Incidental Mutation 'IGL02707:Chd4'
ID 304405
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 # IGL02707
Quality Score
Status
Chromosome 6
Chromosomal Location 125073144-125107554 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 125085730 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Serine at position 875 (A875S)
Ref Sequence ENSEMBL: ENSMUSP00000108009 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056889] [ENSMUST00000112390] [ENSMUST00000112392] [ENSMUST00000124317]
AlphaFold Q6PDQ2
Predicted Effect probably damaging
Transcript: ENSMUST00000056889
AA Change: A868S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000060054
Gene: ENSMUSG00000063870
AA Change: A868S

DomainStartEndE-ValueType
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 damaging
Transcript: ENSMUST00000112390
AA Change: A875S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108009
Gene: ENSMUSG00000063870
AA Change: A875S

DomainStartEndE-ValueType
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 probably damaging
Transcript: ENSMUST00000112392
AA Change: A855S

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000108011
Gene: ENSMUSG00000063870
AA Change: A855S

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138968
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700017B05Rik T C 9: 57,165,928 (GRCm39) T149A probably benign Het
4932414N04Rik A C 2: 68,561,474 (GRCm39) Q267P possibly damaging Het
Actr5 T C 2: 158,478,617 (GRCm39) V489A probably benign Het
Adam26b T C 8: 43,972,895 (GRCm39) probably benign Het
Aff4 A G 11: 53,290,567 (GRCm39) N509S probably benign Het
Arhgap22 C T 14: 33,085,229 (GRCm39) probably benign Het
Arhgap9 C A 10: 127,165,476 (GRCm39) H628Q probably damaging Het
Asap1 A T 15: 64,001,123 (GRCm39) I486N probably damaging Het
Asb15 A T 6: 24,558,787 (GRCm39) probably benign Het
Avil A G 10: 126,842,431 (GRCm39) D70G probably damaging Het
Cct6b T C 11: 82,645,780 (GRCm39) probably benign Het
Cep63 A T 9: 102,464,180 (GRCm39) I717K probably damaging Het
Col4a4 A T 1: 82,471,237 (GRCm39) M706K unknown Het
Cr1l T C 1: 194,806,019 (GRCm39) T155A probably benign Het
Ctnna3 A G 10: 63,339,844 (GRCm39) N10S probably benign Het
Cubn A G 2: 13,450,843 (GRCm39) V854A probably damaging Het
Dgkh T C 14: 78,823,091 (GRCm39) T845A possibly damaging Het
F10 G A 8: 13,098,252 (GRCm39) A152T probably damaging Het
Gabrg3 C A 7: 56,632,439 (GRCm39) E170* probably null Het
Heatr5a A G 12: 51,968,149 (GRCm39) V829A probably benign Het
Htt T A 5: 34,987,225 (GRCm39) probably null Het
Icam4 T C 9: 20,941,770 (GRCm39) Y257H possibly damaging Het
Jph1 A G 1: 17,074,675 (GRCm39) S448P probably benign Het
Kansl1l G A 1: 66,812,604 (GRCm39) L125F probably damaging Het
Kifc1 A T 17: 34,100,467 (GRCm39) C46* probably null Het
Lce3b A G 3: 92,841,193 (GRCm39) D96G unknown Het
Mab21l1 A T 3: 55,690,505 (GRCm39) I31F possibly damaging Het
Mctp2 A G 7: 71,909,089 (GRCm39) Y75H possibly damaging Het
Mesp2 A G 7: 79,461,274 (GRCm39) I200V probably benign Het
Msr1 T C 8: 40,085,870 (GRCm39) probably benign Het
Mtfr2 C T 10: 20,224,084 (GRCm39) T6I probably benign Het
Myo5b T C 18: 74,828,438 (GRCm39) probably benign Het
Myoc T A 1: 162,467,029 (GRCm39) I66N probably benign Het
Or10d1b T C 9: 39,613,937 (GRCm39) I43V probably damaging Het
Or4a70 A T 2: 89,324,171 (GRCm39) Y162N probably damaging Het
Or51k1 A C 7: 103,661,609 (GRCm39) L100W probably damaging Het
Or52n20 T C 7: 104,320,136 (GRCm39) C76R probably damaging Het
Or52n2b A G 7: 104,565,859 (GRCm39) C215R probably damaging Het
Or7a39 T C 10: 78,715,759 (GRCm39) L251S probably damaging Het
Per2 T C 1: 91,378,450 (GRCm39) D33G possibly damaging Het
Pknox1 A G 17: 31,821,793 (GRCm39) I295V possibly damaging Het
Rgs11 G A 17: 26,426,605 (GRCm39) V279I probably benign Het
Rhot2 A G 17: 26,063,270 (GRCm39) S19P probably damaging Het
Rps6kb1 C A 11: 86,426,236 (GRCm39) probably null Het
Serpinb1b C T 13: 33,275,648 (GRCm39) T194I probably benign Het
Smarcad1 T A 6: 65,029,790 (GRCm39) probably benign Het
Stxbp4 A G 11: 90,428,759 (GRCm39) S449P probably benign Het
Thrb A C 14: 18,026,721 (GRCm38) I275L probably benign Het
Tjp1 T A 7: 64,979,431 (GRCm39) K365* probably null Het
Tjp1 T A 7: 64,979,430 (GRCm39) K365I possibly damaging Het
Tm4sf4 C A 3: 57,333,939 (GRCm39) C75* probably null Het
Tmem131 T C 1: 36,864,560 (GRCm39) T558A probably benign Het
Txndc16 T C 14: 45,399,730 (GRCm39) T408A probably benign Het
Ube2j1 T C 4: 33,038,206 (GRCm39) L38P possibly damaging Het
Urb2 T C 8: 124,757,425 (GRCm39) I1044T probably benign Het
Other mutations in Chd4
AlleleSourceChrCoordTypePredicted EffectPPH 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
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 2015-04-16