Incidental Mutation 'R3406:Chd4'
ID 259381
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 040624-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3406 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 125073144-125107554 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 125098970 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Lysine at position 1586 (T1586K)
Ref Sequence ENSEMBL: ENSMUSP00000108009 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056889] [ENSMUST00000112390] [ENSMUST00000112392] [ENSMUST00000124317]
AlphaFold Q6PDQ2
Predicted Effect probably benign
Transcript: ENSMUST00000056889
AA Change: T1579K

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000060054
Gene: ENSMUSG00000063870
AA Change: T1579K

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 benign
Transcript: ENSMUST00000112390
AA Change: T1586K

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000108009
Gene: ENSMUSG00000063870
AA Change: T1586K

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 benign
Transcript: ENSMUST00000112392
AA Change: T1566K

PolyPhen 2 Score 0.037 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000108011
Gene: ENSMUSG00000063870
AA Change: T1566K

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: ENSMUST00000132794
Predicted Effect noncoding transcript
Transcript: ENSMUST00000157583
Meta Mutation Damage Score 0.0600 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 93.4%
Validation Efficiency 98% (52/53)
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: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abhd18 T A 3: 40,859,338 (GRCm39) M1K probably null Het
Adam34l A T 8: 44,079,089 (GRCm39) C378* probably null Het
Bdkrb2 T C 12: 105,558,755 (GRCm39) V332A possibly damaging Het
Cdc27 T C 11: 104,398,026 (GRCm39) E778G probably damaging Het
Cnga3 A G 1: 37,301,146 (GRCm39) E622G probably benign Het
Dbh A G 2: 27,064,977 (GRCm39) D396G possibly damaging Het
Dhodh G A 8: 110,330,107 (GRCm39) R86* probably null Het
Dpt A C 1: 164,624,500 (GRCm39) E67A probably damaging Het
Eif2ak2 A G 17: 79,166,068 (GRCm39) probably benign Het
Esp4 T A 17: 40,913,336 (GRCm39) L68M possibly damaging Het
Exo1 A G 1: 175,733,536 (GRCm39) K787E possibly damaging Het
Fbxo38 T C 18: 62,647,914 (GRCm39) T875A probably damaging Het
Gsdma T C 11: 98,563,964 (GRCm39) probably benign Het
Hemk1 G A 9: 107,214,415 (GRCm39) Q6* probably null Het
Hmcn2 C T 2: 31,323,284 (GRCm39) probably benign Het
Hook2 A G 8: 85,720,613 (GRCm39) probably benign Het
Irx3 A G 8: 92,525,555 (GRCm39) S507P unknown Het
Kazn C A 4: 141,966,506 (GRCm39) probably benign Het
Kcne4 C T 1: 78,795,688 (GRCm39) A112V possibly damaging Het
Lamb1 C T 12: 31,337,528 (GRCm39) R372C probably damaging Het
Lrrc30 A G 17: 67,939,175 (GRCm39) L135P probably damaging Het
Lyst T A 13: 13,809,815 (GRCm39) M495K possibly damaging Het
Mab21l3 C A 3: 101,730,847 (GRCm39) V131F probably damaging Het
Mki67 T A 7: 135,309,204 (GRCm39) T416S probably benign Het
Mlst8 A T 17: 24,697,099 (GRCm39) M56K probably benign Het
Mmp9 A G 2: 164,791,310 (GRCm39) Y160C probably damaging Het
Mslnl A G 17: 25,965,155 (GRCm39) Y507C probably damaging Het
Muc6 G A 7: 141,218,313 (GRCm39) S2120F possibly damaging Het
Myl12a A T 17: 71,301,737 (GRCm39) M130K probably benign Het
Nalf2 A G X: 98,889,109 (GRCm39) I325V probably benign Het
Ncdn C T 4: 126,642,388 (GRCm39) R423Q probably benign Het
Ncf2 A G 1: 152,701,698 (GRCm39) probably benign Het
Nek8 G T 11: 78,061,572 (GRCm39) S319* probably null Het
Or11g7 G A 14: 50,690,653 (GRCm39) C48Y probably benign Het
Or52m2 T C 7: 102,263,993 (GRCm39) M68V possibly damaging Het
Pcdh17 T A 14: 84,684,062 (GRCm39) D176E probably damaging Het
Pcdhb15 C A 18: 37,608,442 (GRCm39) A558E probably benign Het
Plrg1 T A 3: 82,978,526 (GRCm39) W431R probably damaging Het
Rbfox3 T A 11: 118,387,283 (GRCm39) Q277L possibly damaging Het
Rpgrip1 G A 14: 52,382,666 (GRCm39) D600N possibly damaging Het
Siah3 A G 14: 75,763,421 (GRCm39) D224G probably damaging Het
Slc22a6 T C 19: 8,598,675 (GRCm39) L244P probably damaging Het
Stap2 A T 17: 56,304,511 (GRCm39) W374R probably benign Het
Tbck T A 3: 132,432,845 (GRCm39) N418K probably benign Het
Tcp11x2 T C X: 134,555,733 (GRCm39) N474S probably damaging Het
Tenm3 A C 8: 48,681,590 (GRCm39) V2680G probably damaging Het
Thada A T 17: 84,538,213 (GRCm39) probably benign Het
Tlr6 C T 5: 65,110,772 (GRCm39) V712M probably damaging Het
Uvssa G T 5: 33,547,162 (GRCm39) G243C probably damaging Het
Vwa8 T A 14: 79,401,660 (GRCm39) probably benign Het
Znrf2 A T 6: 54,861,776 (GRCm39) N229I 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
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
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
Predicted Primers PCR Primer
(F):5'- CTCAGTTTAGGAGGGCTGTC -3'
(R):5'- TCAGCAGGAGCCTTGTCATC -3'

Sequencing Primer
(F):5'- TCCTAAGAATGGGGCTGGCTC -3'
(R):5'- AGGAGCCTTGTCATCCTCAG -3'
Posted On 2015-01-23