Mutagenetix > Incidental Mutation

Incidental Mutation 'R5579:Mbd5'

438238

Institutional Source

Beutler Lab

Gene Symbol

Mbd5

Ensembl Gene

ENSMUSG00000036792

Gene Name

methyl-CpG binding domain protein 5

Synonyms

C030040A15Rik, OTTMUSG00000012483, 9430004D19Rik

MMRRC Submission

043267-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5579 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

48949508-49325405 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 49272814 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 1103 (T1103A)

Ref Sequence

ENSEMBL: ENSMUSP00000036847 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047413] [ENSMUST00000112754] [ENSMUST00000132717]

AlphaFold

B1AYB6

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047413
AA Change: T1103A

PolyPhen 2 Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000036847
Gene: ENSMUSG00000036792
AA Change: T1103A

Domain	Start	End	E-Value	Type
low complexity region	3	15	N/A	INTRINSIC
Blast:MBD	24	77	9e-11	BLAST
low complexity region	332	342	N/A	INTRINSIC
low complexity region	429	443	N/A	INTRINSIC
low complexity region	459	467	N/A	INTRINSIC
low complexity region	499	512	N/A	INTRINSIC
low complexity region	535	546	N/A	INTRINSIC
low complexity region	571	613	N/A	INTRINSIC
low complexity region	699	719	N/A	INTRINSIC
low complexity region	841	852	N/A	INTRINSIC
low complexity region	912	932	N/A	INTRINSIC
low complexity region	934	948	N/A	INTRINSIC
low complexity region	992	1010	N/A	INTRINSIC
low complexity region	1020	1035	N/A	INTRINSIC
low complexity region	1112	1136	N/A	INTRINSIC
low complexity region	1173	1184	N/A	INTRINSIC
low complexity region	1206	1229	N/A	INTRINSIC
low complexity region	1552	1562	N/A	INTRINSIC
SCOP:d1khca_	1615	1718	2e-17	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112754

SMART Domains

Protein: ENSMUSP00000108374
Gene: ENSMUSG00000036792

Domain	Start	End	E-Value	Type
low complexity region	3	15	N/A	INTRINSIC
Blast:MBD	24	77	8e-11	BLAST
low complexity region	332	342	N/A	INTRINSIC
low complexity region	429	443	N/A	INTRINSIC
low complexity region	459	467	N/A	INTRINSIC
low complexity region	499	512	N/A	INTRINSIC
low complexity region	535	546	N/A	INTRINSIC
low complexity region	571	613	N/A	INTRINSIC
low complexity region	699	719	N/A	INTRINSIC
low complexity region	841	852	N/A	INTRINSIC
low complexity region	912	932	N/A	INTRINSIC
low complexity region	934	948	N/A	INTRINSIC
low complexity region	976	999	N/A	INTRINSIC
low complexity region	1322	1332	N/A	INTRINSIC
SCOP:d1khca_	1385	1488	4e-17	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000122841
AA Change: T842A

SMART Domains

Protein: ENSMUSP00000119317
Gene: ENSMUSG00000036792
AA Change: T842A

Domain	Start	End	E-Value	Type
low complexity region	72	82	N/A	INTRINSIC
low complexity region	169	183	N/A	INTRINSIC
low complexity region	199	207	N/A	INTRINSIC
low complexity region	239	252	N/A	INTRINSIC
low complexity region	275	286	N/A	INTRINSIC
low complexity region	311	353	N/A	INTRINSIC
low complexity region	439	459	N/A	INTRINSIC
low complexity region	581	592	N/A	INTRINSIC
low complexity region	652	672	N/A	INTRINSIC
low complexity region	674	688	N/A	INTRINSIC
low complexity region	732	750	N/A	INTRINSIC
low complexity region	760	775	N/A	INTRINSIC
low complexity region	852	876	N/A	INTRINSIC
low complexity region	913	924	N/A	INTRINSIC
low complexity region	946	969	N/A	INTRINSIC
low complexity region	1011	1022	N/A	INTRINSIC
low complexity region	1056	1064	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000132717
AA Change: T211A

PolyPhen 2 Score 0.128 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000137021
Gene: ENSMUSG00000036792
AA Change: T211A

Domain	Start	End	E-Value	Type
low complexity region	20	40	N/A	INTRINSIC
low complexity region	42	56	N/A	INTRINSIC
low complexity region	100	118	N/A	INTRINSIC
low complexity region	128	143	N/A	INTRINSIC
low complexity region	220	244	N/A	INTRINSIC
low complexity region	281	292	N/A	INTRINSIC
low complexity region	314	337	N/A	INTRINSIC
low complexity region	379	390	N/A	INTRINSIC
low complexity region	424	432	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000199257

Coding Region Coverage

1x: 99.9%
3x: 99.8%
10x: 98.9%
20x: 97.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the methyl-CpG-binding domain (MBD) family. The MBD consists of about 70 residues and is the minimal region required for a methyl-CpG-binding protein binding specifically to methylated DNA. In addition to the MBD domain, this protein contains a PWWP domain (Pro-Trp-Trp-Pro motif), which consists of 100-150 amino acids and is found in numerous proteins that are involved in cell division, growth and differentiation. Mutations in this gene cause mental retardation autosomal dominant type 1. Haploinsufficiency of this gene is associated with a syndrome involving microcephaly, intellectual disabilities, severe speech impairment, and seizures. Alternatively spliced transcript variants have been found, but their full-length nature is not determined. [provided by RefSeq, Mar 2010]
PHENOTYPE: Mice homozgyous for a knock-out allele exhibit severe postnatal growth retardation leading to lethality by P22, decreased body, brain and liver weights, reduced IGF-I and GH levels, and abnormal glucose homeostasis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 114 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810403A07Rik	T	C	3: 88,700,275	S345P	probably benign	Het
6430573F11Rik	T	C	8: 36,512,041	V266A	probably benign	Het
Abca3	G	T	17: 24,376,729	C352F	probably damaging	Het
Abce1	A	T	8: 79,700,586	I237N	possibly damaging	Het
Acrbp	A	G	6: 125,061,099	D421G	probably benign	Het
Adam8	T	A	7: 139,988,984	Y201F	probably benign	Het
Adgrf1	T	A	17: 43,311,064	C731S	probably damaging	Het
AF067063	T	A	13: 119,828,415	M82L	probably benign	Het
Akap8l	A	T	17: 32,321,942	I529N	probably damaging	Het
Akap9	G	A	5: 4,064,714	G114D	possibly damaging	Het
Alox12b	T	A	11: 69,162,932	D158E	probably benign	Het
Ankrd11	A	G	8: 122,884,231	S2639P	probably damaging	Het
Ankrd42	T	C	7: 92,590,182	Y466C	possibly damaging	Het
Apobr	T	C	7: 126,587,675	I786T	probably benign	Het
Arhgef12	C	T	9: 43,010,193	G329R	probably benign	Het
Btnl1	T	C	17: 34,381,552		probably null	Het
Ccdc174	A	G	6: 91,881,350		probably null	Het
Ccdc183	T	C	2: 25,615,422	D177G	possibly damaging	Het
Cd14	A	G	18: 36,726,235	Y56H	probably benign	Het
Cep162	G	A	9: 87,203,671	A1200V	probably benign	Het
Clic3	T	C	2: 25,458,307	L128P	probably damaging	Het
Cntnap5b	A	T	1: 100,383,399	Q539L	probably benign	Het
Cntnap5b	A	T	1: 100,383,395	R538*	probably null	Het
Coq7	A	T	7: 118,517,335	N214K	unknown	Het
Cramp1l	G	A	17: 24,973,113	H1018Y	possibly damaging	Het
Crtac1	T	A	19: 42,304,806	D288V	probably damaging	Het
Dab2ip	C	T	2: 35,715,327	R132*	probably null	Het
Dis3l	C	A	9: 64,330,835	C125F	probably benign	Het
Dnmt1	A	T	9: 20,920,205	V543D	probably damaging	Het
Dock9	A	T	14: 121,599,695	L67Q	probably damaging	Het
Ehbp1	A	T	11: 22,137,846	S413T	probably damaging	Het
Endov	A	G	11: 119,505,097	I158V	probably benign	Het
Epb41l4b	A	G	4: 57,064,802	V469A	possibly damaging	Het
Etf1	G	A	18: 34,913,601	P119S	probably damaging	Het
Fam135a	A	G	1: 24,029,727	L491P	possibly damaging	Het
Fancd2	A	T	6: 113,560,051		probably null	Het
Fank1	T	A	7: 133,869,329		probably null	Het
Fbxo18	A	G	2: 11,748,993	I846T	probably damaging	Het
Gas2l3	T	C	10: 89,414,066	T397A	probably benign	Het
Gga1	T	C	15: 78,893,188	V513A	probably damaging	Het
Ggt1	T	C	10: 75,585,948	V543A	probably damaging	Het
Gm11596	A	T	11: 99,792,891	C134*	probably null	Het
Gnal	C	T	18: 67,088,771	R82C	unknown	Het
Hat1	T	C	2: 71,410,238	V92A	possibly damaging	Het
Icosl	C	T	10: 78,073,763	R181C	probably damaging	Het
Ift46	A	G	9: 44,786,863	M208V	possibly damaging	Het
Ighv1-26	T	C	12: 114,788,599	K42E	possibly damaging	Het
Ipo5	A	G	14: 120,938,613	K617E	probably benign	Het
Irx5	A	G	8: 92,359,913	D208G	probably benign	Het
Itgal	T	G	7: 127,306,929	V397G	probably benign	Het
Itpr2	G	A	6: 146,173,366	R2297*	probably null	Het
Itpr3	A	G	17: 27,113,519	D1779G	probably damaging	Het
Krt4	T	A	15: 101,921,234	E286D	probably benign	Het
Loxl4	C	T	19: 42,604,290	G317E	probably damaging	Het
Mapk6	T	G	9: 75,388,062	H718P	possibly damaging	Het
Mark2	A	C	19: 7,282,816	V14G	probably damaging	Het
Mcph1	A	G	8: 18,632,293	E482G	probably benign	Het
Mme	G	A	3: 63,348,645	E509K	probably damaging	Het
Mrgbp	A	G	2: 180,585,483	T204A	probably damaging	Het
Mycbp2	A	T	14: 103,291,333	F430I	probably damaging	Het
Myo6	A	G	9: 80,217,720	D27G	probably damaging	Het
Ncoa6	A	G	2: 155,406,677	L1569S	probably damaging	Het
Ndc1	T	A	4: 107,380,704	F235Y	possibly damaging	Het
Nmur2	A	T	11: 56,033,009	S240T	probably benign	Het
Olfr1176	A	T	2: 88,340,413	I283F	possibly damaging	Het
Olfr301	T	A	7: 86,412,726	Y121*	probably null	Het
Olfr608	G	A	7: 103,470,914	V292M	probably damaging	Het
Osbpl1a	G	T	18: 12,841,192	A62E	probably damaging	Het
Osbpl1a	A	C	18: 12,892,262	S333A	probably benign	Het
Otud4	C	T	8: 79,664,108	T417I	probably benign	Het
Pagr1a	T	C	7: 127,015,442	E197G	probably damaging	Het
Pcdh18	T	C	3: 49,744,977	Q1012R	probably damaging	Het
Pcdhgb5	A	C	18: 37,731,637	I162L	probably benign	Het
Pdpr	T	A	8: 111,123,816	Y462N	probably damaging	Het
Pkhd1	A	T	1: 20,523,142	H1582Q	probably damaging	Het
Polr1b	A	G	2: 129,110,108	K352R	probably damaging	Het
Poteg	G	A	8: 27,448,037	V12M	probably damaging	Het
Pou2f1	A	C	1: 165,915,162	V54G	probably damaging	Het
Ppme1	A	G	7: 100,344,975	L177P	probably damaging	Het
Prkce	A	G	17: 86,619,948	D550G	probably damaging	Het
Prrc2c	A	G	1: 162,680,758		probably null	Het
Ptpn22	A	G	3: 103,882,139		probably null	Het
Rabif	G	A	1: 134,506,205	V86M	probably damaging	Het
Rbm25	T	A	12: 83,668,507	M484K	probably benign	Het
Rcn2	G	A	9: 56,057,429	A224T	probably benign	Het
Rexo5	T	A	7: 119,834,403		probably null	Het
Rnase1	A	T	14: 51,145,762	I45N	probably benign	Het
Rnmt	T	A	18: 68,306,115	D98E	possibly damaging	Het
Rprd2	A	G	3: 95,785,059	F188L	probably damaging	Het
Scube2	G	A	7: 109,810,737	T643M	probably damaging	Het
Slc7a15	T	C	12: 8,539,344	I68V	probably benign	Het
Slco1a5	A	T	6: 142,242,125	V496D	possibly damaging	Het
Slitrk6	T	G	14: 110,751,217	S353R	possibly damaging	Het
Smpd5	T	A	15: 76,295,125	I53K	possibly damaging	Het
Tas2r108	T	C	6: 40,494,087	S166P	probably benign	Het
Tecpr1	C	A	5: 144,214,344	V245L	possibly damaging	Het
Tenm3	G	T	8: 48,236,764	N1929K	probably damaging	Het
Tigd5	T	G	15: 75,911,025	F412C	probably damaging	Het
Timm17a	A	T	1: 135,306,188	S74T	possibly damaging	Het
Tle1	A	T	4: 72,139,808	L60Q	probably damaging	Het
Tmem132d	T	C	5: 127,796,000	E515G	possibly damaging	Het
Tmem65	T	C	15: 58,794,397	N115S	probably benign	Het
Trmt5	C	A	12: 73,281,652	R259L	possibly damaging	Het
Ttc37	T	C	13: 76,185,200	W25R	probably damaging	Het
Vmn2r50	A	T	7: 10,050,089	W153R	probably benign	Het
Vwa3a	T	G	7: 120,768,173	S184A	probably benign	Het
Zbtb25	A	G	12: 76,349,164	L428P	possibly damaging	Het
Zbtb49	C	T	5: 38,200,816	D698N	probably damaging	Het
Zbtb8os	T	G	4: 129,340,735	D35E	probably damaging	Het
Zfp316	T	C	5: 143,264,491	T56A	unknown	Het
Zfp334	A	T	2: 165,380,487	C545*	probably null	Het
Zmiz1	C	A	14: 25,644,856	S247R	probably damaging	Het
Zscan18	A	G	7: 12,775,381		probably benign	Het
Zzef1	T	C	11: 72,900,637	V2189A	probably damaging	Het

Other mutations in Mbd5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01385:Mbd5	APN	2	49250221	missense	possibly damaging	0.92
IGL01481:Mbd5	APN	2	49278939	missense	possibly damaging	0.90
IGL01639:Mbd5	APN	2	49272308	missense	probably damaging	0.98
IGL02063:Mbd5	APN	2	49274767	missense	probably damaging	1.00
IGL02157:Mbd5	APN	2	49278975	missense	probably benign
IGL02510:Mbd5	APN	2	49257029	missense	probably benign	0.05
IGL02932:Mbd5	APN	2	49279448	missense	possibly damaging	0.66
IGL02973:Mbd5	APN	2	49313709	missense	probably damaging	0.99
IGL03189:Mbd5	APN	2	49257751	missense	probably damaging	0.98
BB003:Mbd5	UTSW	2	49256323	missense	probably damaging	0.99
BB013:Mbd5	UTSW	2	49256323	missense	probably damaging	0.99
F5770:Mbd5	UTSW	2	49316410	missense	probably damaging	0.99
R0391:Mbd5	UTSW	2	49272416	missense	possibly damaging	0.90
R0427:Mbd5	UTSW	2	49279079	missense	probably benign	0.27
R0544:Mbd5	UTSW	2	49257209	missense	possibly damaging	0.54
R0883:Mbd5	UTSW	2	49256689	missense	possibly damaging	0.94
R1072:Mbd5	UTSW	2	49257191	missense	probably damaging	1.00
R1099:Mbd5	UTSW	2	49258144	missense	probably benign	0.06
R1400:Mbd5	UTSW	2	49274776	critical splice donor site	probably null
R1497:Mbd5	UTSW	2	49257381	missense	possibly damaging	0.73
R1552:Mbd5	UTSW	2	49272934	missense	probably damaging	0.99
R1675:Mbd5	UTSW	2	49256218	missense	possibly damaging	0.90
R1710:Mbd5	UTSW	2	49257032	missense	probably benign	0.10
R2085:Mbd5	UTSW	2	49279311	missense	possibly damaging	0.90
R2252:Mbd5	UTSW	2	49257686	missense	probably damaging	1.00
R2473:Mbd5	UTSW	2	49279341	missense	probably benign	0.06
R3966:Mbd5	UTSW	2	49272070	missense	possibly damaging	0.46
R4278:Mbd5	UTSW	2	49272293	missense	probably damaging	0.97
R4348:Mbd5	UTSW	2	49256327	missense	probably benign
R4366:Mbd5	UTSW	2	49272966	missense	probably damaging	0.99
R4428:Mbd5	UTSW	2	49279764	missense	possibly damaging	0.94
R4556:Mbd5	UTSW	2	49279394	missense	probably damaging	1.00
R4600:Mbd5	UTSW	2	49257197	missense	probably benign	0.31
R4689:Mbd5	UTSW	2	49258279	missense	possibly damaging	0.46
R4707:Mbd5	UTSW	2	49250156	missense	probably damaging	0.99
R4718:Mbd5	UTSW	2	49256402	missense	possibly damaging	0.66
R4773:Mbd5	UTSW	2	49274611	missense	probably damaging	1.00
R4846:Mbd5	UTSW	2	49256997	missense	probably damaging	1.00
R5015:Mbd5	UTSW	2	49258196	missense	possibly damaging	0.92
R5059:Mbd5	UTSW	2	49256455	missense	probably damaging	0.96
R5268:Mbd5	UTSW	2	49272094	missense	possibly damaging	0.92
R5479:Mbd5	UTSW	2	49272905	missense	probably damaging	0.99
R5591:Mbd5	UTSW	2	49274669	missense	probably damaging	1.00
R5876:Mbd5	UTSW	2	49274645	missense	probably damaging	0.98
R5886:Mbd5	UTSW	2	49272452	missense	probably damaging	1.00
R5973:Mbd5	UTSW	2	49272389	missense	probably benign	0.23
R6935:Mbd5	UTSW	2	49279812	missense	probably damaging	0.97
R7317:Mbd5	UTSW	2	49279743	missense	probably benign
R7366:Mbd5	UTSW	2	49274568	missense	probably benign
R7385:Mbd5	UTSW	2	49272449	missense	probably benign	0.01
R7402:Mbd5	UTSW	2	49257554	missense	probably damaging	1.00
R7462:Mbd5	UTSW	2	49257880	missense	possibly damaging	0.52
R7549:Mbd5	UTSW	2	49251343	missense	probably damaging	0.97
R7916:Mbd5	UTSW	2	49257106	missense	probably damaging	0.99
R7926:Mbd5	UTSW	2	49256323	missense	probably damaging	0.99
R7960:Mbd5	UTSW	2	49279784	critical splice donor site	probably null
R8273:Mbd5	UTSW	2	49278879	missense	probably damaging	0.99
R8909:Mbd5	UTSW	2	49279221	missense	probably benign	0.13
R9121:Mbd5	UTSW	2	49258090	missense	possibly damaging	0.59
R9149:Mbd5	UTSW	2	49251376	missense	probably damaging	0.98
R9443:Mbd5	UTSW	2	49256700	missense	probably damaging	0.99
R9506:Mbd5	UTSW	2	49272907	missense	probably damaging	0.96
R9566:Mbd5	UTSW	2	49279509	missense	probably damaging	0.96
R9756:Mbd5	UTSW	2	49279271	missense	probably benign	0.07
V7583:Mbd5	UTSW	2	49316410	missense	probably damaging	0.99
Z1176:Mbd5	UTSW	2	49279308	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- TGCCAAGCAATCAGTCAGAC -3'
(R):5'- AAGTAGCTGTGGCACCATAGAG -3'

Sequencing Primer
(F):5'- TCAGTCAGACAACAGCCGAG -3'
(R):5'- AGCTGTGGCACCATAGAGTTACTG -3'

Posted On

2016-10-26