Incidental Mutation 'R5050:Chd4'
ID 394591
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 042640-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5050 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 125073144-125107554 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 125084443 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 692 (Y692H)
Ref Sequence ENSEMBL: ENSMUSP00000108011 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000056889] [ENSMUST00000112390] [ENSMUST00000112392]
AlphaFold Q6PDQ2
Predicted Effect probably damaging
Transcript: ENSMUST00000056889
AA Change: Y705H

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000060054
Gene: ENSMUSG00000063870
AA Change: Y705H

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: Y712H

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000108009
Gene: ENSMUSG00000063870
AA Change: Y712H

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: Y692H

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000108011
Gene: ENSMUSG00000063870
AA Change: Y692H

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
Meta Mutation Damage Score 0.2000 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.6%
  • 10x: 96.7%
  • 20x: 93.6%
Validation Efficiency 100% (69/69)
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ahnak A G 19: 8,989,822 (GRCm39) probably benign Het
Ap3m1 A G 14: 21,094,843 (GRCm39) I108T probably benign Het
Apobec1 T C 6: 122,568,061 (GRCm39) M1V probably null Het
Aqr A T 2: 113,943,090 (GRCm39) L1161* probably null Het
Aqr A T 2: 114,000,506 (GRCm39) probably null Het
Arhgef37 A G 18: 61,637,402 (GRCm39) I420T probably benign Het
Cacna1g C T 11: 94,350,541 (GRCm39) E435K probably damaging Het
Card6 G T 15: 5,129,858 (GRCm39) H513N probably benign Het
Ccdc158 A C 5: 92,814,738 (GRCm39) F29L probably benign Het
Ccr6 T C 17: 8,474,936 (GRCm39) L47S probably damaging Het
Cdc42bpa T A 1: 179,900,018 (GRCm39) Y444* probably null Het
Cdh17 A G 4: 11,784,654 (GRCm39) Y270C probably damaging Het
Cdh9 T C 15: 16,778,233 (GRCm39) F16S probably benign Het
Cdkl1 T C 12: 69,804,014 (GRCm39) K141R probably damaging Het
Cfhr4 T A 1: 139,664,578 (GRCm39) I494F probably damaging Het
Dhrs7 T A 12: 72,704,184 (GRCm39) D104V probably damaging Het
Dhtkd1 A T 2: 5,922,500 (GRCm39) L553Q probably benign Het
Dnah7a T G 1: 53,536,255 (GRCm39) D2596A probably benign Het
Dync1li2 T C 8: 105,164,073 (GRCm39) K151E probably damaging Het
Eno4 C T 19: 58,943,928 (GRCm39) H297Y probably benign Het
Epg5 T A 18: 78,019,156 (GRCm39) D976E possibly damaging Het
Fhip2a T A 19: 57,371,602 (GRCm39) F571L probably damaging Het
Gm4553 C A 7: 141,718,773 (GRCm39) K218N unknown Het
Gpld1 A T 13: 25,146,739 (GRCm39) T234S probably benign Het
Gtpbp6 A T 5: 110,252,567 (GRCm39) probably benign Het
Gucy2g T C 19: 55,229,367 (GRCm39) E101G probably benign Het
Gvin3 T C 7: 106,196,179 (GRCm39) noncoding transcript Het
Hira G A 16: 18,744,609 (GRCm39) R442K possibly damaging Het
Hrh3 A G 2: 179,742,350 (GRCm39) L394P probably damaging Het
Igkv1-110 T A 6: 68,248,176 (GRCm39) F95Y probably damaging Het
Iqgap3 T G 3: 87,997,493 (GRCm39) V223G probably damaging Het
Itpk1 T C 12: 102,671,069 (GRCm39) T3A probably damaging Het
Jag1 A G 2: 136,927,074 (GRCm39) V895A possibly damaging Het
Kazn G A 4: 141,845,514 (GRCm39) probably benign Het
Large2 A T 2: 92,198,124 (GRCm39) L282Q probably benign Het
Lgmn A G 12: 102,369,680 (GRCm39) probably null Het
Lrp4 A T 2: 91,322,767 (GRCm39) I1119F probably benign Het
Map3k19 T C 1: 127,751,299 (GRCm39) H684R probably benign Het
Mier3 C T 13: 111,851,107 (GRCm39) A367V possibly damaging Het
Mpdz A G 4: 81,213,685 (GRCm39) V1579A probably benign Het
Mroh2b A T 15: 4,929,932 (GRCm39) D6V possibly damaging Het
Myh7b A G 2: 155,473,670 (GRCm39) I1568V probably benign Het
Or52e8b T A 7: 104,673,594 (GRCm39) I198F probably damaging Het
Plch2 C T 4: 155,127,766 (GRCm39) probably benign Het
Plek T C 11: 16,945,216 (GRCm39) D38G probably damaging Het
Polr2f A G 15: 79,028,862 (GRCm39) probably benign Het
Samsn1 A G 16: 75,685,645 (GRCm39) S38P probably benign Het
Sf1 C T 19: 6,422,589 (GRCm39) T248I probably damaging Het
Sgms2 C T 3: 131,124,005 (GRCm39) V232M probably benign Het
Sharpin A T 15: 76,232,530 (GRCm39) L160H probably damaging Het
Sympk C T 7: 18,769,967 (GRCm39) R215C probably benign Het
Syn3 T C 10: 86,243,532 (GRCm39) T136A probably benign Het
Tcam1 G A 11: 106,176,278 (GRCm39) V335M possibly damaging Het
Tedc1 G T 12: 113,120,325 (GRCm39) V56L possibly damaging Het
Tenm4 T C 7: 96,544,995 (GRCm39) L2337P probably damaging Het
Ttn G A 2: 76,715,155 (GRCm39) probably benign Het
Tysnd1 T A 10: 61,532,050 (GRCm39) I234N probably damaging Het
Vmn2r51 T C 7: 9,834,349 (GRCm39) K230E 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
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
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'- GTGGATTCTTTGGCTACTCCAC -3'
(R):5'- AAGCACTAGCATCTCCTGGC -3'

Sequencing Primer
(F):5'- GACTGGCCTTGAGCTCAATC -3'
(R):5'- TGGCATCTTTTACCTCCTTATAGAG -3'
Posted On 2016-06-15