Incidental Mutation 'R5578:Chd7'
ID 437293
Institutional Source Beutler Lab
Gene Symbol Chd7
Ensembl Gene ENSMUSG00000041235
Gene Name chromodomain helicase DNA binding protein 7
Synonyms Whi, Dz, Cyn, GENA 47, Cycn, Lda, Flo, Obt, Edy, A730019I05Rik, Todo, GENA 60, WBE1, Gena 52, Mt
MMRRC Submission 043133-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.952) question?
Stock # R5578 (G1)
Quality Score 225
Status Not validated
Chromosome 4
Chromosomal Location 8690406-8867659 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 8847149 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 1631 (T1631A)
Ref Sequence ENSEMBL: ENSMUSP00000059079 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000039267] [ENSMUST00000051558] [ENSMUST00000170391]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000039267
AA Change: T1631A

PolyPhen 2 Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000043903
Gene: ENSMUSG00000041235
AA Change: T1631A

DomainStartEndE-ValueType
low complexity region 11 28 N/A INTRINSIC
low complexity region 48 59 N/A INTRINSIC
low complexity region 107 129 N/A INTRINSIC
low complexity region 152 178 N/A INTRINSIC
low complexity region 194 206 N/A INTRINSIC
low complexity region 385 400 N/A INTRINSIC
low complexity region 491 504 N/A INTRINSIC
low complexity region 512 535 N/A INTRINSIC
low complexity region 585 595 N/A INTRINSIC
low complexity region 632 696 N/A INTRINSIC
low complexity region 721 733 N/A INTRINSIC
low complexity region 735 748 N/A INTRINSIC
low complexity region 759 768 N/A INTRINSIC
CHROMO 789 854 2.54e-9 SMART
CHROMO 870 927 2.94e-5 SMART
low complexity region 928 939 N/A INTRINSIC
DEXDc 954 1155 9.64e-38 SMART
HELICc 1310 1394 1.67e-23 SMART
Blast:DEXDc 1608 1653 8e-16 BLAST
low complexity region 1728 1739 N/A INTRINSIC
internal_repeat_2 1774 1825 1.31e-5 PROSPERO
low complexity region 1831 1846 N/A INTRINSIC
low complexity region 1898 1906 N/A INTRINSIC
low complexity region 1929 1947 N/A INTRINSIC
SANT 1952 2011 9.31e-1 SMART
internal_repeat_2 2079 2126 1.31e-5 PROSPERO
low complexity region 2173 2195 N/A INTRINSIC
low complexity region 2218 2244 N/A INTRINSIC
low complexity region 2387 2407 N/A INTRINSIC
low complexity region 2437 2452 N/A INTRINSIC
BRK 2553 2602 6.57e-23 SMART
BRK 2631 2675 3.77e-23 SMART
low complexity region 2715 2725 N/A INTRINSIC
low complexity region 2746 2758 N/A INTRINSIC
low complexity region 2769 2778 N/A INTRINSIC
low complexity region 2785 2796 N/A INTRINSIC
low complexity region 2810 2821 N/A INTRINSIC
low complexity region 2897 2916 N/A INTRINSIC
low complexity region 2967 2980 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000051558
AA Change: T1631A

PolyPhen 2 Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000059079
Gene: ENSMUSG00000041235
AA Change: T1631A

DomainStartEndE-ValueType
low complexity region 11 28 N/A INTRINSIC
low complexity region 48 59 N/A INTRINSIC
low complexity region 107 129 N/A INTRINSIC
low complexity region 152 178 N/A INTRINSIC
low complexity region 194 206 N/A INTRINSIC
low complexity region 385 400 N/A INTRINSIC
low complexity region 491 504 N/A INTRINSIC
low complexity region 512 535 N/A INTRINSIC
low complexity region 585 595 N/A INTRINSIC
low complexity region 632 696 N/A INTRINSIC
low complexity region 721 733 N/A INTRINSIC
low complexity region 735 748 N/A INTRINSIC
low complexity region 759 768 N/A INTRINSIC
CHROMO 789 854 2.54e-9 SMART
CHROMO 870 927 2.94e-5 SMART
low complexity region 928 939 N/A INTRINSIC
DEXDc 954 1155 9.64e-38 SMART
HELICc 1310 1394 1.67e-23 SMART
Blast:DEXDc 1608 1653 8e-16 BLAST
low complexity region 1728 1739 N/A INTRINSIC
internal_repeat_2 1774 1825 1.31e-5 PROSPERO
low complexity region 1831 1846 N/A INTRINSIC
low complexity region 1898 1906 N/A INTRINSIC
low complexity region 1929 1947 N/A INTRINSIC
SANT 1952 2011 9.31e-1 SMART
internal_repeat_2 2079 2126 1.31e-5 PROSPERO
low complexity region 2173 2195 N/A INTRINSIC
low complexity region 2218 2244 N/A INTRINSIC
low complexity region 2387 2407 N/A INTRINSIC
low complexity region 2437 2452 N/A INTRINSIC
BRK 2553 2602 6.57e-23 SMART
BRK 2631 2675 3.77e-23 SMART
low complexity region 2715 2725 N/A INTRINSIC
low complexity region 2746 2758 N/A INTRINSIC
low complexity region 2769 2778 N/A INTRINSIC
low complexity region 2785 2796 N/A INTRINSIC
low complexity region 2810 2821 N/A INTRINSIC
low complexity region 2897 2916 N/A INTRINSIC
low complexity region 2967 2980 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130709
Predicted Effect probably benign
Transcript: ENSMUST00000170391
SMART Domains Protein: ENSMUSP00000127007
Gene: ENSMUSG00000041235

DomainStartEndE-ValueType
low complexity region 11 28 N/A INTRINSIC
low complexity region 48 59 N/A INTRINSIC
low complexity region 107 129 N/A INTRINSIC
low complexity region 152 178 N/A INTRINSIC
low complexity region 194 206 N/A INTRINSIC
low complexity region 385 400 N/A INTRINSIC
low complexity region 491 504 N/A INTRINSIC
low complexity region 512 535 N/A INTRINSIC
BRK 586 630 3.77e-23 SMART
low complexity region 670 680 N/A INTRINSIC
low complexity region 701 713 N/A INTRINSIC
low complexity region 724 733 N/A INTRINSIC
low complexity region 740 751 N/A INTRINSIC
low complexity region 765 776 N/A INTRINSIC
low complexity region 852 871 N/A INTRINSIC
low complexity region 922 935 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 98.2%
  • 20x: 94.9%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a protein containing two chromodomains and an ATP-binding helicase domain that functions as a regulator of transcription. Mutations in this gene result in an array of development defects, including inner ear problems. Mice defective for this gene exhibit many of the clinical features of the CHARGE syndrome caused by mutations in the homologous gene in human. [provided by RefSeq, Sep 2015]
PHENOTYPE: Heterozygotes for mutations of this gene exhibit a variety of combinations of hyperactivity, circling, head-bobbing, semicircular canal defects, hearing loss, reduced size, and tail-kink. [provided by MGI curators]
Allele List at MGI

All alleles(32) : Targeted, other(4) Gene trapped(19) Chemically induced(9)
Other mutations in this stock
Total: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acap2 A G 16: 30,926,932 (GRCm39) S521P probably benign Het
Aqp11 A G 7: 97,386,665 (GRCm39) F177S probably damaging Het
Arhgap40 G T 2: 158,373,126 (GRCm39) G128V probably damaging Het
Aspm A T 1: 139,398,455 (GRCm39) K1011I probably damaging Het
Cachd1 A G 4: 100,722,203 (GRCm39) T89A probably benign Het
Cep89 ACTCCTCCTCCTCCTCCTCCTCCTC ACTCCTCCTCCTCCTCCTCCTC 7: 35,109,067 (GRCm39) probably benign Het
Cfhr2 A T 1: 139,758,806 (GRCm39) C81* probably null Het
Clca4b T A 3: 144,638,196 (GRCm39) D22V probably benign Het
Csnk2a1-ps3 A G 1: 156,352,800 (GRCm39) M334V probably benign Het
Cybb C G X: 9,316,989 (GRCm39) D246H probably benign Het
Cyp39a1 T A 17: 43,991,031 (GRCm39) N113K possibly damaging Het
Dnah11 A T 12: 117,982,537 (GRCm39) V2544D probably damaging Het
Dnai3 A T 3: 145,802,983 (GRCm39) Y69* probably null Het
Esr1 A C 10: 4,919,164 (GRCm39) Q418P probably damaging Het
Fam89a T A 8: 125,467,968 (GRCm39) K115* probably null Het
Fstl4 T A 11: 53,056,608 (GRCm39) V455D probably damaging Het
Gm20730 T A 6: 43,058,474 (GRCm39) M113L probably benign Het
H2ac21 T C 3: 96,127,554 (GRCm39) V108A probably damaging Het
Hk3 C T 13: 55,159,994 (GRCm39) V327M probably damaging Het
Itm2c T A 1: 85,830,774 (GRCm39) V57E possibly damaging Het
Lrba T C 3: 86,664,814 (GRCm39) Y565H probably benign Het
Mab21l1 C T 3: 55,691,435 (GRCm39) Q341* probably null Het
Mdm2 C T 10: 117,538,192 (GRCm39) E69K possibly damaging Het
Mdn1 A T 4: 32,728,167 (GRCm39) I2709F probably benign Het
Mpp7 T C 18: 7,355,101 (GRCm39) N442D probably benign Het
Ncoa3 A G 2: 165,896,248 (GRCm39) I384V probably benign Het
Pm20d1 A G 1: 131,743,760 (GRCm39) N475S probably benign Het
Rhpn2 A G 7: 35,070,135 (GRCm39) D131G probably damaging Het
S1pr5 T A 9: 21,155,847 (GRCm39) Y193F probably damaging Het
Sdk1 A T 5: 141,598,880 (GRCm39) K182* probably null Het
Slx4 T A 16: 3,804,726 (GRCm39) E696V probably damaging Het
Smyd4 C T 11: 75,295,602 (GRCm39) P753S probably benign Het
Stambp T G 6: 83,538,782 (GRCm39) D206A probably benign Het
Sult5a1 G T 8: 123,869,860 (GRCm39) Y262* probably null Het
Taar1 A T 10: 23,796,718 (GRCm39) I139F possibly damaging Het
Tchh A T 3: 93,351,618 (GRCm39) R353* probably null Het
Thnsl2 C T 6: 71,115,749 (GRCm39) V153I probably benign Het
Trmt5 C T 12: 73,331,837 (GRCm39) probably null Het
Trpa1 T A 1: 14,957,232 (GRCm39) Y728F probably damaging Het
Usp19 T C 9: 108,370,639 (GRCm39) V126A probably benign Het
Vcan A G 13: 89,839,622 (GRCm39) V1974A probably benign Het
Vmn2r120 T A 17: 57,829,514 (GRCm39) H461L probably benign Het
Zfp445 T C 9: 122,682,402 (GRCm39) Y513C probably benign Het
Zfp84 A C 7: 29,474,856 (GRCm39) M43L possibly damaging Het
Other mutations in Chd7
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00422:Chd7 APN 4 8,859,106 (GRCm39) missense probably damaging 1.00
IGL00510:Chd7 APN 4 8,801,404 (GRCm39) missense probably damaging 1.00
IGL00741:Chd7 APN 4 8,839,454 (GRCm39) missense probably damaging 1.00
IGL00796:Chd7 APN 4 8,847,271 (GRCm39) missense possibly damaging 0.95
IGL00907:Chd7 APN 4 8,840,435 (GRCm39) missense probably damaging 0.98
IGL00930:Chd7 APN 4 8,805,181 (GRCm39) missense probably damaging 1.00
IGL01542:Chd7 APN 4 8,859,285 (GRCm39) missense possibly damaging 0.71
IGL01602:Chd7 APN 4 8,833,834 (GRCm39) missense probably damaging 1.00
IGL01605:Chd7 APN 4 8,833,834 (GRCm39) missense probably damaging 1.00
IGL01670:Chd7 APN 4 8,827,033 (GRCm39) missense probably damaging 0.98
IGL02434:Chd7 APN 4 8,752,145 (GRCm39) missense probably benign 0.00
IGL02531:Chd7 APN 4 8,854,134 (GRCm39) missense probably damaging 1.00
IGL02626:Chd7 APN 4 8,826,519 (GRCm39) missense probably damaging 1.00
IGL02961:Chd7 APN 4 8,751,542 (GRCm39) missense probably damaging 1.00
IGL02972:Chd7 APN 4 8,855,174 (GRCm39) missense probably benign 0.30
IGL03329:Chd7 APN 4 8,841,108 (GRCm39) missense probably damaging 1.00
Fili UTSW 4 8,839,523 (GRCm39) missense probably damaging 1.00
D4043:Chd7 UTSW 4 8,862,650 (GRCm39) missense probably damaging 1.00
IGL02991:Chd7 UTSW 4 8,828,398 (GRCm39) missense possibly damaging 0.91
PIT4466001:Chd7 UTSW 4 8,753,101 (GRCm39) missense unknown
PIT4472001:Chd7 UTSW 4 8,753,101 (GRCm39) missense unknown
R0157:Chd7 UTSW 4 8,833,759 (GRCm39) missense probably damaging 1.00
R0179:Chd7 UTSW 4 8,862,516 (GRCm39) missense probably benign 0.22
R0240:Chd7 UTSW 4 8,852,670 (GRCm39) unclassified probably benign
R0388:Chd7 UTSW 4 8,854,560 (GRCm39) missense probably benign 0.27
R0462:Chd7 UTSW 4 8,850,821 (GRCm39) missense probably damaging 1.00
R0512:Chd7 UTSW 4 8,805,139 (GRCm39) intron probably benign
R0657:Chd7 UTSW 4 8,753,141 (GRCm39) missense probably damaging 1.00
R0799:Chd7 UTSW 4 8,801,310 (GRCm39) intron probably benign
R0885:Chd7 UTSW 4 8,866,432 (GRCm39) missense probably damaging 1.00
R1056:Chd7 UTSW 4 8,822,402 (GRCm39) missense possibly damaging 0.50
R1086:Chd7 UTSW 4 8,866,458 (GRCm39) missense probably benign 0.04
R1353:Chd7 UTSW 4 8,839,556 (GRCm39) missense probably damaging 0.99
R1466:Chd7 UTSW 4 8,840,561 (GRCm39) splice site probably null
R1466:Chd7 UTSW 4 8,840,561 (GRCm39) splice site probably null
R1605:Chd7 UTSW 4 8,844,675 (GRCm39) missense probably damaging 1.00
R1693:Chd7 UTSW 4 8,864,307 (GRCm39) critical splice donor site probably null
R1695:Chd7 UTSW 4 8,833,960 (GRCm39) missense probably damaging 1.00
R1938:Chd7 UTSW 4 8,847,200 (GRCm39) missense probably damaging 1.00
R1964:Chd7 UTSW 4 8,865,978 (GRCm39) missense probably damaging 0.96
R2020:Chd7 UTSW 4 8,855,226 (GRCm39) missense probably benign 0.00
R2134:Chd7 UTSW 4 8,753,147 (GRCm39) missense probably damaging 0.99
R2171:Chd7 UTSW 4 8,752,424 (GRCm39) missense probably damaging 1.00
R2271:Chd7 UTSW 4 8,785,532 (GRCm39) missense probably damaging 1.00
R2300:Chd7 UTSW 4 8,855,241 (GRCm39) missense probably benign 0.02
R2355:Chd7 UTSW 4 8,801,350 (GRCm39) missense possibly damaging 0.95
R3153:Chd7 UTSW 4 8,855,174 (GRCm39) missense probably benign 0.30
R3430:Chd7 UTSW 4 8,844,517 (GRCm39) missense probably damaging 0.99
R3746:Chd7 UTSW 4 8,752,537 (GRCm39) missense probably damaging 1.00
R4118:Chd7 UTSW 4 8,865,831 (GRCm39) missense probably damaging 1.00
R4119:Chd7 UTSW 4 8,785,658 (GRCm39) intron probably benign
R4332:Chd7 UTSW 4 8,854,143 (GRCm39) missense probably damaging 1.00
R4402:Chd7 UTSW 4 8,866,353 (GRCm39) missense possibly damaging 0.61
R4571:Chd7 UTSW 4 8,866,217 (GRCm39) missense probably benign 0.09
R4722:Chd7 UTSW 4 8,822,445 (GRCm39) missense probably damaging 1.00
R4821:Chd7 UTSW 4 8,844,706 (GRCm39) missense probably damaging 1.00
R4894:Chd7 UTSW 4 8,838,629 (GRCm39) missense probably damaging 0.99
R5205:Chd7 UTSW 4 8,752,509 (GRCm39) missense possibly damaging 0.60
R5344:Chd7 UTSW 4 8,844,417 (GRCm39) missense probably damaging 1.00
R5484:Chd7 UTSW 4 8,828,258 (GRCm39) missense probably damaging 1.00
R5583:Chd7 UTSW 4 8,752,473 (GRCm39) missense probably damaging 1.00
R5888:Chd7 UTSW 4 8,866,382 (GRCm39) missense probably damaging 0.98
R5905:Chd7 UTSW 4 8,840,553 (GRCm39) missense possibly damaging 0.91
R6091:Chd7 UTSW 4 8,751,875 (GRCm39) missense probably damaging 0.99
R6126:Chd7 UTSW 4 8,826,482 (GRCm39) missense probably damaging 1.00
R6399:Chd7 UTSW 4 8,828,274 (GRCm39) missense probably damaging 1.00
R6751:Chd7 UTSW 4 8,833,866 (GRCm39) missense probably damaging 1.00
R6810:Chd7 UTSW 4 8,839,523 (GRCm39) missense probably damaging 1.00
R6868:Chd7 UTSW 4 8,811,501 (GRCm39) splice site probably null
R6952:Chd7 UTSW 4 8,856,797 (GRCm39) missense probably damaging 1.00
R6986:Chd7 UTSW 4 8,859,285 (GRCm39) missense possibly damaging 0.71
R6990:Chd7 UTSW 4 8,844,525 (GRCm39) missense probably benign 0.28
R7139:Chd7 UTSW 4 8,865,865 (GRCm39) missense probably benign 0.00
R7288:Chd7 UTSW 4 8,847,093 (GRCm39) missense possibly damaging 0.92
R7355:Chd7 UTSW 4 8,752,196 (GRCm39) missense unknown
R7452:Chd7 UTSW 4 8,854,731 (GRCm39) missense probably benign 0.03
R7471:Chd7 UTSW 4 8,859,197 (GRCm39) missense probably damaging 0.96
R7588:Chd7 UTSW 4 8,864,039 (GRCm39) missense probably damaging 1.00
R7711:Chd7 UTSW 4 8,805,234 (GRCm39) missense probably benign 0.00
R7744:Chd7 UTSW 4 8,862,485 (GRCm39) splice site probably null
R7842:Chd7 UTSW 4 8,854,115 (GRCm39) missense probably benign 0.01
R7883:Chd7 UTSW 4 8,826,504 (GRCm39) missense probably damaging 1.00
R7934:Chd7 UTSW 4 8,854,121 (GRCm39) missense probably benign 0.00
R7983:Chd7 UTSW 4 8,844,609 (GRCm39) missense possibly damaging 0.47
R7983:Chd7 UTSW 4 8,752,628 (GRCm39) missense unknown
R8022:Chd7 UTSW 4 8,751,605 (GRCm39) missense unknown
R8161:Chd7 UTSW 4 8,855,038 (GRCm39) missense probably damaging 1.00
R8274:Chd7 UTSW 4 8,839,432 (GRCm39) missense probably damaging 1.00
R8278:Chd7 UTSW 4 8,862,485 (GRCm39) splice site probably null
R8358:Chd7 UTSW 4 8,839,529 (GRCm39) missense probably damaging 1.00
R8464:Chd7 UTSW 4 8,811,465 (GRCm39) missense probably benign 0.06
R8483:Chd7 UTSW 4 8,822,412 (GRCm39) missense possibly damaging 0.65
R8507:Chd7 UTSW 4 8,858,675 (GRCm39) missense probably damaging 1.00
R8535:Chd7 UTSW 4 8,859,211 (GRCm39) missense possibly damaging 0.92
R8695:Chd7 UTSW 4 8,850,812 (GRCm39) missense probably damaging 1.00
R8700:Chd7 UTSW 4 8,833,892 (GRCm39) missense probably damaging 1.00
R8755:Chd7 UTSW 4 8,866,069 (GRCm39) missense probably benign 0.31
R8774:Chd7 UTSW 4 8,854,692 (GRCm39) missense probably damaging 1.00
R8774-TAIL:Chd7 UTSW 4 8,854,692 (GRCm39) missense probably damaging 1.00
R8796:Chd7 UTSW 4 8,838,691 (GRCm39) missense probably damaging 1.00
R8992:Chd7 UTSW 4 8,839,589 (GRCm39) missense probably damaging 1.00
R9018:Chd7 UTSW 4 8,847,083 (GRCm39) missense possibly damaging 0.88
R9122:Chd7 UTSW 4 8,840,510 (GRCm39) missense possibly damaging 0.77
R9131:Chd7 UTSW 4 8,785,642 (GRCm39) missense
R9182:Chd7 UTSW 4 8,838,737 (GRCm39) missense probably damaging 1.00
R9227:Chd7 UTSW 4 8,805,272 (GRCm39) missense probably benign 0.03
R9254:Chd7 UTSW 4 8,752,210 (GRCm39) missense unknown
R9379:Chd7 UTSW 4 8,752,210 (GRCm39) missense unknown
R9388:Chd7 UTSW 4 8,865,756 (GRCm39) missense possibly damaging 0.89
R9455:Chd7 UTSW 4 8,752,061 (GRCm39) missense unknown
R9531:Chd7 UTSW 4 8,858,489 (GRCm39) missense
R9577:Chd7 UTSW 4 8,752,964 (GRCm39) missense unknown
R9634:Chd7 UTSW 4 8,832,499 (GRCm39) missense probably damaging 1.00
Z1176:Chd7 UTSW 4 8,844,313 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TAGAAGTGACTAGTGCCGTTG -3'
(R):5'- CGCAGCCTTTTACCGAATGG -3'

Sequencing Primer
(F):5'- GTGGGTCCAGGATTTCTCAGTCC -3'
(R):5'- TTCTGGTAGCCTTTTGTGACCCAG -3'
Posted On 2016-10-26