Mutagenetix > Incidental Mutation

Incidental Mutation 'R2920:Atrx'

255499

Institutional Source

Beutler Lab

Gene Symbol

Atrx

Ensembl Gene

ENSMUSG00000031229

Gene Name

ATRX, chromatin remodeler

Synonyms

DXHXS6677E, Rad54, 4833408C14Rik, Hp1bp2, Xnp, HP1-BP38, XH2

MMRRC Submission

040505-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.946) question?

Stock #

R2920 (G1)

Quality Score

222

Status

Validated

Chromosome

Chromosomal Location

105797615-105929403 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 105830868 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Aspartic acid at position 1962 (V1962D)

Ref Sequence

ENSEMBL: ENSMUSP00000109203 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000113573] [ENSMUST00000198567]

AlphaFold

Q61687

Predicted Effect

probably benign
Transcript: ENSMUST00000113573
AA Change: V1962D

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000109203
Gene: ENSMUSG00000031229
AA Change: V1962D

Domain	Start	End	E-Value	Type
low complexity region	25	35	N/A	INTRINSIC
low complexity region	66	84	N/A	INTRINSIC
RING	219	267	4.61e-1	SMART
low complexity region	312	322	N/A	INTRINSIC
low complexity region	774	789	N/A	INTRINSIC
low complexity region	822	837	N/A	INTRINSIC
low complexity region	929	946	N/A	INTRINSIC
low complexity region	1021	1039	N/A	INTRINSIC
low complexity region	1130	1143	N/A	INTRINSIC
low complexity region	1145	1165	N/A	INTRINSIC
low complexity region	1179	1194	N/A	INTRINSIC
low complexity region	1238	1245	N/A	INTRINSIC
low complexity region	1264	1279	N/A	INTRINSIC
low complexity region	1309	1318	N/A	INTRINSIC
low complexity region	1341	1354	N/A	INTRINSIC
low complexity region	1373	1386	N/A	INTRINSIC
low complexity region	1407	1416	N/A	INTRINSIC
low complexity region	1430	1454	N/A	INTRINSIC
coiled coil region	1472	1511	N/A	INTRINSIC
DEXDc	1541	1761	2.44e-25	SMART
low complexity region	1898	1932	N/A	INTRINSIC
low complexity region	1947	1959	N/A	INTRINSIC
low complexity region	1969	1982	N/A	INTRINSIC
HELICc	2031	2138	6.1e-17	SMART
low complexity region	2245	2266	N/A	INTRINSIC
low complexity region	2397	2413	N/A	INTRINSIC
low complexity region	2452	2461	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000127221

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000141609

Predicted Effect

probably benign
Transcript: ENSMUST00000198567

SMART Domains

Protein: ENSMUSP00000143007
Gene: ENSMUSG00000031229

Domain	Start	End	E-Value	Type
Pfam:SNF2_N	1	77	3.6e-7	PFAM

Meta Mutation Damage Score

0.0811

Coding Region Coverage

1x: 99.1%
3x: 98.6%
10x: 97.3%
20x: 95.0%

Validation Efficiency

96% (48/50)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene contains an ATPase/helicase domain, and thus it belongs to the SWI/SNF family of chromatin remodeling proteins. This protein is found to undergo cell cycle-dependent phosphorylation, which regulates its nuclear matrix and chromatin association, and suggests its involvement in the gene regulation at interphase and chromosomal segregation in mitosis. Mutations in this gene are associated with an X-linked mental retardation (XLMR) syndrome most often accompanied by alpha-thalassemia (ATRX) syndrome. These mutations have been shown to cause diverse changes in the pattern of DNA methylation, which may provide a link between chromatin remodeling, DNA methylation, and gene expression in developmental processes. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice homozygous for a floxed allele activated in different tissues at different time points can serve as a model of alpha-thalassemia/mental retardation syndrome, nondeletion type, X-linked. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgb	A	G	10: 10,390,243	Y1025H	probably damaging	Het
Adgrv1	C	T	13: 81,448,865	A4122T	probably benign	Het
Aloxe3	C	T	11: 69,142,923	T621I	probably damaging	Het
Atp2b3	A	C	X: 73,533,920	T318P	probably benign	Het
Chl1	C	A	6: 103,695,343	T531K	probably damaging	Het
Clca3b	T	A	3: 144,837,853	D405V	probably benign	Het
Clca3b	C	T	3: 144,846,931	D115N	probably benign	Het
Comtd1	A	G	14: 21,847,618	L149P	possibly damaging	Het
Cops7a	A	G	6: 124,962,362	V108A	probably benign	Het
Crebbp	A	G	16: 4,119,082	V343A	probably damaging	Het
Edrf1	T	A	7: 133,667,572	D1109E	probably benign	Het
Elmo3	A	G	8: 105,308,059	E359G	possibly damaging	Het
Ep400	C	A	5: 110,755,914	G273V	probably damaging	Het
Fgfr3	A	G	5: 33,733,940	N516S	probably damaging	Het
Glb1l	T	A	1: 75,209,190	E31D	probably benign	Het
Gm10093	A	G	17: 78,492,846	D422G	probably damaging	Het
Il12rb2	C	T	6: 67,360,568	V110I	probably damaging	Het
Ints3	T	C	3: 90,393,162	E884G	probably benign	Het
Lin7b	A	G	7: 45,368,397	V170A	possibly damaging	Het
Lrch2	A	T	X: 147,473,030	V750E	probably damaging	Het
Mepe	C	T	5: 104,338,247	R418C	probably damaging	Het
Mettl25	A	T	10: 105,765,177		probably null	Het
Mphosph9	G	A	5: 124,261,006	T982I	probably benign	Het
Mslnl	G	A	17: 25,742,934	V128M	probably damaging	Het
Myo10	G	T	15: 25,801,140	V1472L	probably damaging	Het
Myo9b	A	G	8: 71,325,857	K445R	probably damaging	Het
Ntng2	T	C	2: 29,204,211	M383V	probably benign	Het
Olfr1353	A	C	10: 78,970,012	D121A	probably damaging	Het
Olfr30	T	C	11: 58,455,577	Y124C	probably damaging	Het
Olfr702	C	T	7: 106,824,364	R54Q	probably benign	Het
Pak6	A	T	2: 118,694,007		probably benign	Het
Pcdh8	G	T	14: 79,768,714	P803Q	possibly damaging	Het
Pfkfb3	C	T	2: 11,484,327	V286I	probably benign	Het
Rbp3	C	T	14: 33,956,018	T641M	probably damaging	Het
Rint1	A	G	5: 23,805,402	E203G	probably benign	Het
Sdf2	G	C	11: 78,254,854	V126L	probably damaging	Het
Slc13a5	T	C	11: 72,247,791	E442G	possibly damaging	Het
Slc14a2	G	T	18: 78,158,297	S669*	probably null	Het
Slc38a7	A	G	8: 95,845,943	I157T	possibly damaging	Het
Slc4a5	T	C	6: 83,264,387	L215P	probably damaging	Het
Tbc1d9	T	C	8: 83,210,469	V60A	probably benign	Het
Tcerg1l	T	C	7: 138,248,379	R422G	probably damaging	Het
Tmem107	T	C	11: 69,071,421	L68P	probably damaging	Het
Ugt2b5	A	G	5: 87,125,407	F467L	possibly damaging	Het
Vmn1r19	A	T	6: 57,404,924	N154I	probably benign	Het
Vmn2r69	T	A	7: 85,411,765	I204L	probably benign	Het
Zbtb1	T	A	12: 76,385,845	S202T	possibly damaging	Het

Other mutations in Atrx

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00508:Atrx	APN	X	105823799	missense	probably damaging	0.99
IGL01293:Atrx	APN	X	105876195	missense	probably benign	0.02
IGL01383:Atrx	APN	X	105802075	missense	probably damaging	0.98
IGL01701:Atrx	APN	X	105830920	missense	probably damaging	1.00
IGL02252:Atrx	APN	X	105845823	missense	possibly damaging	0.89
IGL02411:Atrx	APN	X	105830981	missense	possibly damaging	0.82
IGL02929:Atrx	APN	X	105879906	splice site	probably null
IGL03004:Atrx	APN	X	105832509	nonsense	probably null
R1799:Atrx	UTSW	X	105847629	missense	probably damaging	1.00
R3928:Atrx	UTSW	X	105879917	missense	possibly damaging	0.91
R3929:Atrx	UTSW	X	105879917	missense	possibly damaging	0.91
X0028:Atrx	UTSW	X	105877412	missense	probably damaging	0.99
X0060:Atrx	UTSW	X	105847687	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AGACAGAGCAGACTGACTTGC -3'
(R):5'- TATGCTCCCCTAACACAAAGTTCTC -3'

Sequencing Primer
(F):5'- GCAGACTGACTTGCTTACAATTAAAC -3'
(R):5'- AACACAAAGTTCTCTCTCCCTC -3'

Posted On

2014-12-29