Mutagenetix > Incidental Mutation

Incidental Mutation 'R5890:Mecp2'

457139

Institutional Source

Beutler Lab

Gene Symbol

Mecp2

Ensembl Gene

ENSMUSG00000031393

Gene Name

methyl CpG binding protein 2

Synonyms

WBP10, D630021H01Rik, 1500041B07Rik, Mbd5

MMRRC Submission

044091-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.600) question?

Stock #

R5890 (G1)

Quality Score

222

Status

Not validated

Chromosome

Chromosomal Location

73070198-73129296 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 73079043 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 496 (V496M)

Ref Sequence

ENSEMBL: ENSMUSP00000033770 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000033770] [ENSMUST00000100750] [ENSMUST00000123362] [ENSMUST00000140399] [ENSMUST00000170481]

AlphaFold

Q9Z2D6

Predicted Effect

probably damaging
Transcript: ENSMUST00000033770
AA Change: V496M

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

SMART Domains

Protein: ENSMUSP00000033770
Gene: ENSMUSG00000031393
AA Change: V496M

Domain	Start	End	E-Value	Type
low complexity region	2	21	N/A	INTRINSIC
low complexity region	40	61	N/A	INTRINSIC
low complexity region	82	98	N/A	INTRINSIC
MBD	109	186	7.34e-36	SMART
AT_hook	202	214	5.16e0	SMART
low complexity region	248	255	N/A	INTRINSIC
AT_hook	282	294	1.2e2	SMART
low complexity region	357	420	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000100750
AA Change: V479M

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000098314
Gene: ENSMUSG00000031393
AA Change: V479M

Domain	Start	End	E-Value	Type
low complexity region	23	44	N/A	INTRINSIC
low complexity region	65	81	N/A	INTRINSIC
MBD	92	169	7.34e-36	SMART
AT_hook	185	197	5.16e0	SMART
low complexity region	231	238	N/A	INTRINSIC
AT_hook	265	277	1.2e2	SMART
low complexity region	340	403	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000123362

SMART Domains

Protein: ENSMUSP00000118842
Gene: ENSMUSG00000031393

Domain	Start	End	E-Value	Type
low complexity region	23	44	N/A	INTRINSIC
low complexity region	65	81	N/A	INTRINSIC
MBD	92	166	1.19e-21	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000140399

SMART Domains

Protein: ENSMUSP00000119947
Gene: ENSMUSG00000031393

Domain	Start	End	E-Value	Type
low complexity region	2	21	N/A	INTRINSIC
low complexity region	40	61	N/A	INTRINSIC
low complexity region	82	98	N/A	INTRINSIC
MBD	109	183	1.19e-21	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000170481
AA Change: V479M

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000127115
Gene: ENSMUSG00000031393
AA Change: V479M

Domain	Start	End	E-Value	Type
low complexity region	23	44	N/A	INTRINSIC
low complexity region	65	81	N/A	INTRINSIC
MBD	92	169	7.34e-36	SMART
AT_hook	185	197	5.16e0	SMART
low complexity region	231	238	N/A	INTRINSIC
AT_hook	265	277	1.2e2	SMART
low complexity region	340	403	N/A	INTRINSIC

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.6%
20x: 92.9%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. In contrast to other MBD family members, MECP2 is X-linked and subject to X inactivation. MECP2 is dispensible in stem cells, but is essential for embryonic development. MECP2 gene mutations are the cause of most cases of Rett syndrome, a progressive neurologic developmental disorder and one of the most common causes of mental retardation in females. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]
PHENOTYPE: Female mice homozygous or male mice hemizygous for a null allele exhibit premature death, behavioral and neurological abnormalities, abnormal nervous system phenotypes, abnormal breathing, and abnormal hearing. Heterozygous mice exhibit similar behavioral and neurological abnormalities. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc9	A	G	6: 142,550,554 (GRCm39)		probably null	Het
Acsm3	C	A	7: 119,374,457 (GRCm39)	T303N	probably benign	Het
Adamts13	A	T	2: 26,876,603 (GRCm39)	R506W	probably damaging	Het
Adck5	C	T	15: 76,477,785 (GRCm39)	T166M	probably damaging	Het
Adcy8	T	A	15: 64,687,266 (GRCm39)	I413F	probably damaging	Het
Adgrl2	A	T	3: 148,564,811 (GRCm39)	D252E	probably damaging	Het
Aldh16a1	T	A	7: 44,793,969 (GRCm39)	T636S	probably benign	Het
Ampd1	C	A	3: 102,997,391 (GRCm39)	F264L	probably damaging	Het
Arhgap17	T	C	7: 122,885,981 (GRCm39)		probably benign	Het
Babam2	A	G	5: 32,222,151 (GRCm39)		probably benign	Het
Bltp2	C	T	11: 78,164,096 (GRCm39)	Q40*	probably null	Het
Bod1l	T	A	5: 41,977,921 (GRCm39)	E1131V	probably benign	Het
Cbs	C	T	17: 31,832,193 (GRCm39)	V553M	probably damaging	Het
Cd72	T	C	4: 43,454,475 (GRCm39)	K18R	probably damaging	Het
Cep89	A	G	7: 35,128,587 (GRCm39)	Y580C	probably damaging	Het
Chrnb1	T	A	11: 69,683,555 (GRCm39)	I264F	possibly damaging	Het
Cntf	A	G	19: 12,741,357 (GRCm39)	W168R	probably damaging	Het
Cxxc1	T	A	18: 74,354,237 (GRCm39)	D648E	possibly damaging	Het
Cyp2c68	A	T	19: 39,700,936 (GRCm39)	L294Q	probably damaging	Het
Dab2ip	T	C	2: 35,605,414 (GRCm39)	S532P	probably damaging	Het
Defb3	G	A	8: 19,345,200 (GRCm39)	C52Y	probably damaging	Het
Dennd5a	T	G	7: 109,533,428 (GRCm39)	E114A	probably benign	Het
Dnah12	T	C	14: 26,428,039 (GRCm39)	F222L	probably benign	Het
Dock9	A	C	14: 121,905,820 (GRCm39)		probably null	Het
Fras1	A	T	5: 96,793,807 (GRCm39)	H1043L	probably benign	Het
Gamt	C	A	10: 80,095,741 (GRCm39)	R63L	possibly damaging	Het
Gm1527	A	G	3: 28,969,544 (GRCm39)	H298R	probably benign	Het
Gphb5	C	T	12: 75,462,596 (GRCm39)		probably null	Het
Greb1	A	T	12: 16,783,422 (GRCm39)	V104D	possibly damaging	Het
Hck	A	G	2: 152,970,996 (GRCm39)	D86G	probably damaging	Het
Jhy	T	A	9: 40,833,958 (GRCm39)	K321*	probably null	Het
Kcna5	C	T	6: 126,511,699 (GRCm39)	R143H	probably damaging	Het
Kif19a	G	T	11: 114,680,264 (GRCm39)	W867L	possibly damaging	Het
Map3k4	G	A	17: 12,490,303 (GRCm39)	A376V	probably damaging	Het
Mars1	A	T	10: 127,133,914 (GRCm39)	M661K	probably benign	Het
Mfsd2b	A	T	12: 4,917,651 (GRCm39)	C132S	probably damaging	Het
Mfsd4a	T	C	1: 131,966,666 (GRCm39)	Y356C	probably damaging	Het
Mif4gd	G	T	11: 115,500,188 (GRCm39)	A89E	probably benign	Het
Mkln1	A	T	6: 31,467,482 (GRCm39)	E593D	probably benign	Het
Mlh1	G	T	9: 111,057,563 (GRCm39)	N749K	possibly damaging	Het
Mrgprb2	T	A	7: 48,201,707 (GRCm39)	*339C	probably null	Het
Nphp4	T	C	4: 152,631,536 (GRCm39)	V812A	probably benign	Het
Nrcam	G	T	12: 44,623,554 (GRCm39)	V1048L	probably benign	Het
Obsl1	G	A	1: 75,470,503 (GRCm39)	A856V	probably damaging	Het
Osgepl1	T	A	1: 53,357,326 (GRCm39)	F163I	probably damaging	Het
Pcdha6	C	A	18: 37,102,121 (GRCm39)	T438K	possibly damaging	Het
Pcdhb20	A	T	18: 37,638,286 (GRCm39)	M271L	probably benign	Het
Phip	T	C	9: 82,789,005 (GRCm39)	T770A	probably benign	Het
Ppm1d	A	G	11: 85,217,734 (GRCm39)	T166A	probably damaging	Het
Ptprf	A	T	4: 118,081,932 (GRCm39)	I1102K	probably benign	Het
Sbsn	T	C	7: 30,452,692 (GRCm39)	V569A	possibly damaging	Het
Skida1	T	A	2: 18,050,814 (GRCm39)		probably benign	Het
Smg1	T	A	7: 117,789,809 (GRCm39)		probably benign	Het
Sorcs2	A	G	5: 36,386,535 (GRCm39)	Y168H	probably damaging	Het
Sufu	A	T	19: 46,443,172 (GRCm39)		probably null	Het
Tbc1d24	A	T	17: 24,404,500 (GRCm39)	W215R	probably damaging	Het
Tenm4	T	C	7: 96,552,067 (GRCm39)	L2502P	probably damaging	Het
Tgm4	A	T	9: 122,890,703 (GRCm39)	E10V	probably damaging	Het
Trip11	T	C	12: 101,852,231 (GRCm39)	E611G	probably damaging	Het
Ttn	C	A	2: 76,540,243 (GRCm39)	A34248S	possibly damaging	Het
Ube3a	T	A	7: 58,921,776 (GRCm39)	N49K	probably damaging	Het
Ube3c	A	G	5: 29,863,290 (GRCm39)	D855G	possibly damaging	Het
Ugt8a	A	G	3: 125,669,202 (GRCm39)	S301P	probably benign	Het
Wdfy4	T	A	14: 32,824,534 (GRCm39)	N1295I	possibly damaging	Het
Wdr47	G	T	3: 108,517,328 (GRCm39)	G43C	probably damaging	Het
Wdtc1	A	C	4: 133,021,673 (GRCm39)	L601W	unknown	Het
Zfp236	A	G	18: 82,658,276 (GRCm39)	F614S	possibly damaging	Het
Zfp637	T	A	6: 117,822,047 (GRCm39)	D58E	possibly damaging	Het

Other mutations in Mecp2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01520:Mecp2	APN	X	73,079,447 (GRCm39)	missense	possibly damaging	0.53
R1387:Mecp2	UTSW	X	73,079,394 (GRCm39)	missense	possibly damaging	0.93
R1888:Mecp2	UTSW	X	73,080,781 (GRCm39)	missense	probably damaging	1.00
R1888:Mecp2	UTSW	X	73,080,781 (GRCm39)	missense	probably damaging	1.00
R1891:Mecp2	UTSW	X	73,080,781 (GRCm39)	missense	probably damaging	1.00
R1894:Mecp2	UTSW	X	73,080,781 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCAACCTGACTGTGCTTGTC -3'
(R):5'- AGGCTCACTGGAAAGCGATG -3'

Sequencing Primer
(F):5'- GTGCTTGTCGGTAAGAAAAACATCC -3'
(R):5'- TGGCTGCCCCAAGGAGC -3'

Posted On

2017-02-15