Incidental Mutation 'R1478:Chd1'
ID 165662
Institutional Source Beutler Lab
Gene Symbol Chd1
Ensembl Gene ENSMUSG00000023852
Gene Name chromodomain helicase DNA binding protein 1
Synonyms 4930525N21Rik
MMRRC Submission 039531-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1478 (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 C at 15959769 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 663 (F663L)
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: F663L

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000024627
Gene: ENSMUSG00000023852
AA Change: F663L

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: F663L

PolyPhen 2 Score 0.885 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000134091
Gene: ENSMUSG00000023852
AA Change: F663L

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: F47L
SMART Domains Protein: ENSMUSP00000134718
Gene: ENSMUSG00000023852
AA Change: F47L

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: 99.1%
  • 3x: 98.2%
  • 10x: 95.7%
  • 20x: 90.6%
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aacs T A 5: 125,580,287 (GRCm39) I204N possibly damaging Het
Acaca A G 11: 84,263,453 (GRCm39) T2025A probably damaging Het
B4galt3 C T 1: 171,103,938 (GRCm39) R170C probably benign Het
BC028528 T C 3: 95,799,271 (GRCm39) probably null Het
Ccdc73 A T 2: 104,737,955 (GRCm39) Q17L possibly damaging Het
Ccdc73 A G 2: 104,745,012 (GRCm39) T50A possibly damaging Het
Ccdc83 T C 7: 89,908,677 (GRCm39) D19G probably damaging Het
Ccn6 G A 10: 39,029,239 (GRCm39) R230W probably damaging Het
Cct8l1 T C 5: 25,722,767 (GRCm39) V494A probably benign Het
Chn2 A T 6: 54,270,065 (GRCm39) E319V probably damaging Het
Cnnm1 T C 19: 43,460,295 (GRCm39) V679A probably damaging Het
Cntn6 C T 6: 104,753,389 (GRCm39) T447I probably benign Het
Cyp3a11 G T 5: 145,795,581 (GRCm39) L457I probably benign Het
Dera T A 6: 137,807,193 (GRCm39) S214T possibly damaging Het
Dmtf1 A G 5: 9,171,404 (GRCm39) V501A possibly damaging Het
Dnpep A G 1: 75,292,671 (GRCm39) V114A probably damaging Het
Dscam C T 16: 96,592,110 (GRCm39) V722M probably benign Het
Dsp A G 13: 38,365,114 (GRCm39) N499S probably damaging Het
Ecd A T 14: 20,396,725 (GRCm39) Y53* probably null Het
Esyt3 T C 9: 99,200,119 (GRCm39) T692A probably benign Het
Fat1 T A 8: 45,478,659 (GRCm39) N2545K probably damaging Het
Fndc3a A G 14: 72,795,072 (GRCm39) probably null Het
Fscn3 A G 6: 28,430,567 (GRCm39) M246V probably benign Het
Gde1 G T 7: 118,291,007 (GRCm39) T106K probably benign Het
Gjc2 A G 11: 59,068,434 (GRCm39) I16T possibly damaging Het
Hacd4 A T 4: 88,341,260 (GRCm39) M168K probably damaging Het
Hmx3 A G 7: 131,145,826 (GRCm39) E178G probably damaging Het
Htt A G 5: 34,961,171 (GRCm39) Y266C probably damaging Het
Jkampl A T 6: 73,446,039 (GRCm39) L170Q probably damaging Het
Kif27 G T 13: 58,451,359 (GRCm39) R990S probably damaging Het
Krtap22-2 A T 16: 88,807,534 (GRCm39) Y21* probably null Het
Lrrc41 T A 4: 115,952,405 (GRCm39) L661* probably null Het
Lrrc63 T C 14: 75,363,424 (GRCm39) T236A probably benign Het
Mmp13 T C 9: 7,272,892 (GRCm39) L84P probably damaging Het
Myh8 T C 11: 67,183,551 (GRCm39) I754T probably benign Het
Neb A C 2: 52,065,619 (GRCm39) D5961E probably benign Het
Nlrx1 T C 9: 44,175,374 (GRCm39) H134R probably benign Het
Npepps A T 11: 97,117,673 (GRCm39) M542K probably benign Het
Nup160 C T 2: 90,509,743 (GRCm39) probably benign Het
Or3a1c T A 11: 74,045,963 (GRCm39) probably null Het
Or8g33 T A 9: 39,337,888 (GRCm39) T160S possibly damaging Het
Pikfyve T C 1: 65,302,136 (GRCm39) probably null Het
Ppp6r1 A T 7: 4,643,377 (GRCm39) probably null Het
Prss33 A G 17: 24,054,072 (GRCm39) W45R probably damaging Het
Ptprf A T 4: 118,069,302 (GRCm39) Y980* probably null Het
Qrich1 T C 9: 108,436,531 (GRCm39) V743A probably benign Het
Rev3l G A 10: 39,659,329 (GRCm39) probably null Het
Samd9l A T 6: 3,376,369 (GRCm39) N297K probably benign Het
Sap130 A G 18: 31,813,527 (GRCm39) H528R possibly damaging Het
Slc9b2 T C 3: 135,031,863 (GRCm39) V241A probably benign Het
Snx14 A T 9: 88,276,581 (GRCm39) V577E probably benign Het
Srrm2 T C 17: 24,034,876 (GRCm39) S507P probably benign Het
Stat2 A G 10: 128,117,969 (GRCm39) probably null Het
Susd5 T C 9: 113,925,752 (GRCm39) F545S probably benign Het
Tafa2 T A 10: 123,429,401 (GRCm39) M5K possibly damaging Het
Tnnt2 A G 1: 135,775,764 (GRCm39) T107A probably benign Het
Trappc6b T A 12: 59,094,953 (GRCm39) I41F possibly damaging Het
Ttn T A 2: 76,682,417 (GRCm39) probably benign Het
Vmn1r88 A C 7: 12,911,878 (GRCm39) D78A probably damaging Het
Xpc C T 6: 91,485,510 (GRCm39) D122N possibly damaging Het
Xpo1 C T 11: 23,241,623 (GRCm39) A890V probably damaging Het
Zfp493 A G 13: 67,934,680 (GRCm39) H211R probably damaging Het
Zfp958 A T 8: 4,679,190 (GRCm39) H405L 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
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
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'- AGCCTGCCATGAGTTACATCTCCC -3'
(R):5'- AGGACAGCTAACTCTGAGTCCCAC -3'

Sequencing Primer
(F):5'- gcccactcacctatgcac -3'
(R):5'- TATTGCTTCTGTAAAGCACTCATC -3'
Posted On 2014-03-28