Mutagenetix > Incidental Mutation

Incidental Mutation 'R4860:Mbd4'

372403

Institutional Source

Beutler Lab

Gene Symbol

Mbd4

Ensembl Gene

ENSMUSG00000030322

Gene Name

methyl-CpG binding domain protein 4

Synonyms

Med1

MMRRC Submission

042471-MU

Accession Numbers

Essential gene?

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

Stock #

R4860 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

115817658-115830332 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 115825887 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Tyrosine at position 368 (F368Y)

Ref Sequence

ENSEMBL: ENSMUSP00000032469 (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: F368Y

PolyPhen 2 Score 0.513 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000032469
Gene: ENSMUSG00000030322
AA Change: F368Y

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

probably benign
Transcript: ENSMUST00000122816
AA Change: F368Y

PolyPhen 2 Score 0.108 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000145433
Gene: ENSMUSG00000030322
AA Change: F368Y

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

probably benign
Transcript: ENSMUST00000147282
AA Change: F347Y

PolyPhen 2 Score 0.108 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000125619
Gene: ENSMUSG00000030322
AA Change: F347Y

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

Predicted Effect

probably benign
Transcript: ENSMUST00000203643
AA Change: F14Y

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000144930
Gene: ENSMUSG00000030322
AA Change: F14Y

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000203243

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

0.0637

Coding Region Coverage

1x: 98.9%
3x: 97.9%
10x: 95.0%
20x: 87.3%

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030K09Rik	T	C	8: 73,209,267 (GRCm39)	S466P	possibly damaging	Het
Ablim1	T	C	19: 57,068,298 (GRCm39)	T267A	probably damaging	Het
Acap2	A	T	16: 30,922,317 (GRCm39)	L724Q	possibly damaging	Het
Acsbg3	A	G	17: 57,195,655 (GRCm39)	N684S	probably benign	Het
Adcy4	T	C	14: 56,019,384 (GRCm39)	T89A	possibly damaging	Het
Agrp	T	C	8: 106,294,000 (GRCm39)	E41G	probably benign	Het
Ajm1	T	C	2: 25,468,765 (GRCm39)	Y382C	probably damaging	Het
Akr1d1	G	A	6: 37,541,426 (GRCm39)	V308M	probably damaging	Het
Ap1m2	C	T	9: 21,220,970 (GRCm39)	R54Q	probably benign	Het
Arhgap45	T	A	10: 79,862,900 (GRCm39)	V692E	probably damaging	Het
Arid5b	G	T	10: 68,078,925 (GRCm39)	N137K	probably damaging	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
BC048679	T	C	7: 81,145,468 (GRCm39)	N27D	probably benign	Het
Ccdc78	A	G	17: 26,007,674 (GRCm39)	N237S	probably benign	Het
Cd46	G	A	1: 194,744,704 (GRCm39)	L345F	possibly damaging	Het
Cngb3	A	T	4: 19,425,569 (GRCm39)	N459I	possibly damaging	Het
Ctnnd2	A	G	15: 30,881,313 (GRCm39)	E731G	probably damaging	Het
Ctsh	A	G	9: 89,936,601 (GRCm39)	E26G	probably benign	Het
Cul1	G	T	6: 47,494,080 (GRCm39)	K464N	probably benign	Het
Cul1	T	A	6: 47,494,125 (GRCm39)	S479R	probably damaging	Het
Dcaf5	A	T	12: 80,387,006 (GRCm39)	D373E	probably benign	Het
Dhcr7	A	G	7: 143,394,237 (GRCm39)	Q126R	probably benign	Het
Dok2	T	C	14: 71,014,956 (GRCm39)	F228L	probably damaging	Het
Dpep3	T	G	8: 106,702,821 (GRCm39)	I314L	probably benign	Het
Eps8	A	G	6: 137,491,293 (GRCm39)	F362L	probably damaging	Het
Espn	G	T	4: 152,223,303 (GRCm39)	R250S	probably damaging	Het
Faf1	A	C	4: 109,600,093 (GRCm39)	N163H	probably damaging	Het
Fcho1	C	T	8: 72,163,125 (GRCm39)	V635I	probably benign	Het
Garin5b	C	T	7: 4,760,468 (GRCm39)		probably null	Het
Gask1b	C	A	3: 79,843,981 (GRCm39)	S36*	probably null	Het
Gm7579	G	A	7: 141,765,645 (GRCm39)	C17Y	unknown	Het
Gpx8	G	T	13: 113,182,042 (GRCm39)	Y130*	probably null	Het
Gvin1	A	T	7: 105,762,643 (GRCm39)	Y609N	possibly damaging	Het
Hectd4	T	A	5: 121,443,881 (GRCm39)	M30K	probably benign	Het
Iqub	T	C	6: 24,450,841 (GRCm39)	D586G	probably damaging	Het
Klhl25	T	C	7: 75,516,798 (GRCm39)	I568T	probably benign	Het
Larp6	A	G	9: 60,645,093 (GRCm39)	E411G	probably damaging	Het
Lepr	A	C	4: 101,646,534 (GRCm39)	I822L	probably benign	Het
Lrig3	C	A	10: 125,846,921 (GRCm39)	D896E	probably benign	Het
Lrp1	C	T	10: 127,389,693 (GRCm39)	G3114D	probably damaging	Het
Lyset	A	T	12: 102,710,314 (GRCm39)		probably benign	Het
Macf1	A	T	4: 123,380,543 (GRCm39)	Y1263N	probably damaging	Het
Mapk10	T	C	5: 103,138,485 (GRCm39)	D180G	probably damaging	Het
Matr3	T	A	18: 35,714,693 (GRCm39)	V113E	probably damaging	Het
Mcpt8	G	A	14: 56,319,737 (GRCm39)	R238W	probably benign	Het
Mcrip2	G	T	17: 26,083,621 (GRCm39)	T86N	possibly damaging	Het
Mink1	A	G	11: 70,502,418 (GRCm39)	N1043S	probably damaging	Het
Muc4	G	A	16: 32,754,616 (GRCm38)	G1497R	probably benign	Het
Muc4	T	A	16: 32,754,625 (GRCm38)	S1500T	probably benign	Het
Nbeal2	G	A	9: 110,464,262 (GRCm39)	T1128I	probably benign	Het
Nrg2	T	A	18: 36,329,600 (GRCm39)	Y205F	probably damaging	Het
Nubp2	A	G	17: 25,103,430 (GRCm39)	M149T	probably benign	Het
Or4d2b	T	A	11: 87,780,051 (GRCm39)	M224L	probably damaging	Het
Or8d6	G	T	9: 39,853,800 (GRCm39)	M81I	probably benign	Het
Or8j3c	T	C	2: 86,253,301 (GRCm39)	T240A	probably damaging	Het
Pax3	A	G	1: 78,169,093 (GRCm39)	I191T	possibly damaging	Het
Pdcd5	T	C	7: 35,343,135 (GRCm39)	N137D	possibly damaging	Het
Pik3c2a	G	A	7: 115,939,391 (GRCm39)	A1649V	probably damaging	Het
Pkhd1l1	T	C	15: 44,400,774 (GRCm39)	S2183P	possibly damaging	Het
Plekho1	T	A	3: 95,896,305 (GRCm39)	Q388L	possibly damaging	Het
Ppfibp1	A	G	6: 146,892,012 (GRCm39)	T91A	probably benign	Het
Ptger4	G	T	15: 5,272,087 (GRCm39)	N177K	probably benign	Het
Reln	A	G	5: 22,106,749 (GRCm39)	F3207S	probably benign	Het
Rigi	G	T	4: 40,210,000 (GRCm39)	S644R	probably damaging	Het
Ripk4	C	T	16: 97,552,736 (GRCm39)	R194H	probably damaging	Het
Rnf112	A	T	11: 61,343,570 (GRCm39)	C112S	possibly damaging	Het
Rprd1b	T	G	2: 157,916,855 (GRCm39)	Y278*	probably null	Het
Sel1l	A	G	12: 91,798,376 (GRCm39)	L140P	probably damaging	Het
Shroom3	G	T	5: 93,090,945 (GRCm39)	V1151F	probably damaging	Het
Slc38a3	A	G	9: 107,532,263 (GRCm39)	V423A	probably damaging	Het
Slitrk6	T	C	14: 110,989,315 (GRCm39)	T131A	probably damaging	Het
Slmap	A	T	14: 26,181,364 (GRCm39)	V323E	probably benign	Het
Smim6	T	C	11: 115,804,330 (GRCm39)	V39A	probably benign	Het
Sorbs1	T	C	19: 40,325,449 (GRCm39)	T382A	probably benign	Het
Sparc	G	A	11: 55,290,037 (GRCm39)	T218I	possibly damaging	Het
Steap1	A	T	5: 5,786,589 (GRCm39)	F283I	probably damaging	Het
Stil	A	G	4: 114,895,671 (GRCm39)	T586A	probably benign	Het
Tbce	T	A	13: 14,194,380 (GRCm39)	D93V	probably damaging	Het
Tcf12	C	T	9: 71,766,122 (GRCm39)	G504S	probably null	Het
Tex55	A	G	16: 38,648,507 (GRCm39)	S201P	probably damaging	Het
Tle4	A	T	19: 14,441,709 (GRCm39)	I435K	probably benign	Het
Tmem245	A	G	4: 56,899,164 (GRCm39)	F254S	probably damaging	Het
Tubgcp3	T	C	8: 12,699,722 (GRCm39)	K377R	probably benign	Het
Ush2a	A	T	1: 188,285,472 (GRCm39)	T2003S	probably benign	Het
Usp53	A	G	3: 122,755,012 (GRCm39)	S32P	possibly damaging	Het
Vmn1r78	T	A	7: 11,886,683 (GRCm39)	L98Q	probably damaging	Het
Vmn2r116	A	C	17: 23,620,777 (GRCm39)	Q837P	probably benign	Het
Vmn2r3	T	C	3: 64,183,022 (GRCm39)	I226V	probably benign	Het
Vmn2r84	T	A	10: 130,221,712 (GRCm39)	D836V	probably damaging	Het
Vps13d	A	G	4: 144,813,731 (GRCm39)	F165L	probably benign	Het
Vstm4	A	G	14: 32,585,742 (GRCm39)	E103G	possibly damaging	Het
Zfp870	A	T	17: 33,102,314 (GRCm39)	C339*	probably null	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
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'- TAGGGCAGATATTGGGATCAACTG -3'
(R):5'- CTGTGCAAGGGAGACTGTTG -3'

Sequencing Primer
(F):5'- GGGAGAATATATCTGACGCTTGACTC -3'
(R):5'- GTTTCATACAAGTAACTTCTGGCACC -3'

Posted On

2016-03-01