Mutagenetix > Incidental Mutation

Incidental Mutation 'R1489:Mbd3'

163610

Institutional Source

Beutler Lab

Gene Symbol

Mbd3

Ensembl Gene

ENSMUSG00000035478

Gene Name

methyl-CpG binding domain protein 3

Synonyms

MMRRC Submission

039541-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1489 (G1)

Quality Score

216

Status

Validated

Chromosome

Chromosomal Location

80228373-80235365 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to G at 80229740 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Histidine at position 190 (D190H)

Ref Sequence

ENSEMBL: ENSMUSP00000100986 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000092295] [ENSMUST00000105347] [ENSMUST00000105348] [ENSMUST00000105349]

AlphaFold

Q9Z2D8

Predicted Effect

probably damaging
Transcript: ENSMUST00000092295
AA Change: D222H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000089948
Gene: ENSMUSG00000035478
AA Change: D222H

Domain	Start	End	E-Value	Type
MBD	3	76	8.9e-35	SMART
Pfam:MBDa	79	148	8.2e-32	PFAM
Pfam:MBD_C	152	243	4.7e-37	PFAM
low complexity region	268	283	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000105347
AA Change: D198H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000100984
Gene: ENSMUSG00000035478
AA Change: D198H

Domain	Start	End	E-Value	Type
Pfam:MBD	12	48	4.4e-8	PFAM
Pfam:MBD_C	126	219	9.8e-39	PFAM
low complexity region	244	259	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000105348
AA Change: D218H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000100985
Gene: ENSMUSG00000035478
AA Change: D218H

Domain	Start	End	E-Value	Type
MBD	1	44	4.8e-6	SMART
Pfam:MBD_C	146	239	1.7e-35	PFAM
low complexity region	264	279	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000105349
AA Change: D190H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000100986
Gene: ENSMUSG00000035478
AA Change: D190H

Domain	Start	End	E-Value	Type
Pfam:MBD	4	40	4.7e-8	PFAM
Pfam:MBD_C	118	211	1.1e-38	PFAM
low complexity region	236	251	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125618

Predicted Effect

unknown
Transcript: ENSMUST00000142997
AA Change: D121H

SMART Domains

Protein: ENSMUSP00000120675
Gene: ENSMUSG00000035478
AA Change: D121H

Domain	Start	End	E-Value	Type
Pfam:MBDa	1	48	2.4e-25	PFAM
Pfam:MBD_C	52	143	1.3e-37	PFAM
low complexity region	168	183	N/A	INTRINSIC

Meta Mutation Damage Score

0.1544

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.7%
20x: 93.9%

Validation Efficiency

96% (52/54)

MGI Phenotype

FUNCTION: This gene encodes a member of the MBD family of nuclear proteins that contain a methyl-CpG binding domain (MBD). The encoded protein is a component of the nucleosome remodeling and histone deacetylation (NuRD) complex. Deletion of this gene causes embryonic lethality in mice. Embryonic stem cells lacking the encoded protein are severely compromised in their ability to differentiate and fail to commit to developmental lineages in the absence of leukemia inhibitory factor. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2015]
PHENOTYPE: Mice homozygous for disruptions in this gene experience deficiencies as embryos around implantation and die before birth. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700097O09Rik	A	G	12: 55,106,295 (GRCm39)	S143P	possibly damaging	Het
4930522H14Rik	T	C	4: 109,362,654 (GRCm39)	K218E	possibly damaging	Het
Abcb1a	T	A	5: 8,736,300 (GRCm39)		probably null	Het
Adam39	A	G	8: 41,278,031 (GRCm39)	T141A	possibly damaging	Het
Adam6b	T	A	12: 113,455,071 (GRCm39)	S629R	probably benign	Het
Ap3b2	C	A	7: 81,113,438 (GRCm39)	E924*	probably null	Het
Armc3	A	T	2: 19,314,858 (GRCm39)	Y856F	probably benign	Het
Asap1	A	G	15: 64,044,579 (GRCm39)	L142P	probably damaging	Het
Atg9a	T	A	1: 75,162,734 (GRCm39)	D427V	probably damaging	Het
Atl2	G	A	17: 80,160,135 (GRCm39)	A17V	probably benign	Het
Atxn2l	A	T	7: 126,095,639 (GRCm39)	S379T	probably damaging	Het
C1ql3	G	T	2: 13,015,453 (GRCm39)	P69Q	possibly damaging	Het
Cap2	A	T	13: 46,763,111 (GRCm39)	I114F	probably damaging	Het
Ccdc168	A	G	1: 44,096,950 (GRCm39)	F1383L	probably benign	Het
Ccdc168	T	C	1: 44,100,667 (GRCm39)	I144V	probably benign	Het
Cox16	T	C	12: 81,521,389 (GRCm39)	N135S	probably null	Het
Dnajc13	A	T	9: 104,108,234 (GRCm39)	H180Q	possibly damaging	Het
Dpy19l3	A	T	7: 35,424,835 (GRCm39)	Y73*	probably null	Het
Duox2	T	A	2: 122,123,877 (GRCm39)	M436L	probably benign	Het
Exoc6	T	A	19: 37,585,568 (GRCm39)	M481K	possibly damaging	Het
Fbxw2	GCCCCC	GCCCCCCCC	2: 34,702,829 (GRCm39)		probably benign	Het
Fmn1	T	A	2: 113,195,557 (GRCm39)	V419E	unknown	Het
Fndc4	T	C	5: 31,450,795 (GRCm39)	*232W	probably null	Het
Foxc1	C	T	13: 31,992,595 (GRCm39)	R469*	probably null	Het
Fsip2	A	G	2: 82,810,155 (GRCm39)	H2158R	probably benign	Het
Ghdc	C	T	11: 100,659,083 (GRCm39)	G373D	probably benign	Het
Gm10330	A	T	12: 23,830,032 (GRCm39)	S50T	probably benign	Het
Hlx	G	T	1: 184,464,184 (GRCm39)	A52D	probably damaging	Het
Lonrf1	A	G	8: 36,690,108 (GRCm39)	V650A	probably damaging	Het
Map1a	T	C	2: 121,130,918 (GRCm39)	V578A	possibly damaging	Het
Mcpt9	T	C	14: 56,264,976 (GRCm39)	K175R	probably benign	Het
Mia3	A	G	1: 183,120,121 (GRCm39)	S85P	probably benign	Het
Myrip	T	C	9: 120,261,595 (GRCm39)	F403L	probably damaging	Het
Nox4	A	G	7: 86,954,097 (GRCm39)	Y134C	probably damaging	Het
Numb	A	G	12: 83,842,217 (GRCm39)	L642P	probably damaging	Het
Pappa	A	T	4: 65,099,185 (GRCm39)	Y568F	possibly damaging	Het
Pdzrn4	T	C	15: 92,575,593 (GRCm39)	L333P	probably benign	Het
Prl	A	T	13: 27,241,619 (GRCm39)	S3C	probably damaging	Het
Ptprc	T	C	1: 138,047,824 (GRCm39)	T60A	possibly damaging	Het
Rbm10	C	T	X: 20,503,903 (GRCm39)		probably benign	Het
Slc7a7	C	T	14: 54,646,103 (GRCm39)	R120H	probably damaging	Het
Smpd1	T	C	7: 105,205,761 (GRCm39)		probably null	Het
Spta1	A	G	1: 174,058,891 (GRCm39)	E1942G	probably damaging	Het
Tmem38a	A	G	8: 73,333,479 (GRCm39)	Y66C	probably damaging	Het
Tnnt1	A	T	7: 4,510,524 (GRCm39)	Y232*	probably null	Het
Tpte	T	C	8: 22,839,405 (GRCm39)		probably null	Het
Virma	T	C	4: 11,521,164 (GRCm39)	V907A	probably damaging	Het
Vmn1r174	C	T	7: 23,453,981 (GRCm39)	Q216*	probably null	Het
Zswim3	T	C	2: 164,661,901 (GRCm39)	V127A	probably benign	Het

Other mutations in Mbd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00158:Mbd3	APN	10	80,229,717 (GRCm39)	splice site	probably benign
IGL01573:Mbd3	APN	10	80,229,095 (GRCm39)	missense	probably benign	0.03
IGL03080:Mbd3	APN	10	80,229,085 (GRCm39)	missense	probably damaging	1.00
R1500:Mbd3	UTSW	10	80,230,420 (GRCm39)	missense	possibly damaging	0.90
R4454:Mbd3	UTSW	10	80,229,817 (GRCm39)	missense	probably damaging	1.00
R4921:Mbd3	UTSW	10	80,231,410 (GRCm39)	missense	probably damaging	1.00
R7611:Mbd3	UTSW	10	80,231,352 (GRCm39)	missense	probably damaging	0.99
R7659:Mbd3	UTSW	10	80,231,019 (GRCm39)	missense	probably damaging	1.00
X0063:Mbd3	UTSW	10	80,231,287 (GRCm39)	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- ACCCAGCATTTCTAAGCGTGCC -3'
(R):5'- TGGGATGGGGTCATAACTTCCAGG -3'

Sequencing Primer
(F):5'- CTGTCGGGCATCTAAATTGC -3'
(R):5'- GGTCATAACTTCCAGGTAGAGCC -3'

Posted On

2014-03-28