckr	C	T	5: 31,455,644 (GRCm39)	Q66*	probably null	Het
Gm26996	A	T	6: 130,556,317 (GRCm39)		noncoding transcript	Het
Gm9386	C	A	17: 81,246,141 (GRCm39)		noncoding transcript	Het
Gpr6	A	T	10: 40,947,258 (GRCm39)	M108K	possibly damaging	Het
H2-Q10	A	C	17: 35,784,481 (GRCm39)		probably benign	Het
Hpf1	A	G	8: 61,346,841 (GRCm39)	D52G	probably damaging	Het
Jak2	A	G	19: 29,279,377 (GRCm39)	R989G	probably damaging	Het
Kat7	A	G	11: 95,193,949 (GRCm39)		probably benign	Het
Kcnn3	G	T	3: 89,570,031 (GRCm39)	V615F	probably damaging	Het
Lgi1	G	T	19: 38,289,326 (GRCm39)		probably null	Het
Lrrtm4	A	T	6: 80,000,117 (GRCm39)	T510S	possibly damaging	Het
Map7d1	A	G	4: 126,128,114 (GRCm39)		probably null	Het
Mapt	T	C	11: 104,189,786 (GRCm39)	V252A	probably benign	Het
Meig1	T	A	2: 3,412,959 (GRCm39)	I21L	probably benign	Het
Mia3	A	G	1: 183,113,684 (GRCm39)	Y447H	probably damaging	Het
Mrpl46	A	C	7: 78,430,343 (GRCm39)	N142K	probably benign	Het
Myo18a	C	A	11: 77,750,062 (GRCm39)		probably benign	Het
Nup188	A	G	2: 30,216,523 (GRCm39)	T776A	possibly damaging	Het
Oas1h	C	A	5: 121,000,728 (GRCm39)	H113N	probably damaging	Het
Or6c202	T	A	10: 128,996,245 (GRCm39)	T203S	possibly damaging	Het
Or7g18	A	G	9: 18,787,213 (GRCm39)	I197V	probably benign	Het
Or7g27	C	T	9: 19,250,476 (GRCm39)	T240M	probably damaging	Het
Or9i1b	A	T	19: 13,896,817 (GRCm39)	L144F	possibly damaging	Het
Orc3	T	A	4: 34,572,450 (GRCm39)		probably benign	Het
Osbpl3	T	A	6: 50,329,980 (GRCm39)	L65F	probably damaging	Het
Papola	C	A	12: 105,765,912 (GRCm39)	P4Q	probably damaging	Het
Pepd	A	G	7: 34,645,022 (GRCm39)	N151S	probably damaging	Het
Plekhm2	A	G	4: 141,355,150 (GRCm39)	L959P	probably benign	Het
Prpf40a	A	T	2: 53,080,032 (GRCm39)	H82Q	probably damaging	Het
Robo1	C	T	16: 72,768,923 (GRCm39)	T496M	probably benign	Het
Samd9l	T	G	6: 3,372,863 (GRCm39)	Q1466P	probably damaging	Het
Serpina1a	T	C	12: 103,821,022 (GRCm39)	T342A	probably benign	Het
Serpina3i	A	G	12: 104,231,470 (GRCm39)	T36A	probably benign	Het
Serpinb5	G	T	1: 106,800,069 (GRCm39)	L86F	probably damaging	Het
Slc35g1	A	G	19: 38,391,275 (GRCm39)	S186G	possibly damaging	Het
Slco6d1	T	A	1: 98,350,899 (GRCm39)	D126E	probably benign	Het
Smchd1	A	G	17: 71,718,763 (GRCm39)		probably null	Het
Smpdl3a	C	A	10: 57,687,337 (GRCm39)	T355K	probably damaging	Het
Sntg2	A	G	12: 30,423,267 (GRCm39)		probably benign	Het
Sox14	T	A	9: 99,757,284 (GRCm39)	M152L	probably benign	Het
Spats2l	G	T	1: 57,977,085 (GRCm39)	A308S	possibly damaging	Het
Tcf12	T	C	9: 71,777,323 (GRCm39)		probably benign	Het
Tcf7l2	T	A	19: 55,912,504 (GRCm39)	C478*	probably null	Het
Tekt5	A	G	16: 10,200,771 (GRCm39)	L250P	probably damaging	Het
Tmem132d	T	G	5: 128,061,328 (GRCm39)	I425L	probably benign	Het
Tmem174	T	A	13: 98,773,456 (GRCm39)	I125F	probably damaging	Het
Trafd1	T	G	5: 121,512,079 (GRCm39)	I404L	probably benign	Het
Trpm5	G	A	7: 142,636,373 (GRCm39)	P500S	possibly damaging	Het
Trpm6	T	A	19: 18,839,576 (GRCm39)	N1616K	probably benign	Het
Vmn1r4	A	G	6: 56,933,715 (GRCm39)	D73G	possibly damaging	Het
Vmn2r85	T	A	10: 130,254,567 (GRCm39)	I706F	probably benign	Het
Zc3h14	C	G	12: 98,719,107 (GRCm39)	D157E	probably damaging	Het
Zfp982	A	G	4: 147,597,090 (GRCm39)	Q149R	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
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
R8032:Mbd4	UTSW	6	115,821,594 (GRCm39)	missense	probably damaging	1.00
R9707:Mbd4	UTSW	6	115,826,559 (GRCm39)	missense	probably benign	0.04

Predicted Primers

PCR Primer
(F):5'- CACCTGCTGCTTCAGTTGAATG -3'
(R):5'- AGCAGCGGACTGTCTAACTC -3'

Sequencing Primer
(F):5'- GGTGCCAGAAGTTACTTGTATGAAAC -3'
(R):5'- AGCGGACTGTCTAACTCTAACTCG -3'

Posted On

2016-02-04