Mutagenetix > Incidental Mutation

Incidental Mutation 'R5458:Chd1'

432900

Institutional Source

Beutler Lab

Gene Symbol

Chd1

Ensembl Gene

ENSMUSG00000023852

Gene Name

chromodomain helicase DNA binding protein 1

Synonyms

4930525N21Rik

MMRRC Submission

043021-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5458 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

15704967-15772610 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 15738549 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 621 (D621G)

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: D621G

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000024627
Gene: ENSMUSG00000023852
AA Change: D621G

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 damaging
Transcript: ENSMUST00000173311
AA Change: D621G

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000134091
Gene: ENSMUSG00000023852
AA Change: D621G

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

possibly damaging
Transcript: ENSMUST00000174461
AA Change: D5G

PolyPhen 2 Score 0.645 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000134718
Gene: ENSMUSG00000023852
AA Change: D5G

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

0.4367

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 94.9%

Validation Efficiency

98% (54/55)

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: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acrbp	A	G	6: 125,050,050 (GRCm38)		probably benign	Het
Acsl5	A	G	19: 55,294,230 (GRCm38)	D589G	probably damaging	Het
Akap13	T	A	7: 75,586,301 (GRCm38)	L208Q	probably damaging	Het
Ankfn1	C	T	11: 89,434,810 (GRCm38)	R512K	probably benign	Het
Ankhd1	T	C	18: 36,648,485 (GRCm38)	S2197P	probably benign	Het
Ankrd27	A	G	7: 35,591,811 (GRCm38)	N11D	probably damaging	Het
Aspg	T	C	12: 112,120,002 (GRCm38)	V230A	probably damaging	Het
Atp2c1	A	T	9: 105,414,725 (GRCm38)	Y709*	probably null	Het
Atp8b2	T	C	3: 89,946,022 (GRCm38)	N748D	probably benign	Het
B4galnt3	A	G	6: 120,210,385 (GRCm38)	V684A	probably damaging	Het
Bco2	T	C	9: 50,545,344 (GRCm38)		probably null	Het
Bcr	T	C	10: 75,154,960 (GRCm38)	V766A	probably benign	Het
Brca1	T	C	11: 101,517,285 (GRCm38)	N1404S	possibly damaging	Het
Chek1	A	G	9: 36,714,429 (GRCm38)	S307P	probably benign	Het
Dhx29	T	C	13: 112,966,621 (GRCm38)	M1345T	probably benign	Het
Dnah6	T	A	6: 73,086,185 (GRCm38)	T2697S	probably damaging	Het
Ephb4	T	C	5: 137,369,852 (GRCm38)	V753A	probably damaging	Het
Fat1	T	C	8: 45,013,053 (GRCm38)	Y1427H	probably damaging	Het
Fggy	A	G	4: 95,926,743 (GRCm38)	Q445R	probably benign	Het
Fv1	A	G	4: 147,870,269 (GRCm38)	S431G	probably benign	Het
Gm5965	A	T	16: 88,778,507 (GRCm38)	R189S	probably benign	Het
Gnas	A	G	2: 174,298,331 (GRCm38)	I98V	probably benign	Het
Ino80	T	C	2: 119,412,429 (GRCm38)	N1086D	possibly damaging	Het
Lclat1	T	C	17: 73,239,919 (GRCm38)	L277P	probably damaging	Het
Lipc	T	C	9: 70,852,582 (GRCm38)		probably benign	Het
Myo3a	T	C	2: 22,245,550 (GRCm38)	I76T	probably damaging	Het
Nkpd1	C	A	7: 19,524,276 (GRCm38)	A510E	probably damaging	Het
Nlgn2	G	T	11: 69,827,900 (GRCm38)	Q285K	possibly damaging	Het
Olfr284	G	A	15: 98,340,365 (GRCm38)	A208V	probably benign	Het
Pax5	T	C	4: 44,679,526 (GRCm38)	D172G	probably damaging	Het
Pcdh15	T	A	10: 74,504,779 (GRCm38)	V1115D	probably damaging	Het
Pdzd7	T	C	19: 45,027,791 (GRCm38)	S964G	probably benign	Het
Phip	G	T	9: 82,926,500 (GRCm38)	P474Q	probably benign	Het
Pop5	C	T	5: 115,240,437 (GRCm38)		probably benign	Het
Ppfibp1	A	T	6: 147,012,435 (GRCm38)		probably benign	Het
Rdh11	C	T	12: 79,188,505 (GRCm38)	A106T	probably benign	Het
Rin3	A	G	12: 102,373,716 (GRCm38)	T642A	probably damaging	Het
Scmh1	C	T	4: 120,505,281 (GRCm38)		probably benign	Het
Skint2	A	G	4: 112,624,180 (GRCm38)	H80R	possibly damaging	Het
Spata16	A	T	3: 26,777,537 (GRCm38)	N265I	probably damaging	Het
Srpk1	T	C	17: 28,599,472 (GRCm38)		probably null	Het
Tcaf1	T	C	6: 42,686,542 (GRCm38)	T135A	probably benign	Het
Trappc12	A	G	12: 28,746,390 (GRCm38)	V381A	probably damaging	Het
Trim33	T	A	3: 103,330,180 (GRCm38)	I184K	possibly damaging	Het
Unc13a	C	T	8: 71,664,245 (GRCm38)	V62M	probably damaging	Het
Vrk2	A	G	11: 26,498,919 (GRCm38)	V225A	probably damaging	Het
Wdr66	A	G	5: 123,254,445 (GRCm38)		probably benign	Het
Wdr95	C	T	5: 149,564,414 (GRCm38)	P171L	probably damaging	Het
Wsb1	T	C	11: 79,248,436 (GRCm38)	T75A	probably damaging	Het

Other mutations in Chd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00704:Chd1	APN	17	15,732,565 (GRCm38)	missense	probably benign	0.37
IGL01356:Chd1	APN	17	15,749,865 (GRCm38)	missense	probably damaging	1.00
IGL01369:Chd1	APN	17	15,754,997 (GRCm38)	missense	probably damaging	0.97
IGL01519:Chd1	APN	17	17,378,569 (GRCm38)	missense	probably damaging	1.00
IGL01604:Chd1	APN	17	15,770,097 (GRCm38)	missense	possibly damaging	0.95
IGL01635:Chd1	APN	17	17,378,596 (GRCm38)	missense	probably damaging	1.00
IGL01721:Chd1	APN	17	15,770,168 (GRCm38)	missense	probably damaging	1.00
IGL01959:Chd1	APN	17	15,742,173 (GRCm38)	missense	probably damaging	1.00
IGL02367:Chd1	APN	17	17,390,053 (GRCm38)	missense	probably damaging	0.98
IGL02476:Chd1	APN	17	15,734,273 (GRCm38)	missense	probably damaging	1.00
IGL02756:Chd1	APN	17	15,730,807 (GRCm38)	missense	probably damaging	0.97
IGL02817:Chd1	APN	17	15,749,500 (GRCm38)	missense	possibly damaging	0.92
IGL03084:Chd1	APN	17	15,770,298 (GRCm38)	missense	probably benign	0.22
IGL03108:Chd1	APN	17	15,725,281 (GRCm38)	missense	possibly damaging	0.70
Holly	UTSW	17	15,726,283 (GRCm38)	missense	possibly damaging	0.72
R0053:Chd1	UTSW	17	15,747,189 (GRCm38)	missense	probably damaging	1.00
R0053:Chd1	UTSW	17	15,747,189 (GRCm38)	missense	probably damaging	1.00
R0128:Chd1	UTSW	17	17,393,567 (GRCm38)	missense	probably damaging	1.00
R0197:Chd1	UTSW	17	15,725,431 (GRCm38)	missense	probably benign
R0285:Chd1	UTSW	17	17,374,680 (GRCm38)	splice site	probably benign
R0326:Chd1	UTSW	17	15,768,568 (GRCm38)	missense	probably benign
R0326:Chd1	UTSW	17	15,768,566 (GRCm38)	missense	probably damaging	1.00
R0372:Chd1	UTSW	17	17,387,290 (GRCm38)	missense	probably benign	0.14
R0391:Chd1	UTSW	17	15,749,894 (GRCm38)	missense	probably damaging	1.00
R0486:Chd1	UTSW	17	15,734,342 (GRCm38)	missense	probably damaging	0.99
R0637:Chd1	UTSW	17	15,742,288 (GRCm38)	missense	possibly damaging	0.50
R0675:Chd1	UTSW	17	15,758,261 (GRCm38)	unclassified	probably benign
R0701:Chd1	UTSW	17	15,725,431 (GRCm38)	missense	probably benign
R0788:Chd1	UTSW	17	15,707,114 (GRCm38)	missense	possibly damaging	0.86
R0848:Chd1	UTSW	17	15,770,241 (GRCm38)	missense	probably damaging	1.00
R0883:Chd1	UTSW	17	15,725,431 (GRCm38)	missense	probably benign
R1169:Chd1	UTSW	17	15,735,732 (GRCm38)	missense	probably damaging	1.00
R1218:Chd1	UTSW	17	15,725,312 (GRCm38)	missense	probably damaging	1.00
R1370:Chd1	UTSW	17	17,387,480 (GRCm38)	missense	probably benign	0.00
R1470:Chd1	UTSW	17	15,726,283 (GRCm38)	missense	possibly damaging	0.72
R1470:Chd1	UTSW	17	15,726,283 (GRCm38)	missense	possibly damaging	0.72
R1478:Chd1	UTSW	17	15,739,507 (GRCm38)	missense	probably damaging	0.99
R1752:Chd1	UTSW	17	15,743,232 (GRCm38)	critical splice donor site	probably null
R1759:Chd1	UTSW	17	17,387,271 (GRCm38)	missense	probably benign	0.00
R1767:Chd1	UTSW	17	15,770,303 (GRCm38)	missense	probably damaging	1.00
R1938:Chd1	UTSW	17	15,762,486 (GRCm38)	missense	probably benign	0.39
R2007:Chd1	UTSW	17	15,731,006 (GRCm38)	missense	probably damaging	1.00
R2069:Chd1	UTSW	17	15,742,294 (GRCm38)	missense	probably damaging	1.00
R3771:Chd1	UTSW	17	17,374,651 (GRCm38)	missense	probably damaging	1.00
R3773:Chd1	UTSW	17	17,374,651 (GRCm38)	missense	probably damaging	1.00
R3849:Chd1	UTSW	17	15,731,871 (GRCm38)	missense	probably damaging	1.00
R4241:Chd1	UTSW	17	15,770,027 (GRCm38)	nonsense	probably null
R4242:Chd1	UTSW	17	15,770,027 (GRCm38)	nonsense	probably null
R4354:Chd1	UTSW	17	17,390,001 (GRCm38)	missense	probably benign	0.23
R4468:Chd1	UTSW	17	15,760,395 (GRCm38)	missense	probably damaging	0.99
R4469:Chd1	UTSW	17	15,760,395 (GRCm38)	missense	probably damaging	0.99
R4731:Chd1	UTSW	17	17,377,817 (GRCm38)	missense	probably benign	0.36
R4824:Chd1	UTSW	17	15,733,124 (GRCm38)	missense	probably damaging	1.00
R4840:Chd1	UTSW	17	15,768,754 (GRCm38)	missense	probably damaging	1.00
R4840:Chd1	UTSW	17	15,768,753 (GRCm38)	nonsense	probably null
R4880:Chd1	UTSW	17	17,374,654 (GRCm38)	missense	probably damaging	1.00
R4960:Chd1	UTSW	17	15,742,231 (GRCm38)	missense	probably damaging	0.96
R5071:Chd1	UTSW	17	15,762,405 (GRCm38)	missense	probably benign
R5078:Chd1	UTSW	17	15,726,354 (GRCm38)	missense	possibly damaging	0.93
R5114:Chd1	UTSW	17	15,728,198 (GRCm38)	missense	probably benign	0.25
R5268:Chd1	UTSW	17	15,735,743 (GRCm38)	missense	probably damaging	1.00
R5304:Chd1	UTSW	17	15,770,268 (GRCm38)	missense	possibly damaging	0.55
R5304:Chd1	UTSW	17	15,754,951 (GRCm38)	missense	probably benign	0.01
R5307:Chd1	UTSW	17	15,732,570 (GRCm38)	missense	probably damaging	1.00
R5553:Chd1	UTSW	17	17,385,613 (GRCm38)	missense	probably benign	0.17
R5623:Chd1	UTSW	17	15,754,932 (GRCm38)	missense	probably damaging	1.00
R6022:Chd1	UTSW	17	17,377,773 (GRCm38)	missense	probably benign	0.39
R6137:Chd1	UTSW	17	15,758,688 (GRCm38)	missense	probably damaging	1.00
R6257:Chd1	UTSW	17	15,730,203 (GRCm38)	splice site	probably null
R6373:Chd1	UTSW	17	15,738,636 (GRCm38)	missense	probably damaging	1.00
R6458:Chd1	UTSW	17	15,730,602 (GRCm38)	missense	probably benign	0.01
R6476:Chd1	UTSW	17	17,380,988 (GRCm38)	critical splice donor site	probably null
R6508:Chd1	UTSW	17	15,738,633 (GRCm38)	missense	probably benign	0.31
R6553:Chd1	UTSW	17	15,725,430 (GRCm38)	missense	probably benign	0.00
R6745:Chd1	UTSW	17	17,387,167 (GRCm38)	missense	probably benign	0.08
R7107:Chd1	UTSW	17	15,761,366 (GRCm38)	missense	probably damaging	0.98
R7230:Chd1	UTSW	17	15,706,937 (GRCm38)	splice site	probably null
R7317:Chd1	UTSW	17	15,742,274 (GRCm38)	missense	possibly damaging	0.71
R7341:Chd1	UTSW	17	15,770,237 (GRCm38)	missense	probably damaging	0.99
R7421:Chd1	UTSW	17	15,749,398 (GRCm38)	missense	probably benign	0.03
R7704:Chd1	UTSW	17	15,767,475 (GRCm38)	missense	probably benign
R7763:Chd1	UTSW	17	15,733,041 (GRCm38)	missense	probably damaging	1.00
R8156:Chd1	UTSW	17	15,761,404 (GRCm38)	missense	probably benign
R8194:Chd1	UTSW	17	17,374,475 (GRCm38)	start gained	probably benign
R8261:Chd1	UTSW	17	17,387,542 (GRCm38)	missense	probably benign	0.02
R8338:Chd1	UTSW	17	15,769,980 (GRCm38)	missense	probably damaging	1.00
R8401:Chd1	UTSW	17	15,743,211 (GRCm38)	missense	probably damaging	1.00
R8411:Chd1	UTSW	17	15,762,449 (GRCm38)	missense	probably damaging	0.98
R9067:Chd1	UTSW	17	15,730,845 (GRCm38)	missense	possibly damaging	0.49
R9184:Chd1	UTSW	17	15,742,289 (GRCm38)	missense	possibly damaging	0.71
R9210:Chd1	UTSW	17	15,730,505 (GRCm38)	missense	possibly damaging	0.70
R9212:Chd1	UTSW	17	15,730,505 (GRCm38)	missense	possibly damaging	0.70
R9666:Chd1	UTSW	17	15,735,714 (GRCm38)	missense	probably damaging	1.00
R9673:Chd1	UTSW	17	15,768,761 (GRCm38)	missense	probably benign	0.24
Z1176:Chd1	UTSW	17	15,768,733 (GRCm38)	missense	probably damaging	1.00
Z1176:Chd1	UTSW	17	15,766,347 (GRCm38)	missense	probably damaging	0.98
Z1177:Chd1	UTSW	17	15,747,801 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CTTGATTTGAGGATTCCAGTTCAGTC -3'
(R):5'- TGCATCTGAGCACATAAAACCATG -3'

Sequencing Primer
(F):5'- GTGGTCTTGAACTCAGAGATCCAC -3'
(R):5'- ATGAAGCAAGCCGTGTCC -3'

Posted On

2016-10-06