Mutagenetix > Incidental Mutation

Incidental Mutation 'R9184:Chd1'

697270

Institutional Source

Beutler Lab

Gene Symbol

Chd1

Ensembl Gene

ENSMUSG00000023852

Gene Name

chromodomain helicase DNA binding protein 1

Synonyms

4930525N21Rik

MMRRC Submission

068979-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9184 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

15925229-15992872 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 15962551 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 769 (N769K)

Ref Sequence

ENSEMBL: ENSMUSP00000024627 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000024627] [ENSMUST00000173311]

AlphaFold

P40201

Predicted Effect

possibly damaging
Transcript: ENSMUST00000024627
AA Change: N769K

PolyPhen 2 Score 0.712 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000024627
Gene: ENSMUSG00000023852
AA Change: N769K

Domain	Start	End	E-Value	Type
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

probably benign
Transcript: ENSMUST00000173311
AA Change: N769K

PolyPhen 2 Score 0.169 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000134091
Gene: ENSMUSG00000023852
AA Change: N769K

Domain	Start	End	E-Value	Type
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

probably benign
Transcript: ENSMUST00000174461
AA Change: N153K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000134718
Gene: ENSMUSG00000023852
AA Change: N153K

Domain	Start	End	E-Value	Type
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

Meta Mutation Damage Score

0.0662

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

Validation Efficiency

97% (60/62)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6030452D12Rik	T	C	8: 107,233,901 (GRCm39)	V199A	unknown	Het
Abca7	A	G	10: 79,838,690 (GRCm39)	H621R	probably damaging	Het
Adam18	T	A	8: 25,137,847 (GRCm39)	N331I	probably benign	Het
Akt1	A	G	12: 112,621,152 (GRCm39)	S475P	possibly damaging	Het
Arc	A	G	15: 74,543,779 (GRCm39)	V148A	probably damaging	Het
Atg2a	T	C	19: 6,291,887 (GRCm39)	L21P	probably damaging	Het
Bltp2	T	C	11: 78,162,214 (GRCm39)	L692S	probably damaging	Het
C1qtnf2	T	C	11: 43,365,180 (GRCm39)	V25A	probably benign	Het
Cald1	G	T	6: 34,730,512 (GRCm39)	E244D	unknown	Het
Cdc42bpa	T	A	1: 179,972,301 (GRCm39)	F1368I	probably benign	Het
Cfap61	G	A	2: 145,919,308 (GRCm39)	C680Y	probably null	Het
Clasp1	T	A	1: 118,470,908 (GRCm39)	V848E	probably benign	Het
Col15a1	G	C	4: 47,288,200 (GRCm39)		probably benign	Het
Ctsb	G	T	14: 63,375,544 (GRCm39)	G170V	probably damaging	Het
Dnah5	A	G	15: 28,340,552 (GRCm39)	K2320E	probably benign	Het
Fat4	A	T	3: 39,036,592 (GRCm39)	I3415F	probably damaging	Het
Fibcd1	A	G	2: 31,706,488 (GRCm39)	S448P	probably damaging	Het
Filip1	T	C	9: 79,805,542 (GRCm39)	K71E	probably benign	Het
Gad2	G	A	2: 22,558,331 (GRCm39)	V350I	probably benign	Het
Gigyf2	T	A	1: 87,368,311 (GRCm39)	S1032T	possibly damaging	Het
Glis3	T	C	19: 28,509,007 (GRCm39)	T326A	probably damaging	Het
Hspa9	C	T	18: 35,082,168 (GRCm39)	R146H	possibly damaging	Het
Jakmip2	A	G	18: 43,715,352 (GRCm39)	I58T	probably benign	Het
Kcnk15	G	A	2: 163,700,606 (GRCm39)	V282M	probably benign	Het
Klk1b8	A	G	7: 43,602,158 (GRCm39)	N30S	probably benign	Het
Lpin2	T	A	17: 71,540,911 (GRCm39)	Y454*	probably null	Het
Mcam	T	C	9: 44,046,545 (GRCm39)		probably benign	Het
Mms22l	T	C	4: 24,596,182 (GRCm39)	L1047S	probably damaging	Het
Neb	A	G	2: 52,218,767 (GRCm39)	I81T	possibly damaging	Het
Neurod4	A	T	10: 130,106,958 (GRCm39)	D105E	probably damaging	Het
Nlrp1b	A	G	11: 71,072,067 (GRCm39)	L592P	probably damaging	Het
Nnt	C	A	13: 119,518,270 (GRCm39)	K302N	probably damaging	Het
Notch4	T	C	17: 34,806,364 (GRCm39)	F1767S	probably damaging	Het
Or4c103	C	A	2: 88,513,519 (GRCm39)	A186S	possibly damaging	Het
Or4c58	T	A	2: 89,675,294 (GRCm39)	I8F	probably benign	Het
Or7g16	T	C	9: 18,727,138 (GRCm39)	I151V	probably benign	Het
Pcdhga4	A	T	18: 37,820,460 (GRCm39)	I670F	possibly damaging	Het
Pdp1	T	C	4: 11,962,143 (GRCm39)	E75G	possibly damaging	Het
Pds5b	T	A	5: 150,724,249 (GRCm39)	N1275K	probably benign	Het
Pink1	G	T	4: 138,048,321 (GRCm39)	Q134K	probably benign	Het
Poli	T	A	18: 70,642,250 (GRCm39)	H650L	probably damaging	Het
Prickle2	G	A	6: 92,388,505 (GRCm39)	P355L	possibly damaging	Het
Prkaca	G	A	8: 84,717,305 (GRCm39)	G194D	probably benign	Het
Ptgs2	A	T	1: 149,980,175 (GRCm39)	Y371F	probably damaging	Het
Rarb	T	A	14: 16,818,882 (GRCm38)		probably benign	Het
Rarb	C	T	14: 16,818,881 (GRCm38)		probably benign	Het
Safb2	ACTTCTTCT	ACTTCT	17: 56,878,292 (GRCm39)		probably benign	Het
Serpinb1b	T	G	13: 33,269,393 (GRCm39)	V42G	probably damaging	Het
Sgsm2	T	A	11: 74,782,834 (GRCm39)	I41F	possibly damaging	Het
Slc26a5	T	A	5: 22,018,880 (GRCm39)	D653V	probably damaging	Het
Slc26a7	C	T	4: 14,506,630 (GRCm39)	V602M	possibly damaging	Het
Slu7	T	C	11: 43,334,224 (GRCm39)	S417P	probably damaging	Het
Smad2	T	A	18: 76,422,171 (GRCm39)	D194E	probably benign	Het
Sntg1	A	T	1: 8,748,056 (GRCm39)	V112E	probably damaging	Het
Strip1	A	T	3: 107,521,979 (GRCm39)	M733K	probably benign	Het
Szt2	G	A	4: 118,241,726 (GRCm39)	S1655L	possibly damaging	Het
Ttn	A	T	2: 76,599,949 (GRCm39)	I19075N	probably benign	Het
Urb2	C	T	8: 124,771,890 (GRCm39)	T1437I	probably benign	Het
Vmn2r111	T	A	17: 22,790,822 (GRCm39)	I159F	probably benign	Het
Zfp78	T	C	7: 6,382,300 (GRCm39)	V450A	probably damaging	Het
Zmynd11	T	A	13: 9,743,475 (GRCm39)	H314L	probably benign	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
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
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'- AGCTTCAGGATGATGACTAATGC -3'
(R):5'- GAAACAACTCACTGGTTTGAAAGAC -3'

Sequencing Primer
(F):5'- GACTAATGCTGGTTTTAAGCTTTCAC -3'
(R):5'- CCAAAGAGAACTTGACATGAAT -3'

Posted On

2022-02-07