Mutagenetix > Incidental Mutation

Incidental Mutation 'R4454:Mbd3'

329096

Institutional Source

Beutler Lab

Gene Symbol

Mbd3

Ensembl Gene

ENSMUSG00000035478

Gene Name

methyl-CpG binding domain protein 3

Synonyms

MMRRC Submission

041714-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4454 (G1)

Quality Score

195

Status

Validated

Chromosome

Chromosomal Location

80228373-80235365 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 80229817 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Histidine at position 164 (L164H)

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: L196H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000089948
Gene: ENSMUSG00000035478
AA Change: L196H

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: L172H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000100984
Gene: ENSMUSG00000035478
AA Change: L172H

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: L192H

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

SMART Domains

Protein: ENSMUSP00000100985
Gene: ENSMUSG00000035478
AA Change: L192H

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: L164H

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000100986
Gene: ENSMUSG00000035478
AA Change: L164H

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: L95H

SMART Domains

Protein: ENSMUSP00000120675
Gene: ENSMUSG00000035478
AA Change: L95H

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

0.2869

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.3%

Validation Efficiency

100% (51/51)

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ap4e1	T	A	2: 126,889,061 (GRCm39)	F509I	probably damaging	Het
Asmt	A	T	X: 169,106,456 (GRCm39)	M19L	probably benign	Het
Atf6	C	T	1: 170,621,608 (GRCm39)	R471Q	probably damaging	Het
Atp4a	G	A	7: 30,419,650 (GRCm39)	R671Q	probably benign	Het
Baiap3	T	A	17: 25,468,510 (GRCm39)	D250V	probably damaging	Het
C2cd4d	T	A	3: 94,271,054 (GRCm39)	F107I	probably damaging	Het
Cdkn2d	C	G	9: 21,202,185 (GRCm39)	V21L	probably benign	Het
Cldn6	T	C	17: 23,900,060 (GRCm39)		probably null	Het
Cpa5	A	G	6: 30,626,323 (GRCm39)	N228S	possibly damaging	Het
Cracdl	T	C	1: 37,663,834 (GRCm39)	E163G	probably damaging	Het
Crocc	T	C	4: 140,747,716 (GRCm39)	S1478G	possibly damaging	Het
Csmd1	A	T	8: 15,995,011 (GRCm39)	C2675S	probably damaging	Het
Cthrc1	C	A	15: 38,940,408 (GRCm39)	Q4K	probably benign	Het
Ddo	A	T	10: 40,523,543 (GRCm39)	I178F	probably damaging	Het
Dmxl1	A	G	18: 50,026,399 (GRCm39)	T1836A	probably benign	Het
Dnah9	T	G	11: 66,038,215 (GRCm39)	Q107P	probably damaging	Het
Dusp26	A	G	8: 31,584,172 (GRCm39)	N93S	probably damaging	Het
Egr2	GAA	GA	10: 67,375,733 (GRCm39)		probably null	Het
Epha5	T	C	5: 84,304,303 (GRCm39)	I501V	probably damaging	Het
Eya1	C	T	1: 14,253,420 (GRCm39)	V519M	probably damaging	Het
Fam227b	T	A	2: 125,988,188 (GRCm39)		probably benign	Het
Fgd5	C	T	6: 91,966,167 (GRCm39)	S642F	probably damaging	Het
Fsip2	G	T	2: 82,821,120 (GRCm39)	A5618S	possibly damaging	Het
Gm12034	T	A	11: 20,396,476 (GRCm39)		noncoding transcript	Het
Liph	T	C	16: 21,803,018 (GRCm39)	D17G	probably benign	Het
Med4	A	G	14: 73,755,502 (GRCm39)		probably benign	Het
Mslnl	G	A	17: 25,961,908 (GRCm39)	V128M	probably damaging	Het
Nav2	A	T	7: 49,198,292 (GRCm39)		probably null	Het
Or4k1	T	C	14: 50,377,953 (GRCm39)	I48V	probably benign	Het
Or8b1b	C	A	9: 38,375,938 (GRCm39)	F200L	probably benign	Het
Pcdha11	G	A	18: 37,140,426 (GRCm39)	G685D	probably benign	Het
Pgc	A	G	17: 48,043,335 (GRCm39)	I228V	probably benign	Het
Pramel25	A	G	4: 143,519,394 (GRCm39)	S52G	probably benign	Het
Rad51	C	T	2: 118,962,049 (GRCm39)	H199Y	probably damaging	Het
Robo2	A	T	16: 74,149,407 (GRCm39)		probably benign	Het
Sap130	C	T	18: 31,844,413 (GRCm39)	T861I	probably damaging	Het
Sh3tc2	A	T	18: 62,140,844 (GRCm39)	D1061V	probably damaging	Het
Shoc1	T	C	4: 59,092,383 (GRCm39)	D266G	possibly damaging	Het
Snapc3	A	G	4: 83,336,996 (GRCm39)	E119G	probably damaging	Het
Sspo	G	A	6: 48,464,159 (GRCm39)	G3862D	probably benign	Het
Tbc1d16	G	A	11: 119,048,699 (GRCm39)	T318M	possibly damaging	Het
Thrb	T	A	14: 18,011,187 (GRCm38)	W188R	probably damaging	Het
Thsd1	T	C	8: 22,733,594 (GRCm39)	Y214H	probably damaging	Het
Tnfrsf13b	T	C	11: 61,032,264 (GRCm39)	V98A	probably benign	Het
Topbp1	T	C	9: 103,222,070 (GRCm39)	Y1314H	probably damaging	Het
Ttn	C	A	2: 76,616,150 (GRCm39)	V8271L	possibly damaging	Het
Ttn	T	C	2: 76,777,257 (GRCm39)	M1382V	probably benign	Het
Utrn	G	T	10: 12,603,584 (GRCm39)	Q599K	possibly damaging	Het
Zfp995	G	A	17: 22,098,932 (GRCm39)	T434I	probably benign	Het
Zfy1	G	T	Y: 725,518 (GRCm39)	T749K	possibly damaging	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
R1489:Mbd3	UTSW	10	80,229,740 (GRCm39)	missense	probably damaging	1.00
R1500:Mbd3	UTSW	10	80,230,420 (GRCm39)	missense	possibly damaging	0.90
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'- GTCGGGCATCTAAATTGCCTTC -3'
(R):5'- TTCTGGCTGACGAAGACTTGC -3'

Sequencing Primer
(F):5'- GGCATCTAAATTGCCTTCACTCACAG -3'
(R):5'- CCTGGGATGGGGTCATAACTTCC -3'

Posted On

2015-07-21