Mutagenetix > Incidental Mutation

Incidental Mutation 'R6973:Chd4'

543710

Institutional Source

Beutler Lab

Gene Symbol

Chd4

Ensembl Gene

ENSMUSG00000063870

Gene Name

chromodomain helicase DNA binding protein 4

Synonyms

D6Ertd380e, 9530019N15Rik, Mi-2beta

MMRRC Submission

045083-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6973 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

125073144-125107554 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 125099825 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 1666 (N1666D)

Ref Sequence

ENSEMBL: ENSMUSP00000108011 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056889] [ENSMUST00000112390] [ENSMUST00000112392] [ENSMUST00000124317]

AlphaFold

Q6PDQ2

Predicted Effect

possibly damaging
Transcript: ENSMUST00000056889
AA Change: N1679D

PolyPhen 2 Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000060054
Gene: ENSMUSG00000063870
AA Change: N1679D

Domain	Start	End	E-Value	Type
low complexity region	29	45	N/A	INTRINSIC
low complexity region	49	69	N/A	INTRINSIC
low complexity region	80	92	N/A	INTRINSIC
low complexity region	107	144	N/A	INTRINSIC
Pfam:CHDNT	156	210	7.7e-35	PFAM
low complexity region	217	249	N/A	INTRINSIC
low complexity region	271	291	N/A	INTRINSIC
low complexity region	296	318	N/A	INTRINSIC
low complexity region	321	347	N/A	INTRINSIC
PHD	365	408	7.17e-15	SMART
RING	366	407	7.46e-1	SMART
low complexity region	424	443	N/A	INTRINSIC
PHD	444	487	4.41e-15	SMART
RING	445	486	2.63e0	SMART
CHROMO	492	572	8.11e-17	SMART
CHROMO	613	670	1.98e-11	SMART
low complexity region	675	694	N/A	INTRINSIC
DEXDc	715	927	2.73e-37	SMART
low complexity region	1044	1056	N/A	INTRINSIC
HELICc	1073	1157	7.61e-27	SMART
DUF1087	1282	1346	5.56e-33	SMART
DUF1086	1359	1516	4.05e-108	SMART
low complexity region	1526	1540	N/A	INTRINSIC
low complexity region	1560	1578	N/A	INTRINSIC
low complexity region	1590	1633	N/A	INTRINSIC
low complexity region	1635	1653	N/A	INTRINSIC
low complexity region	1661	1674	N/A	INTRINSIC
Pfam:CHDCT2	1727	1899	1.9e-98	PFAM
low complexity region	1903	1915	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000112390
AA Change: N1686D

PolyPhen 2 Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000108009
Gene: ENSMUSG00000063870
AA Change: N1686D

Domain	Start	End	E-Value	Type
low complexity region	29	45	N/A	INTRINSIC
low complexity region	49	69	N/A	INTRINSIC
low complexity region	87	99	N/A	INTRINSIC
low complexity region	114	151	N/A	INTRINSIC
Pfam:CHDNT	164	217	2e-28	PFAM
low complexity region	224	256	N/A	INTRINSIC
low complexity region	278	298	N/A	INTRINSIC
low complexity region	303	325	N/A	INTRINSIC
low complexity region	328	354	N/A	INTRINSIC
PHD	372	415	7.17e-15	SMART
RING	373	414	7.46e-1	SMART
low complexity region	431	450	N/A	INTRINSIC
PHD	451	494	4.41e-15	SMART
RING	452	493	2.63e0	SMART
CHROMO	499	579	8.11e-17	SMART
CHROMO	620	677	1.98e-11	SMART
low complexity region	682	701	N/A	INTRINSIC
DEXDc	722	934	2.73e-37	SMART
low complexity region	1051	1063	N/A	INTRINSIC
HELICc	1080	1164	7.61e-27	SMART
DUF1087	1289	1353	5.56e-33	SMART
DUF1086	1366	1523	4.05e-108	SMART
low complexity region	1533	1547	N/A	INTRINSIC
low complexity region	1567	1585	N/A	INTRINSIC
low complexity region	1597	1640	N/A	INTRINSIC
low complexity region	1642	1660	N/A	INTRINSIC
low complexity region	1668	1681	N/A	INTRINSIC
Pfam:CHDCT2	1735	1906	4.3e-90	PFAM
low complexity region	1910	1922	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000112392
AA Change: N1666D

PolyPhen 2 Score 0.528 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000108011
Gene: ENSMUSG00000063870
AA Change: N1666D

Domain	Start	End	E-Value	Type
low complexity region	29	45	N/A	INTRINSIC
low complexity region	49	69	N/A	INTRINSIC
low complexity region	80	92	N/A	INTRINSIC
low complexity region	107	144	N/A	INTRINSIC
Pfam:CHDNT	156	210	1.1e-34	PFAM
low complexity region	217	249	N/A	INTRINSIC
low complexity region	271	291	N/A	INTRINSIC
low complexity region	296	318	N/A	INTRINSIC
low complexity region	321	347	N/A	INTRINSIC
PHD	352	395	7.17e-15	SMART
RING	353	394	7.46e-1	SMART
low complexity region	411	430	N/A	INTRINSIC
PHD	431	474	4.41e-15	SMART
RING	432	473	2.63e0	SMART
CHROMO	479	559	8.11e-17	SMART
CHROMO	600	657	1.98e-11	SMART
low complexity region	662	681	N/A	INTRINSIC
DEXDc	702	914	2.73e-37	SMART
low complexity region	1031	1043	N/A	INTRINSIC
HELICc	1060	1144	7.61e-27	SMART
DUF1087	1269	1333	5.56e-33	SMART
DUF1086	1346	1503	4.05e-108	SMART
low complexity region	1513	1527	N/A	INTRINSIC
low complexity region	1547	1565	N/A	INTRINSIC
low complexity region	1577	1620	N/A	INTRINSIC
low complexity region	1622	1640	N/A	INTRINSIC
low complexity region	1648	1661	N/A	INTRINSIC
Pfam:CHDCT2	1714	1886	2.8e-98	PFAM
low complexity region	1890	1902	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000124317

SMART Domains

Protein: ENSMUSP00000120704
Gene: ENSMUSG00000063870

Domain	Start	End	E-Value	Type
PDB:3MWY\|W	1	137	2e-13	PDB
DUF1087	141	205	5.56e-33	SMART
low complexity region	209	221	N/A	INTRINSIC
DUF1086	246	403	4.05e-108	SMART
low complexity region	413	427	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

95% (37/39)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The product of this gene belongs to the SNF2/RAD54 helicase family. It represents the main component of the nucleosome remodeling and deacetylase complex and plays an important role in epigenetic transcriptional repression. Patients with dermatomyositis develop antibodies against this protein. Somatic mutations in this gene are associated with serous endometrial tumors. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit embryonic lethality between E3.5 and E4.5, absent blastocoele failure of trophectoderm function and increased apoptosis in blastocysts. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl3	T	C	4: 144,182,760 (GRCm39)	Y236C	probably benign	Het
Adamts12	T	A	15: 11,331,866 (GRCm39)	C1461*	probably null	Het
Akap9	A	G	5: 4,096,699 (GRCm39)	N2525D	possibly damaging	Het
Atp6v1c1	A	G	15: 38,690,794 (GRCm39)	N315S	probably damaging	Het
B3gnt7	G	A	1: 86,233,109 (GRCm39)	M1I	probably null	Het
C2cd4d	G	T	3: 94,271,130 (GRCm39)	R132L	probably damaging	Het
Cd244a	A	G	1: 171,401,775 (GRCm39)	Y167C	probably damaging	Het
Cubn	A	G	2: 13,386,648 (GRCm39)	I1539T	possibly damaging	Het
Dcdc2a	A	T	13: 25,304,372 (GRCm39)		probably benign	Het
Dgka	C	T	10: 128,565,463 (GRCm39)		probably null	Het
Ephb4	T	G	5: 137,368,066 (GRCm39)	V737G	probably damaging	Het
Etv2	T	C	7: 30,334,167 (GRCm39)	N189D	probably benign	Het
Exoc4	G	T	6: 33,556,965 (GRCm39)	C490F	probably damaging	Het
Gatad1	T	C	5: 3,693,540 (GRCm39)	R210G	probably benign	Het
Gpbp1l1	A	G	4: 116,438,479 (GRCm39)	M192V	possibly damaging	Het
Ireb2	A	G	9: 54,789,671 (GRCm39)	K115R	probably benign	Het
Mybpc1	T	C	10: 88,396,223 (GRCm39)	E208G	possibly damaging	Het
Nfic	C	A	10: 81,256,191 (GRCm39)	A158S	probably benign	Het
Nos3	A	T	5: 24,585,241 (GRCm39)	I798L	probably benign	Het
Ntrk1	A	T	3: 87,691,288 (GRCm39)	L292Q	probably damaging	Het
Or52h7	G	A	7: 104,214,183 (GRCm39)	V252I	probably benign	Het
Or8u3-ps	C	T	2: 85,953,198 (GRCm39)	T310I	probably benign	Het
Pcdhb2	G	C	18: 37,429,416 (GRCm39)	R463P	probably benign	Het
Pcdhgb6	A	T	18: 37,875,526 (GRCm39)	D78V	possibly damaging	Het
Peg10	CATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAGGATC	CATC	6: 4,756,431 (GRCm39)		probably benign	Het
Prelid3b	C	A	2: 174,311,155 (GRCm39)	W59L	probably benign	Het
Prex2	T	G	1: 11,182,967 (GRCm39)	S405R	probably damaging	Het
Rp1	G	A	1: 4,422,217 (GRCm39)	Q248*	probably null	Het
Rspo4	T	A	2: 151,709,735 (GRCm39)	C47S	probably damaging	Het
Ryr3	C	A	2: 112,596,656 (GRCm39)	M2499I	probably damaging	Het
Smarca5	A	G	8: 81,431,380 (GRCm39)	Y946H	probably damaging	Het
Spata31d1e	A	G	13: 59,890,521 (GRCm39)	I433T	probably benign	Het
Tcn2	T	C	11: 3,867,649 (GRCm39)	*431W	probably null	Het
Tert	A	G	13: 73,776,107 (GRCm39)	E286G	probably benign	Het
Tnni3	A	G	7: 4,521,416 (GRCm39)	I196T	possibly damaging	Het
Unc79	T	C	12: 102,964,699 (GRCm39)	I49T	possibly damaging	Het
Zfp687	A	G	3: 94,916,688 (GRCm39)	S813P	possibly damaging	Het
Znfx1	T	A	2: 166,898,681 (GRCm39)	H81L	probably benign	Het

Other mutations in Chd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00573:Chd4	APN	6	125,086,860 (GRCm39)	missense	probably damaging	1.00
IGL00917:Chd4	APN	6	125,081,909 (GRCm39)	missense	possibly damaging	0.95
IGL01088:Chd4	APN	6	125,099,431 (GRCm39)	unclassified	probably benign
IGL02005:Chd4	APN	6	125,105,779 (GRCm39)	missense	possibly damaging	0.71
IGL02405:Chd4	APN	6	125,074,190 (GRCm39)	missense	probably benign	0.06
IGL02707:Chd4	APN	6	125,085,730 (GRCm39)	missense	probably damaging	1.00
IGL02976:Chd4	APN	6	125,098,331 (GRCm39)	missense	probably damaging	1.00
IGL03001:Chd4	APN	6	125,078,529 (GRCm39)	missense	possibly damaging	0.93
FR4304:Chd4	UTSW	6	125,099,107 (GRCm39)	unclassified	probably benign
FR4589:Chd4	UTSW	6	125,099,102 (GRCm39)	unclassified	probably benign
FR4589:Chd4	UTSW	6	125,099,096 (GRCm39)	missense	probably benign	0.02
FR4737:Chd4	UTSW	6	125,099,094 (GRCm39)	unclassified	probably benign
FR4976:Chd4	UTSW	6	125,099,094 (GRCm39)	unclassified	probably benign
R0311:Chd4	UTSW	6	125,078,628 (GRCm39)	missense	probably benign	0.15
R0414:Chd4	UTSW	6	125,084,443 (GRCm39)	missense	probably damaging	1.00
R0647:Chd4	UTSW	6	125,086,086 (GRCm39)	missense	probably damaging	1.00
R0656:Chd4	UTSW	6	125,079,930 (GRCm39)	missense	probably damaging	0.98
R1342:Chd4	UTSW	6	125,074,151 (GRCm39)	missense	probably benign	0.40
R1651:Chd4	UTSW	6	125,100,547 (GRCm39)	missense	possibly damaging	0.92
R1850:Chd4	UTSW	6	125,098,619 (GRCm39)	missense	probably damaging	1.00
R2190:Chd4	UTSW	6	125,091,260 (GRCm39)	missense	probably benign	0.18
R2192:Chd4	UTSW	6	125,082,320 (GRCm39)	missense	probably damaging	0.99
R2858:Chd4	UTSW	6	125,081,849 (GRCm39)	missense	probably damaging	0.99
R3406:Chd4	UTSW	6	125,098,970 (GRCm39)	missense	probably benign	0.09
R3431:Chd4	UTSW	6	125,097,523 (GRCm39)	splice site	probably benign
R4330:Chd4	UTSW	6	125,078,565 (GRCm39)	missense	probably benign	0.29
R4394:Chd4	UTSW	6	125,098,581 (GRCm39)	missense	probably damaging	0.99
R4538:Chd4	UTSW	6	125,097,649 (GRCm39)	missense	probably damaging	0.99
R4664:Chd4	UTSW	6	125,078,465 (GRCm39)	missense	possibly damaging	0.58
R4805:Chd4	UTSW	6	125,105,908 (GRCm39)	missense	possibly damaging	0.86
R5050:Chd4	UTSW	6	125,084,443 (GRCm39)	missense	probably damaging	1.00
R5055:Chd4	UTSW	6	125,077,949 (GRCm39)	missense	possibly damaging	0.65
R5232:Chd4	UTSW	6	125,098,273 (GRCm39)	missense	probably damaging	1.00
R5314:Chd4	UTSW	6	125,077,551 (GRCm39)	missense	probably damaging	0.96
R5343:Chd4	UTSW	6	125,097,326 (GRCm39)	missense	probably damaging	1.00
R5502:Chd4	UTSW	6	125,082,239 (GRCm39)	missense	possibly damaging	0.83
R5613:Chd4	UTSW	6	125,097,509 (GRCm39)	missense	probably damaging	0.99
R6211:Chd4	UTSW	6	125,078,248 (GRCm39)	missense	possibly damaging	0.82
R6606:Chd4	UTSW	6	125,086,389 (GRCm39)	missense	probably damaging	0.99
R6753:Chd4	UTSW	6	125,091,263 (GRCm39)	missense	probably benign	0.01
R6808:Chd4	UTSW	6	125,099,086 (GRCm39)	missense	possibly damaging	0.53
R6939:Chd4	UTSW	6	125,083,501 (GRCm39)	missense	probably damaging	0.99
R6968:Chd4	UTSW	6	125,085,281 (GRCm39)	missense	probably damaging	1.00
R6992:Chd4	UTSW	6	125,091,339 (GRCm39)	missense	probably benign	0.14
R7058:Chd4	UTSW	6	125,085,405 (GRCm39)	missense	possibly damaging	0.74
R7081:Chd4	UTSW	6	125,106,948 (GRCm39)	missense	unknown
R7253:Chd4	UTSW	6	125,083,555 (GRCm39)	splice site	probably null
R7423:Chd4	UTSW	6	125,105,822 (GRCm39)	missense	possibly damaging	0.92
R7535:Chd4	UTSW	6	125,105,836 (GRCm39)	missense	probably benign	0.32
R7566:Chd4	UTSW	6	125,078,866 (GRCm39)	missense	possibly damaging	0.86
R8053:Chd4	UTSW	6	125,105,779 (GRCm39)	nonsense	probably null
R8155:Chd4	UTSW	6	125,082,287 (GRCm39)	missense	probably benign	0.00
R8711:Chd4	UTSW	6	125,100,485 (GRCm39)	unclassified	probably benign
R8783:Chd4	UTSW	6	125,100,347 (GRCm39)	missense	possibly damaging	0.53
R9020:Chd4	UTSW	6	125,084,469 (GRCm39)	missense	probably damaging	1.00
R9093:Chd4	UTSW	6	125,090,974 (GRCm39)	missense	probably benign	0.13
R9417:Chd4	UTSW	6	125,097,688 (GRCm39)	missense	probably damaging	0.99
R9509:Chd4	UTSW	6	125,099,485 (GRCm39)	missense	possibly damaging	0.96
RF046:Chd4	UTSW	6	125,099,094 (GRCm39)	unclassified	probably benign
RF052:Chd4	UTSW	6	125,099,108 (GRCm39)	unclassified	probably benign
RF058:Chd4	UTSW	6	125,099,094 (GRCm39)	unclassified	probably benign
RF060:Chd4	UTSW	6	125,099,108 (GRCm39)	unclassified	probably benign
X0025:Chd4	UTSW	6	125,083,430 (GRCm39)	nonsense	probably null
X0027:Chd4	UTSW	6	125,079,127 (GRCm39)	missense	probably damaging	0.98
X0063:Chd4	UTSW	6	125,090,978 (GRCm39)	missense	probably damaging	1.00
Z1176:Chd4	UTSW	6	125,078,561 (GRCm39)	missense	probably benign	0.36
Z1176:Chd4	UTSW	6	125,077,823 (GRCm39)	missense	possibly damaging	0.93

Predicted Primers

PCR Primer
(F):5'- TTTCCAAATGTAGTTGTTAGGGAGC -3'
(R):5'- CGCTAACATAGAGCCCAGAAGG -3'

Sequencing Primer
(F):5'- GAGCTGGCTGGTGATGC -3'
(R):5'- TAGAGCCCAGAAGGACAAACAGTC -3'

Posted On

2019-05-13