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 15704967-15772610 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 17374651 bp (GRCm38)
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
1700061G19Rik T C 17: 56,876,262 (GRCm38) M1T probably null Het
1810041L15Rik A T 15: 84,406,685 (GRCm38) Y120* probably null Het
A2ml1 T A 6: 128,555,083 (GRCm38) K899N probably benign Het
Adgrv1 G A 13: 81,499,043 (GRCm38) S3126L probably damaging Het
Apba3 C A 10: 81,272,609 (GRCm38) probably null Het
Apobec4 G T 1: 152,756,805 (GRCm38) A195S probably benign Het
Asap3 C T 4: 136,227,575 (GRCm38) T72I probably benign Het
BC067074 A G 13: 113,318,209 (GRCm38) E263G probably benign Het
Cand2 T A 6: 115,785,217 (GRCm38) H201Q probably damaging Het
Cd109 CATTTATTTATTTATTTATTTATTTATTTATTTAT CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT 9: 78,712,500 (GRCm38) probably benign Het
Csgalnact2 T C 6: 118,126,219 (GRCm38) K19E probably benign Het
Cyp17a1 T G 19: 46,669,723 (GRCm38) K250T probably damaging Het
Ddx41 G A 13: 55,534,480 (GRCm38) R205W possibly damaging Het
Dgcr8 T C 16: 18,256,775 (GRCm38) D712G probably damaging Het
Dsg2 T C 18: 20,591,862 (GRCm38) W442R probably damaging Het
Elavl2 C T 4: 91,264,088 (GRCm38) G131R probably damaging Het
Elf1 T C 14: 79,567,210 (GRCm38) V105A possibly damaging Het
Ercc6l2 A G 13: 63,841,450 (GRCm38) D270G probably damaging Het
Fmn1 T G 2: 113,582,118 (GRCm38) S996A probably damaging Het
Frmd4a A T 2: 4,590,622 (GRCm38) E109D probably damaging Het
Fry A T 5: 150,398,198 (GRCm38) R999S probably damaging Het
Gak G A 5: 108,582,672 (GRCm38) T956I probably benign Het
Gm6614 T C 6: 141,972,335 (GRCm38) K605R probably benign Het
Gm9008 C T 6: 76,496,959 (GRCm38) V225I probably benign Het
Gps2 T C 11: 69,916,101 (GRCm38) F21L probably damaging Het
Grhl3 C T 4: 135,555,847 (GRCm38) W303* probably null Het
Hmcn2 C T 2: 31,360,896 (GRCm38) T790M probably damaging Het
Lrp5 G A 19: 3,612,330 (GRCm38) R173C probably damaging Het
Matk T A 10: 81,258,297 (GRCm38) L21Q probably benign Het
Mthfr T C 4: 148,044,450 (GRCm38) V160A probably benign Het
Nhlrc4 T A 17: 25,943,393 (GRCm38) K127* probably null Het
Nsd1 G A 13: 55,246,673 (GRCm38) V696I probably benign Het
Nup210l T G 3: 90,119,894 (GRCm38) Y194* probably null Het
Olfr1497 T A 19: 13,795,204 (GRCm38) M136L probably benign Het
Olfr345 A T 2: 36,640,321 (GRCm38) Y94F probably benign Het
Olfr57 G A 10: 79,035,180 (GRCm38) C128Y possibly damaging Het
Olfr90 G T 17: 37,086,065 (GRCm38) Y33* probably null Het
Pcdhb15 T A 18: 37,475,890 (GRCm38) V725D probably benign Het
Pes1 A G 11: 3,975,548 (GRCm38) Y221C probably damaging Het
Prkd3 T C 17: 78,959,106 (GRCm38) I603V possibly damaging Het
Ptpn13 A G 5: 103,477,121 (GRCm38) E97G probably damaging Het
Ptpro T A 6: 137,443,594 (GRCm38) V1007D probably damaging Het
Ptprs T C 17: 56,428,978 (GRCm38) T152A possibly damaging Het
Rims1 T C 1: 22,421,810 (GRCm38) D842G probably damaging Het
Rin2 C T 2: 145,860,446 (GRCm38) T354I probably benign Het
Rngtt T C 4: 33,330,889 (GRCm38) I164T probably damaging Het
Scn9a T C 2: 66,483,648 (GRCm38) N1909D probably benign Het
Ska3 C T 14: 57,810,077 (GRCm38) V334I probably benign Het
Srebf2 A G 15: 82,182,108 (GRCm38) K579R probably benign Het
Stxbp5 G A 10: 9,768,927 (GRCm38) T960I probably damaging Het
Suco A T 1: 161,843,996 (GRCm38) probably null Het
Tecta T C 9: 42,330,996 (GRCm38) T2094A probably damaging Het
Tenm4 A T 7: 96,694,880 (GRCm38) R227W probably damaging Het
Tmem131l A G 3: 83,898,586 (GRCm38) S1517P probably damaging Het
Trio A G 15: 27,748,091 (GRCm38) S2492P probably damaging Het
Tsg101 T C 7: 46,889,615 (GRCm38) *254W probably null Het
Ttn T C 2: 76,771,367 (GRCm38) T16872A probably benign Het
Ugt2b38 A G 5: 87,424,095 (GRCm38) V26A probably damaging Het
Upb1 T A 10: 75,439,838 (GRCm38) probably null Het
Vmn1r32 T A 6: 66,553,367 (GRCm38) I142F probably benign Het
Vmn1r60 C A 7: 5,544,711 (GRCm38) C130F possibly damaging Het
Vmn2r101 A G 17: 19,589,657 (GRCm38) D235G probably benign Het
Wnk1 C T 6: 120,002,280 (GRCm38) R282Q possibly damaging Het
Xrn2 T C 2: 147,061,287 (GRCm38) V765A probably benign Het
Zbed4 T C 15: 88,780,847 (GRCm38) S373P probably benign Het
Zfp251 A G 15: 76,853,636 (GRCm38) I414T possibly damaging Het
Zfp423 A T 8: 87,780,512 (GRCm38) L1047Q probably benign Het
Zfp426 A T 9: 20,473,117 (GRCm38) probably null Het
Zfp61 T C 7: 24,295,981 (GRCm38) M1V probably null Het
Other mutations in Chd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00704:Chd1 APN 17 15,732,565 (GRCm38) missense probably benign 0.37
IGL01356:Chd1 APN 17 15,749,865 (GRCm38) missense probably damaging 1.00
IGL01369:Chd1 APN 17 15,754,997 (GRCm38) missense probably damaging 0.97
IGL01519:Chd1 APN 17 17,378,569 (GRCm38) missense probably damaging 1.00
IGL01604:Chd1 APN 17 15,770,097 (GRCm38) missense possibly damaging 0.95
IGL01635:Chd1 APN 17 17,378,596 (GRCm38) missense probably damaging 1.00
IGL01721:Chd1 APN 17 15,770,168 (GRCm38) missense probably damaging 1.00
IGL01959:Chd1 APN 17 15,742,173 (GRCm38) missense probably damaging 1.00
IGL02367:Chd1 APN 17 17,390,053 (GRCm38) missense probably damaging 0.98
IGL02476:Chd1 APN 17 15,734,273 (GRCm38) missense probably damaging 1.00
IGL02756:Chd1 APN 17 15,730,807 (GRCm38) missense probably damaging 0.97
IGL02817:Chd1 APN 17 15,749,500 (GRCm38) missense possibly damaging 0.92
IGL03084:Chd1 APN 17 15,770,298 (GRCm38) missense probably benign 0.22
IGL03108:Chd1 APN 17 15,725,281 (GRCm38) missense possibly damaging 0.70
Holly UTSW 17 15,726,283 (GRCm38) missense possibly damaging 0.72
R0053:Chd1 UTSW 17 15,747,189 (GRCm38) missense probably damaging 1.00
R0053:Chd1 UTSW 17 15,747,189 (GRCm38) missense probably damaging 1.00
R0128:Chd1 UTSW 17 17,393,567 (GRCm38) missense probably damaging 1.00
R0197:Chd1 UTSW 17 15,725,431 (GRCm38) missense probably benign
R0285:Chd1 UTSW 17 17,374,680 (GRCm38) splice site probably benign
R0326:Chd1 UTSW 17 15,768,568 (GRCm38) missense probably benign
R0326:Chd1 UTSW 17 15,768,566 (GRCm38) missense probably damaging 1.00
R0372:Chd1 UTSW 17 17,387,290 (GRCm38) missense probably benign 0.14
R0391:Chd1 UTSW 17 15,749,894 (GRCm38) missense probably damaging 1.00
R0486:Chd1 UTSW 17 15,734,342 (GRCm38) missense probably damaging 0.99
R0637:Chd1 UTSW 17 15,742,288 (GRCm38) missense possibly damaging 0.50
R0675:Chd1 UTSW 17 15,758,261 (GRCm38) unclassified probably benign
R0701:Chd1 UTSW 17 15,725,431 (GRCm38) missense probably benign
R0788:Chd1 UTSW 17 15,707,114 (GRCm38) missense possibly damaging 0.86
R0848:Chd1 UTSW 17 15,770,241 (GRCm38) missense probably damaging 1.00
R0883:Chd1 UTSW 17 15,725,431 (GRCm38) missense probably benign
R1169:Chd1 UTSW 17 15,735,732 (GRCm38) missense probably damaging 1.00
R1218:Chd1 UTSW 17 15,725,312 (GRCm38) missense probably damaging 1.00
R1370:Chd1 UTSW 17 17,387,480 (GRCm38) missense probably benign 0.00
R1470:Chd1 UTSW 17 15,726,283 (GRCm38) missense possibly damaging 0.72
R1470:Chd1 UTSW 17 15,726,283 (GRCm38) missense possibly damaging 0.72
R1478:Chd1 UTSW 17 15,739,507 (GRCm38) missense probably damaging 0.99
R1752:Chd1 UTSW 17 15,743,232 (GRCm38) critical splice donor site probably null
R1759:Chd1 UTSW 17 17,387,271 (GRCm38) missense probably benign 0.00
R1767:Chd1 UTSW 17 15,770,303 (GRCm38) missense probably damaging 1.00
R1938:Chd1 UTSW 17 15,762,486 (GRCm38) missense probably benign 0.39
R2007:Chd1 UTSW 17 15,731,006 (GRCm38) missense probably damaging 1.00
R2069:Chd1 UTSW 17 15,742,294 (GRCm38) missense probably damaging 1.00
R3771:Chd1 UTSW 17 17,374,651 (GRCm38) missense probably damaging 1.00
R3849:Chd1 UTSW 17 15,731,871 (GRCm38) missense probably damaging 1.00
R4241:Chd1 UTSW 17 15,770,027 (GRCm38) nonsense probably null
R4242:Chd1 UTSW 17 15,770,027 (GRCm38) nonsense probably null
R4354:Chd1 UTSW 17 17,390,001 (GRCm38) missense probably benign 0.23
R4468:Chd1 UTSW 17 15,760,395 (GRCm38) missense probably damaging 0.99
R4469:Chd1 UTSW 17 15,760,395 (GRCm38) missense probably damaging 0.99
R4731:Chd1 UTSW 17 17,377,817 (GRCm38) missense probably benign 0.36
R4824:Chd1 UTSW 17 15,733,124 (GRCm38) missense probably damaging 1.00
R4840:Chd1 UTSW 17 15,768,754 (GRCm38) missense probably damaging 1.00
R4840:Chd1 UTSW 17 15,768,753 (GRCm38) nonsense probably null
R4880:Chd1 UTSW 17 17,374,654 (GRCm38) missense probably damaging 1.00
R4960:Chd1 UTSW 17 15,742,231 (GRCm38) missense probably damaging 0.96
R5071:Chd1 UTSW 17 15,762,405 (GRCm38) missense probably benign
R5078:Chd1 UTSW 17 15,726,354 (GRCm38) missense possibly damaging 0.93
R5114:Chd1 UTSW 17 15,728,198 (GRCm38) missense probably benign 0.25
R5268:Chd1 UTSW 17 15,735,743 (GRCm38) missense probably damaging 1.00
R5304:Chd1 UTSW 17 15,770,268 (GRCm38) missense possibly damaging 0.55
R5304:Chd1 UTSW 17 15,754,951 (GRCm38) missense probably benign 0.01
R5307:Chd1 UTSW 17 15,732,570 (GRCm38) missense probably damaging 1.00
R5458:Chd1 UTSW 17 15,738,549 (GRCm38) missense probably damaging 1.00
R5553:Chd1 UTSW 17 17,385,613 (GRCm38) missense probably benign 0.17
R5623:Chd1 UTSW 17 15,754,932 (GRCm38) missense probably damaging 1.00
R6022:Chd1 UTSW 17 17,377,773 (GRCm38) missense probably benign 0.39
R6137:Chd1 UTSW 17 15,758,688 (GRCm38) missense probably damaging 1.00
R6257:Chd1 UTSW 17 15,730,203 (GRCm38) splice site probably null
R6373:Chd1 UTSW 17 15,738,636 (GRCm38) missense probably damaging 1.00
R6458:Chd1 UTSW 17 15,730,602 (GRCm38) missense probably benign 0.01
R6476:Chd1 UTSW 17 17,380,988 (GRCm38) critical splice donor site probably null
R6508:Chd1 UTSW 17 15,738,633 (GRCm38) missense probably benign 0.31
R6553:Chd1 UTSW 17 15,725,430 (GRCm38) missense probably benign 0.00
R6745:Chd1 UTSW 17 17,387,167 (GRCm38) missense probably benign 0.08
R7107:Chd1 UTSW 17 15,761,366 (GRCm38) missense probably damaging 0.98
R7230:Chd1 UTSW 17 15,706,937 (GRCm38) splice site probably null
R7317:Chd1 UTSW 17 15,742,274 (GRCm38) missense possibly damaging 0.71
R7341:Chd1 UTSW 17 15,770,237 (GRCm38) missense probably damaging 0.99
R7421:Chd1 UTSW 17 15,749,398 (GRCm38) missense probably benign 0.03
R7704:Chd1 UTSW 17 15,767,475 (GRCm38) missense probably benign
R7763:Chd1 UTSW 17 15,733,041 (GRCm38) missense probably damaging 1.00
R8156:Chd1 UTSW 17 15,761,404 (GRCm38) missense probably benign
R8194:Chd1 UTSW 17 17,374,475 (GRCm38) start gained probably benign
R8261:Chd1 UTSW 17 17,387,542 (GRCm38) missense probably benign 0.02
R8338:Chd1 UTSW 17 15,769,980 (GRCm38) missense probably damaging 1.00
R8401:Chd1 UTSW 17 15,743,211 (GRCm38) missense probably damaging 1.00
R8411:Chd1 UTSW 17 15,762,449 (GRCm38) missense probably damaging 0.98
R9067:Chd1 UTSW 17 15,730,845 (GRCm38) missense possibly damaging 0.49
R9184:Chd1 UTSW 17 15,742,289 (GRCm38) missense possibly damaging 0.71
R9210:Chd1 UTSW 17 15,730,505 (GRCm38) missense possibly damaging 0.70
R9212:Chd1 UTSW 17 15,730,505 (GRCm38) missense possibly damaging 0.70
R9666:Chd1 UTSW 17 15,735,714 (GRCm38) missense probably damaging 1.00
R9673:Chd1 UTSW 17 15,768,761 (GRCm38) missense probably benign 0.24
Z1176:Chd1 UTSW 17 15,768,733 (GRCm38) missense probably damaging 1.00
Z1176:Chd1 UTSW 17 15,766,347 (GRCm38) missense probably damaging 0.98
Z1177:Chd1 UTSW 17 15,747,801 (GRCm38) 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