Mutagenetix > Incidental Mutation

Incidental Mutation 'R6952:Chd7'

543273

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

045064-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.952) question?

Stock #

R6952 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

8690406-8867659 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 8856797 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Leucine at position 136 (H136L)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000039267] [ENSMUST00000051558] [ENSMUST00000170391]

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000039267
AA Change: H2290L

PolyPhen 2 Score 0.565 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000043903
Gene: ENSMUSG00000041235
AA Change: H2290L

Domain	Start	End	E-Value	Type
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

possibly damaging
Transcript: ENSMUST00000051558
AA Change: H2290L

PolyPhen 2 Score 0.565 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000059079
Gene: ENSMUSG00000041235
AA Change: H2290L

Domain	Start	End	E-Value	Type
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: ENSMUST00000170391

SMART Domains

Protein: ENSMUSP00000127007
Gene: ENSMUSG00000041235

Domain	Start	End	E-Value	Type
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

Predicted Effect

probably damaging
Transcript: ENSMUST00000222546
AA Change: H136L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

Meta Mutation Damage Score

0.2026

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.0%

Validation Efficiency

100% (44/44)

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
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcf3	T	G	16: 20,368,484 (GRCm39)		probably null	Het
Acap1	C	A	11: 69,776,343 (GRCm39)	V219L	probably benign	Het
Arpp21	G	A	9: 111,955,550 (GRCm39)	P530S	probably damaging	Het
Atp6v1b1	T	C	6: 83,731,792 (GRCm39)	V224A	probably damaging	Het
Brd3	T	C	2: 27,344,371 (GRCm39)	D453G	probably damaging	Het
Btbd10	A	T	7: 112,951,150 (GRCm39)		probably null	Het
Ccdc148	T	C	2: 58,713,657 (GRCm39)	H498R	probably damaging	Het
Cga	A	T	4: 34,905,171 (GRCm39)	Y65F	possibly damaging	Het
Chit1	T	C	1: 134,071,022 (GRCm39)	Y34H	probably damaging	Het
Cimap2	C	G	4: 106,467,596 (GRCm39)		probably null	Het
Dapk2	C	G	9: 66,161,904 (GRCm39)	R271G	probably benign	Het
Dnhd1	T	G	7: 105,362,895 (GRCm39)	V3819G	probably damaging	Het
Dsg3	A	T	18: 20,658,216 (GRCm39)	I276F	possibly damaging	Het
Dusp1	T	C	17: 26,726,577 (GRCm39)	S162G	probably benign	Het
Entrep1	A	T	19: 23,962,082 (GRCm39)	M307K	possibly damaging	Het
Gga2	C	A	7: 121,598,111 (GRCm39)	A328S	probably benign	Het
Gpr183	A	G	14: 122,191,897 (GRCm39)	I208T	possibly damaging	Het
Haspin	T	C	11: 73,026,971 (GRCm39)	D706G	possibly damaging	Het
Hdac5	T	C	11: 102,095,786 (GRCm39)	I338V	probably benign	Het
Ik	C	T	18: 36,886,613 (GRCm39)	R362C	probably damaging	Het
Kdm4c	T	G	4: 74,275,587 (GRCm39)	C754W	probably damaging	Het
Limk1	T	A	5: 134,699,332 (GRCm39)	I142F	possibly damaging	Het
Mccc2	T	C	13: 100,104,234 (GRCm39)	E305G	probably benign	Het
Mdm1	A	G	10: 118,003,962 (GRCm39)	D639G	probably damaging	Het
Mefv	T	G	16: 3,528,744 (GRCm39)	T566P	probably damaging	Het
Mep1b	G	A	18: 21,221,727 (GRCm39)	V226I	probably benign	Het
Mgmt	T	C	7: 136,553,064 (GRCm39)	M19T	probably benign	Het
Mrgpra6	A	T	7: 46,835,693 (GRCm39)	S243T	probably benign	Het
Myh7	C	T	14: 55,229,197 (GRCm39)	R169Q	probably damaging	Het
Myo1b	T	C	1: 51,801,668 (GRCm39)	I917V	probably damaging	Het
Or4a80	A	T	2: 89,582,971 (GRCm39)	M67K	possibly damaging	Het
Phlpp1	T	C	1: 106,100,209 (GRCm39)	L159P	probably benign	Het
Plekhh3	T	C	11: 101,056,482 (GRCm39)	E371G	probably damaging	Het
Rps6ka2	C	A	17: 7,495,377 (GRCm39)	D21E	probably benign	Het
Slc47a1	T	A	11: 61,235,280 (GRCm39)	M518L	probably benign	Het
Slitrk6	T	C	14: 110,987,974 (GRCm39)	T578A	probably benign	Het
Syne2	A	T	12: 75,974,205 (GRCm39)	K1133N	possibly damaging	Het
Taco1	T	C	11: 105,963,942 (GRCm39)	S234P	probably benign	Het
Trpv4	G	A	5: 114,771,263 (GRCm39)	S422F	probably damaging	Het
Tvp23b	T	A	11: 62,775,952 (GRCm39)	D97E	possibly damaging	Het
Vmn1r37	A	T	6: 66,708,523 (GRCm39)	I13L	probably benign	Het
Vrk2	T	A	11: 26,485,597 (GRCm39)	K130N	probably damaging	Het
Wdfy4	C	T	14: 32,681,923 (GRCm39)	R3016Q	probably damaging	Het
Zfp383	T	C	7: 29,614,380 (GRCm39)	S212P	probably benign	Het

Other mutations in Chd7

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
R5578:Chd7	UTSW	4	8,847,149 (GRCm39)	missense	probably benign	0.09
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
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'- TCCGTGCATTCTGGCTATGAG -3'
(R):5'- AGATCAACGGTTCTGCTCGC -3'

Sequencing Primer
(F):5'- GGCTATGAGTGCTGCACATAACTC -3'
(R):5'- TTTGAGCTTCCACGTTATCTAATAC -3'

Posted On

2018-11-28