Mutagenetix > Incidental Mutation

Incidental Mutation 'R4921:Mbd3'

378610

Institutional Source

Beutler Lab

Gene Symbol

Mbd3

Ensembl Gene

ENSMUSG00000035478

Gene Name

methyl-CpG binding domain protein 3

Synonyms

MMRRC Submission

042523-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4921 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

80392539-80399550 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 80395576 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Serine at position 12 (R12S)

Ref Sequence

ENSEMBL: ENSMUSP00000100985 (fasta)

Gene Model

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

AlphaFold

Q9Z2D8

Predicted Effect

probably damaging
Transcript: ENSMUST00000092295
AA Change: R44S

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000089948
Gene: ENSMUSG00000035478
AA Change: R44S

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

possibly damaging
Transcript: ENSMUST00000105347
AA Change: R20S

PolyPhen 2 Score 0.795 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000100984
Gene: ENSMUSG00000035478
AA Change: R20S

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: R12S

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

SMART Domains

Protein: ENSMUSP00000100985
Gene: ENSMUSG00000035478
AA Change: R12S

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: R12S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000100986
Gene: ENSMUSG00000035478
AA Change: R12S

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

probably benign
Transcript: ENSMUST00000142997

SMART Domains

Protein: ENSMUSP00000120675
Gene: ENSMUSG00000035478

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

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.7%
20x: 90.3%

Validation Efficiency

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: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522L14Rik	A	T	5: 109,737,796	N65K	probably benign	Het
Abcc9	T	C	6: 142,590,436	Y1524C	probably benign	Het
Acap1	A	G	11: 69,887,193	I102T	probably damaging	Het
Acvr2a	T	C	2: 48,893,541	V284A	possibly damaging	Het
Adam3	T	C	8: 24,684,614	M712V	probably benign	Het
Adck1	T	C	12: 88,441,138	V213A	probably benign	Het
Adgrl3	G	T	5: 81,512,110	W242L	probably damaging	Het
Alk	T	C	17: 71,904,315	T857A	probably benign	Het
Alms1	A	G	6: 85,628,546	T2393A	probably benign	Het
Ank3	C	T	10: 70,002,109	P240L	probably damaging	Het
Ankrd35	C	A	3: 96,684,824	L809M	possibly damaging	Het
Birc6	T	A	17: 74,650,099	L3690Q	probably damaging	Het
Bmp3	C	A	5: 98,872,061	F114L	probably damaging	Het
Cage1	G	A	13: 38,019,208	H627Y	probably benign	Het
Cars	T	C	7: 143,569,475	D468G	probably damaging	Het
Ccdc148	T	C	2: 58,829,802	E487G	probably damaging	Het
Ccdc80	A	T	16: 45,118,167	I746F	probably damaging	Het
Ccl25	A	G	8: 4,353,913	Q119R	possibly damaging	Het
Cdh24	C	T	14: 54,633,215	D178N	probably damaging	Het
Cdk12	A	T	11: 98,222,687	T766S	unknown	Het
Chst15	T	A	7: 132,247,884	T443S	probably benign	Het
Cnbp	T	C	6: 87,845,146	D125G	possibly damaging	Het
Cntn2	A	T	1: 132,516,032	V1003E	possibly damaging	Het
Crct1	A	G	3: 93,014,825		probably benign	Het
Dand5	C	T	8: 84,816,484	C121Y	probably damaging	Het
Dmkn	A	T	7: 30,771,233	D382V	probably damaging	Het
Dnase2b	T	A	3: 146,593,441	T86S	probably damaging	Het
Dusp8	GCCACCACCACCACCACCACCACC	GCCACCACCACCACCACCACC	7: 142,082,154		probably benign	Het
Eef1akmt1	C	T	14: 57,550,632	V90M	probably damaging	Het
Egfl7	G	T	2: 26,590,980	W168L	probably benign	Het
Ep400	A	G	5: 110,665,810	C2908R	probably damaging	Het
Espl1	A	G	15: 102,315,241	K1076E	probably damaging	Het
Exoc4	A	G	6: 33,910,517	N747D	probably benign	Het
Fancm	T	C	12: 65,077,141	V191A	probably benign	Het
Fbxo17	A	G	7: 28,732,789	D97G	probably benign	Het
Fer1l6	G	T	15: 58,600,311		probably null	Het
Flt4	T	C	11: 49,627,143	W337R	probably damaging	Het
Fpr-rs7	T	C	17: 20,113,820	H136R	possibly damaging	Het
Frem3	T	A	8: 80,613,136	I686N	possibly damaging	Het
Galnt9	A	G	5: 110,577,449	K84R	probably damaging	Het
Gfm2	T	A	13: 97,175,676	M760K	probably damaging	Het
Glis3	T	C	19: 28,666,104	T13A	probably damaging	Het
Gm13078	A	T	4: 143,728,326	K398M	possibly damaging	Het
H2-K1	A	G	17: 33,997,076	V323A	possibly damaging	Het
Hbb-bs	G	A	7: 103,826,720	A130V	probably damaging	Het
Herc2	T	A	7: 56,229,690	H4685Q	probably benign	Het
Ighv5-9-1	C	T	12: 113,736,294	R56H	possibly damaging	Het
Itgb4	A	G	11: 116,006,605	N1548S	probably benign	Het
Itpr3	T	C	17: 27,098,005	Y745H	probably damaging	Het
Kank3	G	T	17: 33,817,200	G14V	probably damaging	Het
Kif24	G	T	4: 41,394,329	S982Y	probably damaging	Het
Kifc5b	C	T	17: 26,921,023	R53W	probably damaging	Het
Krt39	A	G	11: 99,514,749	S442P	possibly damaging	Het
Lcat	G	A	8: 105,942,442	P67L	possibly damaging	Het
Maml2	T	C	9: 13,621,175	S562P	probably damaging	Het
Map3k8	G	A	18: 4,349,124	R65W	possibly damaging	Het
Msr1	T	C	8: 39,624,251	E106G	possibly damaging	Het
Myh4	T	A	11: 67,254,028	L1256Q	probably damaging	Het
Mypn	G	A	10: 63,147,936	T511M	possibly damaging	Het
Nub1	A	T	5: 24,701,469	N331I	probably benign	Het
Nup107	A	G	10: 117,770,511	V440A	possibly damaging	Het
Ofcc1	A	G	13: 40,214,517	F174L	probably benign	Het
Olfr1497	T	C	19: 13,795,465	I49V	probably benign	Het
Olfr597	A	T	7: 103,320,543	N44I	probably damaging	Het
Olfr975	A	C	9: 39,950,225	V182G	probably damaging	Het
Parp2	C	A	14: 50,819,268	L310I	probably damaging	Het
Pcdh20	A	G	14: 88,469,726	V46A	probably benign	Het
Pcdhgb6	A	G	18: 37,743,472	D411G	probably damaging	Het
Pkd1l2	T	C	8: 117,054,885	E807G	probably benign	Het
Pkd1l2	A	T	8: 117,072,549	N267K	probably damaging	Het
Rell1	C	A	5: 63,936,033	M126I	probably damaging	Het
Robo4	G	A	9: 37,402,560	E36K	probably benign	Het
Rpgrip1l	T	C	8: 91,261,009	S807G	probably benign	Het
Rpl10a	T	C	17: 28,330,852	V169A	probably benign	Het
Rubcn	C	T	16: 32,847,294	V166I	probably damaging	Het
Sall2	T	C	14: 52,315,393	E113G	possibly damaging	Het
Sars2	T	C	7: 28,752,438	S423P	possibly damaging	Het
Scaper	A	G	9: 55,892,235	I182T	probably benign	Het
Selp	A	G	1: 164,141,397	D522G	possibly damaging	Het
Sema4b	T	A	7: 80,198,756	I35N	possibly damaging	Het
Sgce	A	T	6: 4,694,153	F268I	probably damaging	Het
Slc14a2	G	T	18: 78,192,188	A258E	probably damaging	Het
Slc17a9	T	C	2: 180,735,949	Y213H	probably benign	Het
Slc22a7	T	G	17: 46,436,933	I233L	probably benign	Het
Slc35f1	A	G	10: 53,062,602	Q210R	probably damaging	Het
Slc6a21	A	G	7: 45,288,310	E350G	possibly damaging	Het
Spata21	A	T	4: 141,112,091	D639V	probably damaging	Het
Svil	A	G	18: 5,108,631	D1519G	probably damaging	Het
Tbccd1	T	C	16: 22,841,899	T56A	probably benign	Het
Tigit	A	T	16: 43,662,017	I118N	probably damaging	Het
Tlr11	A	T	14: 50,362,885	Q776L	possibly damaging	Het
Tspan12	A	C	6: 21,835,449	I9S	possibly damaging	Het
Unc5c	T	A	3: 141,788,966	Y347N	probably damaging	Het
Unk	A	G	11: 116,054,945	T481A	probably benign	Het
Vmn1r192	A	C	13: 22,187,480	V190G	probably damaging	Het
Vnn3	A	T	10: 23,864,575	M259L	probably benign	Het
Zan	T	C	5: 137,408,370		probably benign	Het
Zdhhc6	T	C	19: 55,313,210	H113R	probably damaging	Het

Other mutations in Mbd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00158:Mbd3	APN	10	80393883	splice site	probably benign
IGL01573:Mbd3	APN	10	80393261	missense	probably benign	0.03
IGL03080:Mbd3	APN	10	80393251	missense	probably damaging	1.00
R1489:Mbd3	UTSW	10	80393906	missense	probably damaging	1.00
R1500:Mbd3	UTSW	10	80394586	missense	possibly damaging	0.90
R4454:Mbd3	UTSW	10	80393983	missense	probably damaging	1.00
R7611:Mbd3	UTSW	10	80395518	missense	probably damaging	0.99
R7659:Mbd3	UTSW	10	80395185	missense	probably damaging	1.00
X0063:Mbd3	UTSW	10	80395453	missense	probably benign	0.01

Predicted Primers

PCR Primer
(F):5'- TACTGACTCGATGGCGATAGAC -3'
(R):5'- ACCTCATAGGGCCTCCTTAG -3'

Sequencing Primer
(F):5'- CGATAGACGCTAACCCAGAGG -3'
(R):5'- TAGGCTTCCCAGATGAACTGTAGC -3'

Posted On

2016-04-15