Mutagenetix > Incidental Mutation

Incidental Mutation 'R3771:Chd1'

273312

Institutional Source

Beutler Lab

Gene Symbol

Chd1

Ensembl Gene

ENSMUSG00000023852

Gene Name

chromodomain helicase DNA binding protein 1

Synonyms

4930525N21Rik

MMRRC Submission

040747-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R3771 (G1)

Quality Score

225

Status

Validated

Chromosome

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

Domain	Start	End	E-Value	Type
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

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

99% (69/70)

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: 65 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aanat	G	T	11: 116,487,697 (GRCm39)	G132V	probably damaging	Het
Abcb11	T	A	2: 69,159,720 (GRCm39)		probably benign	Het
Adam26b	T	A	8: 43,973,751 (GRCm39)	D417V	probably damaging	Het
Ank1	T	C	8: 23,613,913 (GRCm39)	S1482P	probably benign	Het
Aoc1l2	T	C	6: 48,908,130 (GRCm39)	Y377H	probably damaging	Het
Armc2	C	T	10: 41,798,223 (GRCm39)	V768M	probably damaging	Het
Ascc3	C	T	10: 50,596,814 (GRCm39)		probably benign	Het
Birc6	T	A	17: 74,925,424 (GRCm39)		probably benign	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,619,782 (GRCm39)		probably benign	Het
Cdh12	A	T	15: 21,578,640 (GRCm39)		probably benign	Het
Clstn2	A	G	9: 97,464,615 (GRCm39)	I180T	probably damaging	Het
Cxcr6	A	G	9: 123,639,550 (GRCm39)	I184V	probably benign	Het
Dagla	G	A	19: 10,225,831 (GRCm39)	P778S	possibly damaging	Het
Ddx19b	T	C	8: 111,747,613 (GRCm39)	K107R	probably benign	Het
Dpyd	G	A	3: 119,205,927 (GRCm39)		probably null	Het
Elf1	T	C	14: 79,804,650 (GRCm39)	V105A	possibly damaging	Het
Fam13a	T	G	6: 58,964,171 (GRCm39)	K87T	probably benign	Het
Fap	C	A	2: 62,363,354 (GRCm39)	S359I	probably damaging	Het
Fbxo39	T	C	11: 72,208,041 (GRCm39)	I131T	possibly damaging	Het
Fmn1	T	G	2: 113,412,463 (GRCm39)	S996A	probably damaging	Het
Gm5866	T	C	5: 52,740,088 (GRCm39)		noncoding transcript	Het
Hmcn2	C	T	2: 31,250,908 (GRCm39)	T790M	probably damaging	Het
Irf2bp2	T	C	8: 127,318,550 (GRCm39)	K339E	probably damaging	Het
Kat6b	A	G	14: 21,567,166 (GRCm39)	D75G	probably damaging	Het
Kcnab3	A	G	11: 69,219,389 (GRCm39)	T127A	probably damaging	Het
Kdm5b	G	T	1: 134,541,083 (GRCm39)	C725F	probably damaging	Het
Lrp5	G	A	19: 3,662,330 (GRCm39)	R173C	probably damaging	Het
Lrrn3	T	A	12: 41,502,869 (GRCm39)	I483L	probably damaging	Het
Man2c1	C	A	9: 57,047,661 (GRCm39)		probably benign	Het
Med23	G	T	10: 24,778,099 (GRCm39)	G810C	probably damaging	Het
Nhlrc4	T	A	17: 26,162,367 (GRCm39)	K127*	probably null	Het
Numb	T	C	12: 83,846,350 (GRCm39)	D344G	probably damaging	Het
Nup210l	T	G	3: 90,027,201 (GRCm39)	Y194*	probably null	Het
Ogg1	T	C	6: 113,310,804 (GRCm39)	V317A	possibly damaging	Het
Or1o2	T	A	17: 37,542,356 (GRCm39)	I302F	possibly damaging	Het
Or6c69c	A	G	10: 129,911,143 (GRCm39)	Y288C	probably damaging	Het
Pclo	A	T	5: 14,589,422 (GRCm39)		probably null	Het
Pnpt1	T	C	11: 29,088,174 (GRCm39)	M195T	probably benign	Het
Polr3c	T	A	3: 96,633,170 (GRCm39)	T43S	probably damaging	Het
Ptprs	T	C	17: 56,735,978 (GRCm39)	T152A	possibly damaging	Het
Rasl10b	A	T	11: 83,309,349 (GRCm39)	T134S	probably benign	Het
Rin2	C	T	2: 145,702,366 (GRCm39)	T354I	probably benign	Het
Rnf39	T	C	17: 37,258,121 (GRCm39)	W96R	probably damaging	Het
Ros1	G	T	10: 52,005,087 (GRCm39)	A949E	probably damaging	Het
Rwdd2a	A	C	9: 86,456,214 (GRCm39)	N130T	possibly 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
Srebf2	A	G	15: 82,066,309 (GRCm39)	K579R	probably benign	Het
Sun1	A	G	5: 139,224,575 (GRCm39)		probably benign	Het
Tc2n	T	A	12: 101,660,833 (GRCm39)	Q133L	possibly damaging	Het
Tecta	T	C	9: 42,242,292 (GRCm39)	T2094A	probably damaging	Het
Tex2	T	C	11: 106,437,720 (GRCm39)	D650G	unknown	Het
Trio	A	G	15: 27,748,177 (GRCm39)	S2492P	probably damaging	Het
Ttn	T	C	2: 76,601,711 (GRCm39)	T16872A	probably benign	Het
Ugcg	T	C	4: 59,189,690 (GRCm39)	F16S	probably benign	Het
Usp16	T	C	16: 87,255,571 (GRCm39)	M1T	probably null	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
Vpreb3	A	T	10: 75,775,800 (GRCm39)	V26E	probably benign	Het
Vps39	C	T	2: 120,172,497 (GRCm39)	V179I	possibly damaging	Het
Xrn2	T	C	2: 146,903,207 (GRCm39)	V765A	probably benign	Het
Zfp251	A	G	15: 76,737,836 (GRCm39)	I414T	possibly damaging	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

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- TGAGCACGTGTTCTTACCTAGC -3'
(R):5'- GTAAGCACATCTGCAGCAAAAG -3'

Sequencing Primer
(F):5'- GCACGTGTTCTTACCTAGCGATAAG -3'
(R):5'- TTCACAAAGCTTCATGAAAATCAGAC -3'

Posted On

2015-03-25