Incidental Mutation 'IGL03001:Chd4'
ID 407361
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 # IGL03001
Quality Score
Status
Chromosome 6
Chromosomal Location 125073144-125107554 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 125078529 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Glutamic Acid at position 217 (A217E)
Ref Sequence ENSEMBL: ENSMUSP00000108011 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056889] [ENSMUST00000112390] [ENSMUST00000112392] [ENSMUST00000155261]
AlphaFold Q6PDQ2
Predicted Effect possibly damaging
Transcript: ENSMUST00000056889
AA Change: A217E

PolyPhen 2 Score 0.780 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000060054
Gene: ENSMUSG00000063870
AA Change: A217E

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: A224E

PolyPhen 2 Score 0.913 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000108009
Gene: ENSMUSG00000063870
AA Change: A224E

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: A217E

PolyPhen 2 Score 0.934 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000108011
Gene: ENSMUSG00000063870
AA Change: A217E

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: ENSMUST00000155261
SMART Domains Protein: ENSMUSP00000122806
Gene: ENSMUSG00000063870

DomainStartEndE-ValueType
Blast:DEXDc 4 25 1e-5 BLAST
low complexity region 29 45 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155932
Predicted Effect noncoding transcript
Transcript: ENSMUST00000183346
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acan A C 7: 78,761,042 (GRCm39) D1918A probably damaging Het
Ahcy C A 2: 154,906,748 (GRCm39) D182Y probably damaging Het
Aldob T G 4: 49,542,844 (GRCm39) D110A probably damaging Het
Alkbh8 A T 9: 3,344,602 (GRCm39) M53L probably benign Het
Aqr T C 2: 113,977,400 (GRCm39) D363G probably benign Het
Asxl3 A G 18: 22,650,455 (GRCm39) R815G probably damaging Het
Atf4 T A 15: 80,140,858 (GRCm39) W83R probably damaging Het
Baz1a A T 12: 54,969,896 (GRCm39) M587K possibly damaging Het
Btbd8 T C 5: 107,645,708 (GRCm39) I9T probably damaging Het
Cactin T A 10: 81,161,568 (GRCm39) I700N probably damaging Het
Catsperg2 T C 7: 29,424,504 (GRCm39) S95G probably benign Het
Cd1d1 C T 3: 86,905,468 (GRCm39) S175N probably benign Het
Cnbd2 T C 2: 156,175,554 (GRCm39) probably null Het
Cntnap5c G A 17: 58,362,634 (GRCm39) C329Y probably damaging Het
Col12a1 C T 9: 79,540,955 (GRCm39) G2391R probably damaging Het
Col5a3 T A 9: 20,719,040 (GRCm39) D238V unknown Het
Cuedc1 T C 11: 88,073,315 (GRCm39) V160A probably benign Het
Depdc5 T C 5: 33,102,434 (GRCm39) V342A possibly damaging Het
Dnah6 T C 6: 73,126,123 (GRCm39) D1338G probably benign Het
Dpyd T C 3: 118,710,891 (GRCm39) V433A probably benign Het
Epb41l5 T C 1: 119,545,374 (GRCm39) H179R probably damaging Het
Fbf1 T C 11: 116,056,712 (GRCm39) probably benign Het
Flnb T C 14: 7,934,680 (GRCm38) S2251P probably damaging Het
Fsip2 A T 2: 82,820,968 (GRCm39) probably benign Het
Grin2b C T 6: 135,716,113 (GRCm39) V735M probably damaging Het
Itpr3 T G 17: 27,308,586 (GRCm39) probably benign Het
Lingo4 C T 3: 94,309,703 (GRCm39) R214C probably damaging Het
Lrp1b C T 2: 40,817,901 (GRCm39) R2329H probably damaging Het
Lrrc47 T C 4: 154,100,450 (GRCm39) L342P probably damaging Het
Mmp15 T C 8: 96,094,845 (GRCm39) S240P probably damaging Het
Ndufaf4 T A 4: 24,901,747 (GRCm39) N95K probably benign Het
Nms C T 1: 38,980,993 (GRCm39) P60S probably benign Het
Npas3 A T 12: 53,547,975 (GRCm39) Y77F probably damaging Het
Or2ak7 T G 11: 58,574,702 (GRCm39) M1R probably null Het
Or51f5 G T 7: 102,424,460 (GRCm39) C243F probably damaging Het
Or5d43 T A 2: 88,105,189 (GRCm39) D68V probably damaging Het
Or8d2b A G 9: 38,789,374 (GRCm39) M301V probably benign Het
Or9m2 T A 2: 87,820,493 (GRCm39) Y13N probably benign Het
Or9s27 T A 1: 92,516,273 (GRCm39) S74T probably damaging Het
Picalm T C 7: 89,831,454 (GRCm39) V429A probably benign Het
Pkhd1l1 T A 15: 44,421,400 (GRCm39) I3056N probably damaging Het
Pomt1 G T 2: 32,134,338 (GRCm39) M286I probably benign Het
Popdc2 A T 16: 38,189,881 (GRCm39) Y176F probably benign Het
Psg21 A T 7: 18,386,410 (GRCm39) M192K probably benign Het
Psma1 C A 7: 113,865,674 (GRCm39) A219S probably benign Het
Rad21l T G 2: 151,510,389 (GRCm39) H22P probably damaging Het
Rnf213 A G 11: 119,370,767 (GRCm39) T4791A probably damaging Het
Sdk2 A G 11: 113,712,452 (GRCm39) V1609A probably benign Het
Sema3e T A 5: 14,291,057 (GRCm39) S606T probably benign Het
Slc16a4 A T 3: 107,218,858 (GRCm39) R486S possibly damaging Het
Slc17a3 T C 13: 24,040,767 (GRCm39) L331P probably damaging Het
Slc38a11 A T 2: 65,184,159 (GRCm39) V164D probably damaging Het
Slc38a6 A G 12: 73,383,827 (GRCm39) I173V probably benign Het
Synpo2 T C 3: 122,873,604 (GRCm39) T1121A probably benign Het
Tfcp2 T C 15: 100,426,302 (GRCm39) D83G possibly damaging Het
Thnsl1 A G 2: 21,216,455 (GRCm39) T70A probably damaging Het
Tnfrsf21 A G 17: 43,398,786 (GRCm39) I631V probably damaging Het
Tor2a C A 2: 32,647,329 (GRCm39) H6Q possibly damaging Het
Ttn T C 2: 76,565,267 (GRCm39) N19993S probably benign Het
Vps53 T C 11: 76,029,150 (GRCm39) E119G probably damaging Het
Zkscan6 T C 11: 65,705,495 (GRCm39) W69R probably damaging Het
Zng1 T C 19: 24,900,002 (GRCm39) K301E probably benign Het
Zswim8 T C 14: 20,764,459 (GRCm39) S610P probably damaging 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
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
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 2016-08-02