Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL00917:Chd4'

27614

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Chd4

Ensembl Gene

ENSMUSG00000063870

Gene Name

chromodomain helicase DNA binding protein 4

Synonyms

D6Ertd380e, 9530019N15Rik, Mi-2beta

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL00917

Quality Score

Status

Chromosome

Chromosomal Location

125073144-125107554 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 125081909 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glutamine at position 514 (R514Q)

Ref Sequence

ENSEMBL: ENSMUSP00000060054 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056889] [ENSMUST00000112390] [ENSMUST00000112392] [ENSMUST00000155261]

AlphaFold

Q6PDQ2

Predicted Effect

possibly damaging
Transcript: ENSMUST00000056889
AA Change: R514Q

PolyPhen 2 Score 0.948 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000060054
Gene: ENSMUSG00000063870
AA Change: R514Q

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

probably benign
Transcript: ENSMUST00000112390
AA Change: R521Q

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000108009
Gene: ENSMUSG00000063870
AA Change: R521Q

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: R501Q

PolyPhen 2 Score 0.890 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000108011
Gene: ENSMUSG00000063870
AA Change: R501Q

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: ENSMUST00000155261

SMART Domains

Protein: ENSMUSP00000122806
Gene: ENSMUSG00000063870

Domain	Start	End	E-Value	Type
Blast:DEXDc	4	25	1e-5	BLAST
low complexity region	29	45	N/A	INTRINSIC

Coding Region Coverage

Validation Efficiency

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: 34 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	A	T	16: 20,241,107 (GRCm39)	V26E	probably benign	Het
Adcy4	T	A	14: 56,011,120 (GRCm39)		probably null	Het
Adgrl3	C	T	5: 81,841,421 (GRCm39)	T766I	possibly damaging	Het
Atad2b	A	T	12: 5,015,837 (GRCm39)		probably benign	Het
Atp8b4	A	T	2: 126,216,453 (GRCm39)	S664R	probably benign	Het
Cand1	A	C	10: 119,046,841 (GRCm39)	I883S	possibly damaging	Het
Cfap53	A	G	18: 74,432,367 (GRCm39)	D85G	probably benign	Het
Cnst	T	C	1: 179,452,557 (GRCm39)		probably benign	Het
Col6a6	T	C	9: 105,661,453 (GRCm39)		probably benign	Het
Cux2	A	C	5: 122,007,168 (GRCm39)	L831R	probably null	Het
Elf2	T	A	3: 51,215,467 (GRCm39)		probably benign	Het
Frey1	T	A	2: 92,213,563 (GRCm39)	S39T	probably benign	Het
Glp1r	A	G	17: 31,138,443 (GRCm39)		probably benign	Het
Hus1b	A	G	13: 31,131,527 (GRCm39)	M44T	probably benign	Het
Mbd6	A	G	10: 127,119,988 (GRCm39)		probably benign	Het
Med31	T	A	11: 72,102,905 (GRCm39)		probably null	Het
Mmrn1	C	T	6: 60,952,894 (GRCm39)	Q392*	probably null	Het
Mrpl3	T	G	9: 104,934,240 (GRCm39)	V121G	probably damaging	Het
Or10am5	A	G	7: 6,517,577 (GRCm39)	S284P	probably damaging	Het
Or14c46	A	T	7: 85,918,649 (GRCm39)	M116K	probably damaging	Het
Palld	A	G	8: 61,968,969 (GRCm39)	V879A	possibly damaging	Het
Pkn2	G	T	3: 142,559,386 (GRCm39)	D46E	probably damaging	Het
Prkdc	T	A	16: 15,557,428 (GRCm39)	C2244S	probably damaging	Het
Prss50	T	A	9: 110,691,474 (GRCm39)	H259Q	possibly damaging	Het
Rab8b	C	T	9: 66,761,969 (GRCm39)	W102*	probably null	Het
Rad54l2	A	T	9: 106,587,638 (GRCm39)	L709Q	possibly damaging	Het
Rapgef1	T	C	2: 29,592,535 (GRCm39)	V471A	probably benign	Het
Rbms3	A	G	9: 116,939,183 (GRCm39)	S27P	probably damaging	Het
Rpl35a	A	G	16: 32,879,101 (GRCm39)	K73E	possibly damaging	Het
Sugct	A	T	13: 17,032,503 (GRCm39)	Y416*	probably null	Het
Top2b	A	G	14: 16,407,354 (GRCm38)	I713V	probably benign	Het
Unc79	A	T	12: 103,054,766 (GRCm39)	R777S	possibly damaging	Het
Vps37a	T	A	8: 40,993,779 (GRCm39)	M258K	probably benign	Het
Zfp944	G	A	17: 22,558,765 (GRCm39)	L161F	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
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
R6973:Chd4	UTSW	6	125,099,825 (GRCm39)	missense	possibly damaging	0.53
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

Posted On

2013-04-17