Incidental Mutation 'IGL02005:Chd4'
ID 183137
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 # IGL02005
Quality Score
Status
Chromosome 6
Chromosomal Location 125073144-125107554 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 125105779 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Lysine at position 1786 (E1786K)
Ref Sequence ENSEMBL: ENSMUSP00000108011 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000044200] [ENSMUST00000056889] [ENSMUST00000112390] [ENSMUST00000112392] [ENSMUST00000204185]
AlphaFold Q6PDQ2
Predicted Effect probably benign
Transcript: ENSMUST00000044200
SMART Domains Protein: ENSMUSP00000047123
Gene: ENSMUSG00000038279

DomainStartEndE-ValueType
low complexity region 41 57 N/A INTRINSIC
low complexity region 97 109 N/A INTRINSIC
low complexity region 166 176 N/A INTRINSIC
Pfam:Methyltr_RsmF_N 268 359 2.9e-12 PFAM
Pfam:Nol1_Nop2_Fmu 362 570 2e-86 PFAM
Pfam:P120R 609 630 2.7e-11 PFAM
Pfam:P120R 663 685 1.1e-12 PFAM
low complexity region 729 745 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000056889
AA Change: E1799K

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000060054
Gene: ENSMUSG00000063870
AA Change: E1799K

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 possibly damaging
Transcript: ENSMUST00000112390
AA Change: E1806K

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000108009
Gene: ENSMUSG00000063870
AA Change: E1806K

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 possibly damaging
Transcript: ENSMUST00000112392
AA Change: E1786K

PolyPhen 2 Score 0.707 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000108011
Gene: ENSMUSG00000063870
AA Change: E1786K

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: ENSMUST00000204185
SMART Domains Protein: ENSMUSP00000145333
Gene: ENSMUSG00000038279

DomainStartEndE-ValueType
low complexity region 41 57 N/A INTRINSIC
low complexity region 97 109 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: 52 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933434E20Rik A G 3: 89,965,927 (GRCm39) D141G probably damaging Het
Ankhd1 T G 18: 36,781,479 (GRCm39) L2177R probably damaging Het
Arhgap23 A T 11: 97,382,045 (GRCm39) D1136V probably damaging Het
Atp6v1b1 A G 6: 83,730,896 (GRCm39) probably benign Het
Atxn1 T C 13: 45,721,701 (GRCm39) T65A probably benign Het
Bbs4 A G 9: 59,243,638 (GRCm39) probably benign Het
Bms1 G A 6: 118,381,546 (GRCm39) T664M probably damaging Het
Bod1l T C 5: 41,973,682 (GRCm39) D2544G probably benign Het
Cdhr2 C T 13: 54,867,576 (GRCm39) H469Y probably benign Het
Cep57l1 T C 10: 41,616,957 (GRCm39) D110G probably benign Het
Cltc T C 11: 86,621,045 (GRCm39) K321E possibly damaging Het
Col6a2 T C 10: 76,446,007 (GRCm39) D383G probably damaging Het
Crcp T G 5: 130,071,074 (GRCm39) C58G probably benign Het
Ctc1 A G 11: 68,921,975 (GRCm39) Y807C probably damaging Het
Eml4 T A 17: 83,785,132 (GRCm39) probably benign Het
Glce A T 9: 61,967,859 (GRCm39) L431I probably damaging Het
Glp1r C A 17: 31,143,585 (GRCm39) T207K probably benign Het
Gm28042 G A 2: 119,865,115 (GRCm39) V247I possibly damaging Het
Gvin-ps5 G T 7: 105,928,627 (GRCm39) F423L unknown Het
Hcrtr1 T A 4: 130,031,056 (GRCm39) H76L probably benign Het
Hoxb13 G A 11: 96,085,435 (GRCm39) G56D probably damaging Het
Hykk A G 9: 54,827,842 (GRCm39) E27G possibly damaging Het
Kars1 A T 8: 112,726,736 (GRCm39) L321* probably null Het
Klhl12 A T 1: 134,391,652 (GRCm39) T95S possibly damaging Het
Klhl14 A T 18: 21,757,668 (GRCm39) Y347* probably null Het
Kmt5b A G 19: 3,836,538 (GRCm39) H25R possibly damaging Het
Krtap12-1 T A 10: 77,556,823 (GRCm39) V122D probably damaging Het
Lrrc66 T C 5: 73,766,077 (GRCm39) D322G possibly damaging Het
Lrrc8b T A 5: 105,628,920 (GRCm39) V422D probably benign Het
Med12l T G 3: 59,152,368 (GRCm39) M1051R probably damaging Het
Mmrn1 A G 6: 60,937,728 (GRCm39) Y242C probably damaging Het
Ncf2 A T 1: 152,692,803 (GRCm39) I107L possibly damaging Het
Or6b13 C T 7: 139,782,345 (GRCm39) E113K probably damaging Het
Pdlim4 T C 11: 53,950,810 (GRCm39) D93G probably benign Het
Pgap1 C A 1: 54,590,214 (GRCm39) A75S probably damaging Het
Pkd1 A G 17: 24,804,978 (GRCm39) D3209G possibly damaging Het
Prcp T C 7: 92,577,032 (GRCm39) S319P probably benign Het
Rasal2 G A 1: 156,984,568 (GRCm39) Q1035* probably null Het
Ryr3 A T 2: 112,493,608 (GRCm39) probably benign Het
Scaf8 T C 17: 3,236,145 (GRCm39) I544T probably damaging Het
Svep1 A T 4: 58,069,056 (GRCm39) V2910E possibly damaging Het
Tln2 C T 9: 67,299,787 (GRCm39) R155Q possibly damaging Het
Trpm7 A T 2: 126,655,104 (GRCm39) L1278H probably damaging Het
Tti2 G T 8: 31,645,858 (GRCm39) G391C probably damaging Het
Ttn C T 2: 76,778,363 (GRCm39) M1295I possibly damaging Het
Ttn T C 2: 76,554,313 (GRCm39) probably benign Het
Vmn1r170 G A 7: 23,306,338 (GRCm39) V247M probably damaging Het
Wdr48 T C 9: 119,734,455 (GRCm39) Y125H probably damaging Het
Wdtc1 C T 4: 133,036,225 (GRCm39) R105H probably benign Het
Zc3h11a A G 1: 133,549,880 (GRCm39) S699P probably benign Het
Zkscan14 C T 5: 145,132,419 (GRCm39) V371I probably benign Het
Zzef1 A T 11: 72,779,125 (GRCm39) Y1862F 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
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 2014-05-07