Incidental Mutation 'R4960:Chd1'
ID 382326
Institutional Source Beutler Lab
Gene Symbol Chd1
Ensembl Gene ENSMUSG00000023852
Gene Name chromodomain helicase DNA binding protein 1
Synonyms 4930525N21Rik
MMRRC Submission 042557-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4960 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 15925229-15992872 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 15962493 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 750 (M750K)
Ref Sequence ENSEMBL: ENSMUSP00000024627 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000024627] [ENSMUST00000173311]
AlphaFold P40201
Predicted Effect probably damaging
Transcript: ENSMUST00000024627
AA Change: M750K

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000024627
Gene: ENSMUSG00000023852
AA Change: M750K

DomainStartEndE-ValueType
low complexity region 17 67 N/A INTRINSIC
low complexity region 105 115 N/A INTRINSIC
low complexity region 116 136 N/A INTRINSIC
low complexity region 151 175 N/A INTRINSIC
low complexity region 213 230 N/A INTRINSIC
CHROMO 268 355 6.43e-20 SMART
CHROMO 385 443 1.19e-14 SMART
DEXDc 475 672 3.44e-34 SMART
Blast:DEXDc 692 786 2e-54 BLAST
low complexity region 787 799 N/A INTRINSIC
HELICc 816 900 8.48e-25 SMART
Blast:DEXDc 955 1234 1e-112 BLAST
PDB:4B4C|A 1119 1320 1e-132 PDB
low complexity region 1325 1348 N/A INTRINSIC
low complexity region 1377 1388 N/A INTRINSIC
DUF4208 1396 1500 5.54e-51 SMART
low complexity region 1507 1516 N/A INTRINSIC
low complexity region 1538 1549 N/A INTRINSIC
low complexity region 1626 1650 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000173311
AA Change: M750K

PolyPhen 2 Score 0.839 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000134091
Gene: ENSMUSG00000023852
AA Change: M750K

DomainStartEndE-ValueType
low complexity region 17 67 N/A INTRINSIC
low complexity region 105 115 N/A INTRINSIC
low complexity region 116 136 N/A INTRINSIC
low complexity region 151 175 N/A INTRINSIC
low complexity region 213 230 N/A INTRINSIC
CHROMO 268 355 6.43e-20 SMART
CHROMO 385 443 1.19e-14 SMART
DEXDc 475 672 3.44e-34 SMART
Blast:DEXDc 692 786 2e-54 BLAST
low complexity region 787 799 N/A INTRINSIC
HELICc 816 900 8.48e-25 SMART
Blast:DEXDc 955 1078 2e-38 BLAST
Predicted Effect unknown
Transcript: ENSMUST00000174461
AA Change: M134K
SMART Domains Protein: ENSMUSP00000134718
Gene: ENSMUSG00000023852
AA Change: M134K

DomainStartEndE-ValueType
Pfam:SNF2_N 1 148 3.6e-34 PFAM
low complexity region 172 184 N/A INTRINSIC
HELICc 201 285 8.48e-25 SMART
Blast:DEXDc 340 516 1e-47 BLAST
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 93.8%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit complete embryonic lethality associated with arrest of epiblast development due to increased apoptosis and cell cycle defects, abnormal rostral-caudal axis patterning, and failure to gastrulate. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 102 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc9 A T 6: 142,566,509 (GRCm39) probably null Het
Abtb3 A C 10: 85,487,526 (GRCm39) N998T probably benign Het
Adamts20 T C 15: 94,277,655 (GRCm39) H269R probably benign Het
Adamtsl1 C T 4: 86,342,410 (GRCm39) Q1642* probably null Het
Adamtsl3 A C 7: 82,216,185 (GRCm39) T863P probably damaging Het
Adcy3 G T 12: 4,184,896 (GRCm39) V191L probably benign Het
Akap9 G T 5: 4,007,664 (GRCm39) R244L probably benign Het
Anapc1 C T 2: 128,526,514 (GRCm39) V95M probably benign Het
Arhgap17 G T 7: 122,886,149 (GRCm39) probably benign Het
Art2b T A 7: 101,229,437 (GRCm39) Y154F probably damaging Het
Atrn C T 2: 130,836,967 (GRCm39) R1144* probably null Het
Atxn3 T C 12: 101,914,638 (GRCm39) S29G possibly damaging Het
Batf3 C T 1: 190,830,707 (GRCm39) P18S probably benign Het
Bmal1 T A 7: 112,898,642 (GRCm39) probably null Het
Bmpr1b A T 3: 141,576,546 (GRCm39) C96S probably damaging Het
Bola1 A G 3: 96,104,370 (GRCm39) S75P probably benign Het
Cela3a G A 4: 137,129,959 (GRCm39) R221* probably null Het
Chat A G 14: 32,142,771 (GRCm39) V406A possibly damaging Het
Clip1 T A 5: 123,792,066 (GRCm39) K35* probably null Het
Cnr2 G A 4: 135,644,918 (GRCm39) G332D probably benign Het
Cnrip1 A G 11: 17,002,228 (GRCm39) D20G probably damaging Het
Col2a1 T C 15: 97,874,030 (GRCm39) Y1384C unknown Het
Col6a3 T A 1: 90,731,940 (GRCm39) I831F probably damaging Het
Cp G A 3: 20,027,961 (GRCm39) V456I probably damaging Het
Cspp1 T A 1: 10,196,688 (GRCm39) N900K probably damaging Het
Ctbp2 T C 7: 132,615,967 (GRCm39) I323V probably benign Het
Ctnna2 C T 6: 77,630,094 (GRCm39) R120H probably damaging Het
Cyp2a12 A G 7: 26,733,575 (GRCm39) H318R probably benign Het
Cyp2c66 A T 19: 39,151,766 (GRCm39) probably null Het
Cyp2j8 T C 4: 96,395,614 (GRCm39) T4A probably benign Het
Cyp4v3 A G 8: 45,773,674 (GRCm39) V165A possibly damaging Het
D5Ertd579e G A 5: 36,773,571 (GRCm39) R275* probably null Het
Deup1 G T 9: 15,512,264 (GRCm39) Q160K possibly damaging Het
Dhx36 A T 3: 62,404,280 (GRCm39) I221K probably damaging Het
Dnah7b T A 1: 46,272,886 (GRCm39) M2338K probably benign Het
Dync2li1 T G 17: 84,940,969 (GRCm39) L62V probably benign Het
Ephb3 A G 16: 21,039,245 (GRCm39) K367R probably benign Het
Etv3 A G 3: 87,435,368 (GRCm39) K80E probably damaging Het
Flacc1 T A 1: 58,706,965 (GRCm39) E234V probably damaging Het
Gdap1l1 T C 2: 163,295,779 (GRCm39) F346L probably benign Het
Gm4787 C T 12: 81,426,090 (GRCm39) V23M probably damaging Het
Greb1l T A 18: 10,547,306 (GRCm39) I1508N probably damaging Het
Heatr5b G A 17: 79,139,013 (GRCm39) T43I probably benign Het
Hephl1 T C 9: 14,997,586 (GRCm39) Y360C probably damaging Het
Itgam A C 7: 127,715,012 (GRCm39) T865P possibly damaging Het
Kcnma1 T C 14: 24,054,186 (GRCm39) probably benign Het
Kidins220 T A 12: 25,042,259 (GRCm39) C185* probably null Het
Klhl35 G T 7: 99,118,275 (GRCm39) G273V probably damaging Het
Lama5 A G 2: 179,850,045 (GRCm39) probably null Het
Lamc3 A G 2: 31,805,966 (GRCm39) Q689R probably benign Het
Lnx2 C T 5: 146,955,850 (GRCm39) V649I probably benign Het
Lrrc43 A G 5: 123,637,675 (GRCm39) I281V probably benign Het
Ly6g6d C A 17: 35,290,730 (GRCm39) A67S probably benign Het
Map1b A G 13: 99,568,720 (GRCm39) S1334P probably benign Het
Mast1 T A 8: 85,644,500 (GRCm39) T810S probably benign Het
Matcap1 G T 8: 106,009,843 (GRCm39) R369S probably damaging Het
Mbnl1 A G 3: 60,503,117 (GRCm39) M1V probably null Het
Mc5r T G 18: 68,471,890 (GRCm39) M83R possibly damaging Het
Mkln1 T C 6: 31,435,941 (GRCm39) F300S probably damaging Het
Mrgpre A T 7: 143,335,088 (GRCm39) C138* probably null Het
Mtarc2 T A 1: 184,566,116 (GRCm39) M186L probably benign Het
Ncbp1 C T 4: 46,165,273 (GRCm39) Q529* probably null Het
Nherf1 A G 11: 115,067,289 (GRCm39) D180G probably benign Het
Nrcam A G 12: 44,613,082 (GRCm39) D591G probably benign Het
Nrxn3 A T 12: 88,761,971 (GRCm39) H6L possibly damaging Het
Nsmaf T A 4: 6,423,342 (GRCm39) D342V probably damaging Het
Oip5 TGAGAAA T 2: 119,448,342 (GRCm39) probably benign Het
Omt2a T A 9: 78,220,305 (GRCm39) E31D possibly damaging Het
Or4f62 A G 2: 111,986,697 (GRCm39) T134A probably benign Het
Or52n2b A G 7: 104,565,915 (GRCm39) I196T probably benign Het
Or5ac20 A G 16: 59,104,348 (GRCm39) S171P probably benign Het
Or6c88 A C 10: 129,406,895 (GRCm39) I124L probably damaging Het
Or9a2 C A 6: 41,749,003 (GRCm39) V77F probably damaging Het
Phyhipl A G 10: 70,404,815 (GRCm39) V131A probably benign Het
Pik3r5 A G 11: 68,384,464 (GRCm39) M619V probably benign Het
Pramel19 T C 4: 101,798,661 (GRCm39) Y211H probably benign Het
Ptprg A T 14: 12,237,837 (GRCm38) E1431D probably benign Het
Rnf20 A G 4: 49,638,029 (GRCm39) T85A probably damaging Het
Rtn3 A T 19: 7,433,886 (GRCm39) I683K probably damaging Het
Rwdd3 A G 3: 120,952,470 (GRCm39) F174L probably damaging Het
Ryr1 T C 7: 28,778,208 (GRCm39) Q2096R possibly damaging Het
Scrn1 T C 6: 54,511,407 (GRCm39) D111G probably damaging Het
Sema3e A G 5: 14,302,646 (GRCm39) R724G possibly damaging Het
She A G 3: 89,741,544 (GRCm39) M232V possibly damaging Het
Skic3 T A 13: 76,333,275 (GRCm39) V1508E possibly damaging Het
Slc25a54 A T 3: 109,020,132 (GRCm39) N382I possibly damaging Het
Slc26a2 T C 18: 61,331,875 (GRCm39) M519V probably damaging Het
Slc9a1 T A 4: 133,097,967 (GRCm39) L38H probably damaging Het
Snap47 A T 11: 59,319,369 (GRCm39) D256E probably damaging Het
Tacc3 A G 5: 33,829,326 (GRCm39) T610A probably benign Het
Tbc1d30 G A 10: 121,103,121 (GRCm39) T637M probably benign Het
Tbcd T A 11: 121,464,681 (GRCm39) M572K probably benign Het
Thoc7 A T 14: 13,953,460 (GRCm38) D68E probably benign Het
Tmpo G A 10: 90,989,171 (GRCm39) T250M probably damaging Het
Tmtc1 TGTCCGCCAGGCCCTTGCCCCAGAAGTC TGTC 6: 148,345,445 (GRCm39) probably benign Het
Tnfaip1 A T 11: 78,418,396 (GRCm39) C224S possibly damaging Het
Tshz1 T C 18: 84,032,987 (GRCm39) T474A probably benign Het
Tspoap1 C T 11: 87,657,222 (GRCm39) Q345* probably null Het
Ttc21a A G 9: 119,774,067 (GRCm39) E258G possibly damaging Het
Ttyh1 T C 7: 4,131,225 (GRCm39) L232P probably damaging Het
Usp2 T A 9: 43,987,110 (GRCm39) L136Q probably damaging Het
Usp31 T C 7: 121,247,868 (GRCm39) S1192G probably damaging Het
Other mutations in Chd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00704:Chd1 APN 17 15,952,827 (GRCm39) missense probably benign 0.37
IGL01356:Chd1 APN 17 15,970,127 (GRCm39) missense probably damaging 1.00
IGL01369:Chd1 APN 17 15,975,259 (GRCm39) missense probably damaging 0.97
IGL01519:Chd1 APN 17 17,598,831 (GRCm39) missense probably damaging 1.00
IGL01604:Chd1 APN 17 15,990,359 (GRCm39) missense possibly damaging 0.95
IGL01635:Chd1 APN 17 17,598,858 (GRCm39) missense probably damaging 1.00
IGL01721:Chd1 APN 17 15,990,430 (GRCm39) missense probably damaging 1.00
IGL01959:Chd1 APN 17 15,962,435 (GRCm39) missense probably damaging 1.00
IGL02367:Chd1 APN 17 17,610,315 (GRCm39) missense probably damaging 0.98
IGL02476:Chd1 APN 17 15,954,535 (GRCm39) missense probably damaging 1.00
IGL02756:Chd1 APN 17 15,951,069 (GRCm39) missense probably damaging 0.97
IGL02817:Chd1 APN 17 15,969,762 (GRCm39) missense possibly damaging 0.92
IGL03084:Chd1 APN 17 15,990,560 (GRCm39) missense probably benign 0.22
IGL03108:Chd1 APN 17 15,945,543 (GRCm39) missense possibly damaging 0.70
Holly UTSW 17 15,946,545 (GRCm39) missense possibly damaging 0.72
R0053:Chd1 UTSW 17 15,967,451 (GRCm39) missense probably damaging 1.00
R0053:Chd1 UTSW 17 15,967,451 (GRCm39) missense probably damaging 1.00
R0128:Chd1 UTSW 17 17,613,829 (GRCm39) missense probably damaging 1.00
R0197:Chd1 UTSW 17 15,945,693 (GRCm39) missense probably benign
R0285:Chd1 UTSW 17 17,594,942 (GRCm39) splice site probably benign
R0326:Chd1 UTSW 17 15,988,830 (GRCm39) missense probably benign
R0326:Chd1 UTSW 17 15,988,828 (GRCm39) missense probably damaging 1.00
R0372:Chd1 UTSW 17 17,607,552 (GRCm39) missense probably benign 0.14
R0391:Chd1 UTSW 17 15,970,156 (GRCm39) missense probably damaging 1.00
R0486:Chd1 UTSW 17 15,954,604 (GRCm39) missense probably damaging 0.99
R0637:Chd1 UTSW 17 15,962,550 (GRCm39) missense possibly damaging 0.50
R0675:Chd1 UTSW 17 15,978,523 (GRCm39) unclassified probably benign
R0701:Chd1 UTSW 17 15,945,693 (GRCm39) missense probably benign
R0788:Chd1 UTSW 17 15,927,376 (GRCm39) missense possibly damaging 0.86
R0848:Chd1 UTSW 17 15,990,503 (GRCm39) missense probably damaging 1.00
R0883:Chd1 UTSW 17 15,945,693 (GRCm39) missense probably benign
R1169:Chd1 UTSW 17 15,955,994 (GRCm39) missense probably damaging 1.00
R1218:Chd1 UTSW 17 15,945,574 (GRCm39) missense probably damaging 1.00
R1370:Chd1 UTSW 17 17,607,742 (GRCm39) missense probably benign 0.00
R1470:Chd1 UTSW 17 15,946,545 (GRCm39) missense possibly damaging 0.72
R1470:Chd1 UTSW 17 15,946,545 (GRCm39) missense possibly damaging 0.72
R1478:Chd1 UTSW 17 15,959,769 (GRCm39) missense probably damaging 0.99
R1752:Chd1 UTSW 17 15,963,494 (GRCm39) critical splice donor site probably null
R1759:Chd1 UTSW 17 17,607,533 (GRCm39) missense probably benign 0.00
R1767:Chd1 UTSW 17 15,990,565 (GRCm39) missense probably damaging 1.00
R1938:Chd1 UTSW 17 15,982,748 (GRCm39) missense probably benign 0.39
R2007:Chd1 UTSW 17 15,951,268 (GRCm39) missense probably damaging 1.00
R2069:Chd1 UTSW 17 15,962,556 (GRCm39) missense probably damaging 1.00
R3771:Chd1 UTSW 17 17,594,913 (GRCm39) missense probably damaging 1.00
R3773:Chd1 UTSW 17 17,594,913 (GRCm39) missense probably damaging 1.00
R3849:Chd1 UTSW 17 15,952,133 (GRCm39) missense probably damaging 1.00
R4241:Chd1 UTSW 17 15,990,289 (GRCm39) nonsense probably null
R4242:Chd1 UTSW 17 15,990,289 (GRCm39) nonsense probably null
R4354:Chd1 UTSW 17 17,610,263 (GRCm39) missense probably benign 0.23
R4468:Chd1 UTSW 17 15,980,657 (GRCm39) missense probably damaging 0.99
R4469:Chd1 UTSW 17 15,980,657 (GRCm39) missense probably damaging 0.99
R4731:Chd1 UTSW 17 17,598,079 (GRCm39) missense probably benign 0.36
R4824:Chd1 UTSW 17 15,953,386 (GRCm39) missense probably damaging 1.00
R4840:Chd1 UTSW 17 15,989,016 (GRCm39) missense probably damaging 1.00
R4840:Chd1 UTSW 17 15,989,015 (GRCm39) nonsense probably null
R4880:Chd1 UTSW 17 17,594,916 (GRCm39) missense probably damaging 1.00
R5071:Chd1 UTSW 17 15,982,667 (GRCm39) missense probably benign
R5078:Chd1 UTSW 17 15,946,616 (GRCm39) missense possibly damaging 0.93
R5114:Chd1 UTSW 17 15,948,460 (GRCm39) missense probably benign 0.25
R5268:Chd1 UTSW 17 15,956,005 (GRCm39) missense probably damaging 1.00
R5304:Chd1 UTSW 17 15,990,530 (GRCm39) missense possibly damaging 0.55
R5304:Chd1 UTSW 17 15,975,213 (GRCm39) missense probably benign 0.01
R5307:Chd1 UTSW 17 15,952,832 (GRCm39) missense probably damaging 1.00
R5458:Chd1 UTSW 17 15,958,811 (GRCm39) missense probably damaging 1.00
R5553:Chd1 UTSW 17 17,605,875 (GRCm39) missense probably benign 0.17
R5623:Chd1 UTSW 17 15,975,194 (GRCm39) missense probably damaging 1.00
R6022:Chd1 UTSW 17 17,598,035 (GRCm39) missense probably benign 0.39
R6137:Chd1 UTSW 17 15,978,950 (GRCm39) missense probably damaging 1.00
R6257:Chd1 UTSW 17 15,950,465 (GRCm39) splice site probably null
R6373:Chd1 UTSW 17 15,958,898 (GRCm39) missense probably damaging 1.00
R6458:Chd1 UTSW 17 15,950,864 (GRCm39) missense probably benign 0.01
R6476:Chd1 UTSW 17 17,601,250 (GRCm39) critical splice donor site probably null
R6508:Chd1 UTSW 17 15,958,895 (GRCm39) missense probably benign 0.31
R6553:Chd1 UTSW 17 15,945,692 (GRCm39) missense probably benign 0.00
R6745:Chd1 UTSW 17 17,607,429 (GRCm39) missense probably benign 0.08
R7107:Chd1 UTSW 17 15,981,628 (GRCm39) missense probably damaging 0.98
R7230:Chd1 UTSW 17 15,927,199 (GRCm39) splice site probably null
R7317:Chd1 UTSW 17 15,962,536 (GRCm39) missense possibly damaging 0.71
R7341:Chd1 UTSW 17 15,990,499 (GRCm39) missense probably damaging 0.99
R7421:Chd1 UTSW 17 15,969,660 (GRCm39) missense probably benign 0.03
R7704:Chd1 UTSW 17 15,987,737 (GRCm39) missense probably benign
R7763:Chd1 UTSW 17 15,953,303 (GRCm39) missense probably damaging 1.00
R8156:Chd1 UTSW 17 15,981,666 (GRCm39) missense probably benign
R8194:Chd1 UTSW 17 17,594,737 (GRCm39) start gained probably benign
R8261:Chd1 UTSW 17 17,607,804 (GRCm39) missense probably benign 0.02
R8338:Chd1 UTSW 17 15,990,242 (GRCm39) missense probably damaging 1.00
R8401:Chd1 UTSW 17 15,963,473 (GRCm39) missense probably damaging 1.00
R8411:Chd1 UTSW 17 15,982,711 (GRCm39) missense probably damaging 0.98
R9067:Chd1 UTSW 17 15,951,107 (GRCm39) missense possibly damaging 0.49
R9184:Chd1 UTSW 17 15,962,551 (GRCm39) missense possibly damaging 0.71
R9210:Chd1 UTSW 17 15,950,767 (GRCm39) missense possibly damaging 0.70
R9212:Chd1 UTSW 17 15,950,767 (GRCm39) missense possibly damaging 0.70
R9666:Chd1 UTSW 17 15,955,976 (GRCm39) missense probably damaging 1.00
R9673:Chd1 UTSW 17 15,989,023 (GRCm39) missense probably benign 0.24
Z1176:Chd1 UTSW 17 15,988,995 (GRCm39) missense probably damaging 1.00
Z1176:Chd1 UTSW 17 15,986,609 (GRCm39) missense probably damaging 0.98
Z1177:Chd1 UTSW 17 15,968,063 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AACCACGAGCTTCAGGATG -3'
(R):5'- ACAACTCACTGGTTTGAAAGAC -3'

Sequencing Primer
(F):5'- CCACGAGCTTCAGGATGATGAC -3'
(R):5'- ACATTAACCAAAGAGAACTTGACATG -3'
Posted On 2016-04-27