Mutagenetix > Incidental Mutation

Incidental Mutation 'R7723:Mbd4'

595336

Institutional Source

Beutler Lab

Gene Symbol

Mbd4

Ensembl Gene

ENSMUSG00000030322

Gene Name

methyl-CpG binding domain protein 4

Synonyms

Med1

MMRRC Submission

045779-MU

Accession Numbers

Essential gene?

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

Stock #

R7723 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

115817658-115830332 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 115822324 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Glutamine at position 428 (H428Q)

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

possibly damaging
Transcript: ENSMUST00000032469
AA Change: H428Q

PolyPhen 2 Score 0.469 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000032469
Gene: ENSMUSG00000030322
AA Change: H428Q

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

probably benign
Transcript: ENSMUST00000203643
AA Change: H49Q

PolyPhen 2 Score 0.347 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000144930
Gene: ENSMUSG00000030322
AA Change: H49Q

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

100% (57/57)

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Apbb1ip	G	A	2: 22,761,574 (GRCm39)		probably null	Het
Brinp3	C	T	1: 146,577,409 (GRCm39)	T148I	probably damaging	Het
C1qa	A	T	4: 136,623,744 (GRCm39)	C153*	probably null	Het
Camkk1	G	T	11: 72,928,058 (GRCm39)	R363L	probably benign	Het
Ccdc80	T	G	16: 44,946,798 (GRCm39)		probably null	Het
Cenpu	T	C	8: 47,029,349 (GRCm39)	S351P	probably damaging	Het
Chd9	C	T	8: 91,741,837 (GRCm39)	L1609F	unknown	Het
Cnr1	T	A	4: 33,944,416 (GRCm39)	I268N	probably damaging	Het
Cyp3a59	A	T	5: 146,016,154 (GRCm39)	I4F	probably benign	Het
Dph6	A	G	2: 114,475,236 (GRCm39)	V93A	probably damaging	Het
Egf	T	A	3: 129,499,786 (GRCm39)	M785L	probably benign	Het
Fbn1	A	T	2: 125,223,954 (GRCm39)	C598*	probably null	Het
Fer	T	C	17: 64,203,273 (GRCm39)	S68P	probably damaging	Het
Herc1	C	T	9: 66,279,158 (GRCm39)	T22I	probably benign	Het
Kat2b	A	G	17: 53,945,415 (GRCm39)	D278G	possibly damaging	Het
Kdm1a	C	T	4: 136,285,060 (GRCm39)	V520I	probably benign	Het
Lrrc4c	G	T	2: 97,460,999 (GRCm39)	V542L	possibly damaging	Het
Lrrtm3	T	C	10: 63,924,427 (GRCm39)	T247A	possibly damaging	Het
Macf1	T	C	4: 123,326,717 (GRCm39)	S4929G	probably benign	Het
Mink1	C	G	11: 70,503,736 (GRCm39)	Q1183E	probably benign	Het
Myo9a	C	T	9: 59,687,141 (GRCm39)	P82L	probably damaging	Het
Nts	T	C	10: 102,320,784 (GRCm39)	T102A	probably damaging	Het
Nup35	T	C	2: 80,486,375 (GRCm39)	I230T	possibly damaging	Het
Nwd2	A	T	5: 63,965,347 (GRCm39)	T1644S	possibly damaging	Het
Nynrin	T	A	14: 56,109,502 (GRCm39)	N1536K	possibly damaging	Het
Or10d5j	A	T	9: 39,867,920 (GRCm39)	Y104N	possibly damaging	Het
Or13p10	A	G	4: 118,522,914 (GRCm39)	S67G	probably benign	Het
Or2at4	A	G	7: 99,384,884 (GRCm39)	Y178C	possibly damaging	Het
Or2l13b	A	T	16: 19,349,358 (GRCm39)	L104*	probably null	Het
Or5d44	A	C	2: 88,141,819 (GRCm39)	V107G	possibly damaging	Het
Palld	C	T	8: 62,164,492 (GRCm39)	V400I	probably damaging	Het
Pank2	T	C	2: 131,122,258 (GRCm39)	V261A	probably damaging	Het
Pcdhb3	C	A	18: 37,435,565 (GRCm39)	N510K	probably damaging	Het
Pfkfb2	A	T	1: 130,635,325 (GRCm39)	Y79N	probably damaging	Het
Phc2	C	T	4: 128,616,882 (GRCm39)	A385V	probably benign	Het
Prob1	T	C	18: 35,785,942 (GRCm39)	T771A	possibly damaging	Het
Psmb6	T	C	11: 70,417,396 (GRCm39)	V109A	possibly damaging	Het
Ptcd1	T	C	5: 145,091,639 (GRCm39)	T487A	probably damaging	Het
Ralgapa1	A	T	12: 55,788,298 (GRCm39)	M595K	probably benign	Het
Rps12	A	T	10: 23,662,752 (GRCm39)	V14D	probably benign	Het
Scn3b	C	A	9: 40,199,693 (GRCm39)	S203*	probably null	Het
Serinc1	G	A	10: 57,403,918 (GRCm39)	P15L	probably benign	Het
Six2	A	G	17: 85,995,103 (GRCm39)	I93T	probably benign	Het
Slco1a1	T	A	6: 141,854,795 (GRCm39)	I619F	probably damaging	Het
Snx25	A	C	8: 46,491,516 (GRCm39)	V858G	probably damaging	Het
Sspo	G	A	6: 48,441,572 (GRCm39)	C1903Y	probably damaging	Het
Tas2r116	T	A	6: 132,832,867 (GRCm39)	I156N	probably benign	Het
Tasp1	G	T	2: 139,827,051 (GRCm39)	T189K	probably damaging	Het
Tdrd6	A	T	17: 43,936,851 (GRCm39)	M1399K	probably benign	Het
Tecta	C	A	9: 42,278,232 (GRCm39)	C1092F	probably damaging	Het
Tmem150a	G	A	6: 72,336,057 (GRCm39)	V215I	probably damaging	Het
Tmem176b	C	T	6: 48,812,869 (GRCm39)	V109I	probably benign	Het
Trav8d-1	T	A	14: 53,016,321 (GRCm39)	I69K	probably damaging	Het
Ttn	A	T	2: 76,638,419 (GRCm39)	L13954I	probably damaging	Het
Veph1	C	A	3: 66,113,093 (GRCm39)	C237F	possibly damaging	Het
Vmn1r121	G	A	7: 20,832,119 (GRCm39)	T107I	probably damaging	Het
Zdhhc13	G	A	7: 48,458,567 (GRCm39)	M300I	probably benign	Het
Zfp608	T	C	18: 55,030,673 (GRCm39)	D1089G	probably 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
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'- GAAATCAATGACCACCTGGC -3'
(R):5'- ACCTTTCCCTAAGCAGAATGG -3'

Sequencing Primer
(F):5'- CCTGGCCCTCAGTATTAAAAAGAATG -3'
(R):5'- GGGGACATTCCAAGTCT -3'

Posted On

2019-11-12