Incidental Mutation 'R3773:Chd1'
ID 273465
Institutional Source Beutler Lab
Gene Symbol Chd1
Ensembl Gene ENSMUSG00000023852
Gene Name chromodomain helicase DNA binding protein 1
Synonyms 4930525N21Rik
MMRRC Submission 040749-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3773 (G1)
Quality Score 225
Status Not validated
Chromosome 17
Chromosomal Location 15925229-15992872 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 17594913 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 16 (D16G)
Ref Sequence ENSEMBL: ENSMUSP00000156350 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000024620] [ENSMUST00000232199] [ENSMUST00000232396]
AlphaFold P40201
Predicted Effect probably damaging
Transcript: ENSMUST00000024620
AA Change: D16G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000024620
Gene: ENSMUSG00000116564
AA Change: D16G

DomainStartEndE-ValueType
Pfam:Rio2_N 9 91 9.5e-36 PFAM
Pfam:Kdo 105 193 6.3e-8 PFAM
Pfam:RIO1 108 284 1.7e-57 PFAM
Pfam:APH 194 278 3.2e-8 PFAM
low complexity region 326 340 N/A INTRINSIC
low complexity region 501 518 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000232199
Predicted Effect noncoding transcript
Transcript: ENSMUST00000232288
Predicted Effect probably damaging
Transcript: ENSMUST00000232396
AA Change: D16G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
Meta Mutation Damage Score 0.6931 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.2%
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: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A2ml1 T A 6: 128,532,046 (GRCm39) K899N probably benign Het
Acsbg3 T C 17: 57,183,262 (GRCm39) M1T probably null Het
Adgrv1 G A 13: 81,647,162 (GRCm39) S3126L probably damaging Het
Apba3 C A 10: 81,108,443 (GRCm39) probably null Het
Apobec4 G T 1: 152,632,556 (GRCm39) A195S probably benign Het
Asap3 C T 4: 135,954,886 (GRCm39) T72I probably benign Het
Cand2 T A 6: 115,762,178 (GRCm39) H201Q probably damaging Het
Cd109 CATTTATTTATTTATTTATTTATTTATTTATTTAT CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT 9: 78,619,782 (GRCm39) probably benign Het
Csgalnact2 T C 6: 118,103,180 (GRCm39) K19E probably benign Het
Cspg4b A G 13: 113,454,743 (GRCm39) E263G probably benign Het
Cyp17a1 T G 19: 46,658,162 (GRCm39) K250T probably damaging Het
Ddx41 G A 13: 55,682,293 (GRCm39) R205W possibly damaging Het
Dgcr8 T C 16: 18,074,639 (GRCm39) D712G probably damaging Het
Dsg2 T C 18: 20,724,919 (GRCm39) W442R probably damaging Het
Elavl2 C T 4: 91,152,325 (GRCm39) G131R probably damaging Het
Elf1 T C 14: 79,804,650 (GRCm39) V105A possibly damaging Het
Ercc6l2 A G 13: 63,989,264 (GRCm39) D270G probably damaging Het
Fmn1 T G 2: 113,412,463 (GRCm39) S996A probably damaging Het
Frmd4a A T 2: 4,595,433 (GRCm39) E109D probably damaging Het
Fry A T 5: 150,321,663 (GRCm39) R999S probably damaging Het
Gak G A 5: 108,730,538 (GRCm39) T956I probably benign Het
Gps2 T C 11: 69,806,927 (GRCm39) F21L probably damaging Het
Grhl3 C T 4: 135,283,158 (GRCm39) W303* probably null Het
Hmcn2 C T 2: 31,250,908 (GRCm39) T790M probably damaging Het
Lrp5 G A 19: 3,662,330 (GRCm39) R173C probably damaging Het
Matk T A 10: 81,094,131 (GRCm39) L21Q probably benign Het
Mthfr T C 4: 148,128,907 (GRCm39) V160A probably benign Het
Nhlrc4 T A 17: 26,162,367 (GRCm39) K127* probably null Het
Nsd1 G A 13: 55,394,486 (GRCm39) V696I probably benign Het
Nup210l T G 3: 90,027,201 (GRCm39) Y194* probably null Het
Or1j16 A T 2: 36,530,333 (GRCm39) Y94F probably benign Het
Or2h2 G T 17: 37,396,957 (GRCm39) Y33* probably null Het
Or7a41 G A 10: 78,871,014 (GRCm39) C128Y possibly damaging Het
Or9q2 T A 19: 13,772,568 (GRCm39) M136L probably benign Het
Pcdhb15 T A 18: 37,608,943 (GRCm39) V725D probably benign Het
Pes1 A G 11: 3,925,548 (GRCm39) Y221C probably damaging Het
Prkd3 T C 17: 79,266,535 (GRCm39) I603V possibly damaging Het
Ptpn13 A G 5: 103,624,987 (GRCm39) E97G probably damaging Het
Ptpro T A 6: 137,420,592 (GRCm39) V1007D probably damaging Het
Ptprs T C 17: 56,735,978 (GRCm39) T152A possibly damaging Het
Rims1 T C 1: 22,492,034 (GRCm39) D842G probably damaging Het
Rin2 C T 2: 145,702,366 (GRCm39) T354I probably benign Het
Rnf26rt C T 6: 76,473,942 (GRCm39) V225I probably benign Het
Rngtt T C 4: 33,330,889 (GRCm39) I164T probably damaging Het
Scn9a T C 2: 66,313,992 (GRCm39) N1909D probably benign Het
Shisal1 A T 15: 84,290,886 (GRCm39) Y120* probably null Het
Ska3 C T 14: 58,047,534 (GRCm39) V334I probably benign Het
Slco1a8 T C 6: 141,918,061 (GRCm39) K605R probably benign Het
Srebf2 A G 15: 82,066,309 (GRCm39) K579R probably benign Het
Stxbp5 G A 10: 9,644,671 (GRCm39) T960I probably damaging Het
Suco A T 1: 161,671,565 (GRCm39) probably null Het
Tecta T C 9: 42,242,292 (GRCm39) T2094A probably damaging Het
Tenm4 A T 7: 96,344,087 (GRCm39) R227W probably damaging Het
Tmem131l A G 3: 83,805,893 (GRCm39) S1517P probably damaging Het
Trio A G 15: 27,748,177 (GRCm39) S2492P probably damaging Het
Tsg101 T C 7: 46,539,363 (GRCm39) *254W probably null Het
Ttn T C 2: 76,601,711 (GRCm39) T16872A probably benign Het
Ugt2b38 A G 5: 87,571,954 (GRCm39) V26A probably damaging Het
Upb1 T A 10: 75,275,672 (GRCm39) probably null Het
Vmn1r32 T A 6: 66,530,351 (GRCm39) I142F probably benign Het
Vmn1r60 C A 7: 5,547,710 (GRCm39) C130F possibly damaging Het
Vmn2r101 A G 17: 19,809,919 (GRCm39) D235G probably benign Het
Wnk1 C T 6: 119,979,241 (GRCm39) R282Q possibly damaging Het
Xrn2 T C 2: 146,903,207 (GRCm39) V765A probably benign Het
Zbed4 T C 15: 88,665,050 (GRCm39) S373P probably benign Het
Zfp251 A G 15: 76,737,836 (GRCm39) I414T possibly damaging Het
Zfp423 A T 8: 88,507,140 (GRCm39) L1047Q probably benign Het
Zfp426 A T 9: 20,384,413 (GRCm39) probably null Het
Zfp61 T C 7: 23,995,406 (GRCm39) M1V probably null 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
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
R4960:Chd1 UTSW 17 15,962,493 (GRCm39) missense probably damaging 0.96
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'- GAGCACGTGTTCTTACCTAGCG -3'
(R):5'- ACGTAAGCACATCTGCAGC -3'

Sequencing Primer
(F):5'- GCACGTGTTCTTACCTAGCGATAAG -3'
(R):5'- GTAAGCACATCTGCAGCAAAAG -3'
Posted On 2015-03-25