Mutagenetix > Incidental Mutation

Incidental Mutation 'R3929:Atrx'

308660

Institutional Source

Beutler Lab

Gene Symbol

Atrx

Ensembl Gene

ENSMUSG00000031229

Gene Name

ATRX, chromatin remodeler

Synonyms

alpha thalassemia/mental retardation syndrome X-linked, Hp1bp2, Xnp, DXHXS6677E, 4833408C14Rik, XH2, Rad54, HP1-BP38

MMRRC Submission

040824-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.948) question?

Stock #

R3929 (G1)

Quality Score

222

Status

Not validated

Chromosome

Chromosomal Location

104841221-104972978 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 104923523 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Valine at position 157 (I157V)

Ref Sequence

ENSEMBL: ENSMUSP00000143565 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000101305] [ENSMUST00000113573] [ENSMUST00000128968] [ENSMUST00000134381] [ENSMUST00000134507] [ENSMUST00000154866] [ENSMUST00000198441] [ENSMUST00000150914] [ENSMUST00000197302] [ENSMUST00000198448] [ENSMUST00000199233] [ENSMUST00000198209] [ENSMUST00000137453]

AlphaFold

Q61687

Predicted Effect

probably benign
Transcript: ENSMUST00000101305

SMART Domains

Protein: ENSMUSP00000098863
Gene: ENSMUSG00000031229

Domain	Start	End	E-Value	Type
low complexity region	40	50	N/A	INTRINSIC
low complexity region	81	99	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000113573
AA Change: I195V

PolyPhen 2 Score 0.353 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000109203
Gene: ENSMUSG00000031229
AA Change: I195V

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

noncoding transcript
Transcript: ENSMUST00000123174

Predicted Effect

possibly damaging
Transcript: ENSMUST00000128968
AA Change: I156V

PolyPhen 2 Score 0.751 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000121416
Gene: ENSMUSG00000031229
AA Change: I156V

Domain	Start	End	E-Value	Type
low complexity region	25	35	N/A	INTRINSIC
low complexity region	66	84	N/A	INTRINSIC
RING	180	228	2.2e-3	SMART
low complexity region	273	283	N/A	INTRINSIC
low complexity region	735	750	N/A	INTRINSIC
low complexity region	783	798	N/A	INTRINSIC
low complexity region	890	907	N/A	INTRINSIC
low complexity region	982	993	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133543

Predicted Effect

probably benign
Transcript: ENSMUST00000134381
AA Change: I102V

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000122875
Gene: ENSMUSG00000031229
AA Change: I102V

Domain	Start	End	E-Value	Type
low complexity region	11	29	N/A	INTRINSIC
RING	126	174	4.61e-1	SMART
low complexity region	219	229	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000134507
AA Change: I118V

PolyPhen 2 Score 0.013 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000123085
Gene: ENSMUSG00000031229
AA Change: I118V

Domain	Start	End	E-Value	Type
low complexity region	27	45	N/A	INTRINSIC
RING	142	190	4.61e-1	SMART
low complexity region	235	245	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000154866
AA Change: I139V

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000121291
Gene: ENSMUSG00000031229
AA Change: I139V

Domain	Start	End	E-Value	Type
low complexity region	11	29	N/A	INTRINSIC
PDB:2LD1\|A	103	208	6e-77	PDB
SCOP:d1fp0a1	157	208	5e-7	SMART
Blast:RING	163	208	5e-27	BLAST

Predicted Effect

possibly damaging
Transcript: ENSMUST00000198441
AA Change: I157V

PolyPhen 2 Score 0.908 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000143565
Gene: ENSMUSG00000031229
AA Change: I157V

Domain	Start	End	E-Value	Type
low complexity region	25	35	N/A	INTRINSIC
low complexity region	66	84	N/A	INTRINSIC
PDB:2JM1\|A	123	174	3e-32	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000150914
AA Change: I156V

PolyPhen 2 Score 0.066 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000122034
Gene: ENSMUSG00000031229
AA Change: I156V

Domain	Start	End	E-Value	Type
low complexity region	27	45	N/A	INTRINSIC
RING	180	228	4.61e-1	SMART
low complexity region	273	283	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000197302
AA Change: I109V

PolyPhen 2 Score 0.174 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000143163
Gene: ENSMUSG00000031229
AA Change: I109V

Domain	Start	End	E-Value	Type
PDB:2JM1\|A	72	134	6e-42	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000198448
AA Change: I140V

PolyPhen 2 Score 0.056 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000143090
Gene: ENSMUSG00000031229
AA Change: I140V

Domain	Start	End	E-Value	Type
low complexity region	11	29	N/A	INTRINSIC
RING	164	212	2.2e-3	SMART
low complexity region	257	267	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000199233
AA Change: I102V

PolyPhen 2 Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000143015
Gene: ENSMUSG00000031229
AA Change: I102V

Domain	Start	End	E-Value	Type
low complexity region	11	29	N/A	INTRINSIC
PDB:2JM1\|A	68	158	2e-64	PDB
SCOP:d1fp0a1	120	154	9e-6	SMART
Blast:RING	126	158	9e-17	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000200471

Predicted Effect

probably benign
Transcript: ENSMUST00000198209

SMART Domains

Protein: ENSMUSP00000142726
Gene: ENSMUSG00000031229

Domain	Start	End	E-Value	Type
low complexity region	50	67	N/A	INTRINSIC
low complexity region	142	160	N/A	INTRINSIC
internal_repeat_1	171	196	2.95e-5	PROSPERO
internal_repeat_1	218	241	2.95e-5	PROSPERO
low complexity region	251	264	N/A	INTRINSIC
low complexity region	266	286	N/A	INTRINSIC
low complexity region	300	315	N/A	INTRINSIC
low complexity region	359	366	N/A	INTRINSIC
low complexity region	385	400	N/A	INTRINSIC
low complexity region	422	431	N/A	INTRINSIC
low complexity region	454	467	N/A	INTRINSIC
low complexity region	486	499	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000137453

SMART Domains

Protein: ENSMUSP00000120246
Gene: ENSMUSG00000031229

Domain	Start	End	E-Value	Type
low complexity region	11	29	N/A	INTRINSIC

Meta Mutation Damage Score

0.1216

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.5%
20x: 95.5%

Validation Efficiency

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: 33 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ak5	A	C	3: 152,373,444 (GRCm39)	L18R	probably damaging	Het
C9	T	A	15: 6,496,939 (GRCm39)	I212N	probably benign	Het
Cabin1	T	C	10: 75,587,452 (GRCm39)		probably null	Het
Ccnf	A	G	17: 24,453,356 (GRCm39)	V361A	probably damaging	Het
Ctps1	T	A	4: 120,399,093 (GRCm39)	H553L	probably benign	Het
Dmrta1	C	T	4: 89,579,681 (GRCm39)	Q214*	probably null	Het
E230025N22Rik	T	C	18: 36,824,625 (GRCm39)	D112G	probably damaging	Het
Frat1	T	C	19: 41,819,087 (GRCm39)	C161R	probably damaging	Het
H1f8	A	G	6: 115,925,757 (GRCm39)	K185E	probably benign	Het
Itpr2	C	A	6: 146,275,857 (GRCm39)		probably null	Het
Klhl40	A	G	9: 121,609,742 (GRCm39)	D509G	probably benign	Het
Muc5ac	T	C	7: 141,356,629 (GRCm39)	V1072A	probably benign	Het
Nav3	A	G	10: 109,520,064 (GRCm39)	Y2340H	probably damaging	Het
Or10ak9	T	C	4: 118,726,179 (GRCm39)	L66P	probably damaging	Het
Or2y17	A	T	11: 49,231,820 (GRCm39)	M154L	probably benign	Het
Or51a43	C	T	7: 103,717,791 (GRCm39)	C149Y	probably benign	Het
Or5be3	T	A	2: 86,864,428 (GRCm39)	I46F	possibly damaging	Het
Or6c2	G	A	10: 129,362,100 (GRCm39)	M1I	probably null	Het
Prdm10	T	C	9: 31,258,432 (GRCm39)	I619T	probably damaging	Het
Rp1	T	C	1: 4,422,868 (GRCm39)	T71A	probably damaging	Het
Rpusd4	A	G	9: 35,183,876 (GRCm39)	I202V	probably benign	Het
Sin3a	A	G	9: 57,025,421 (GRCm39)	N1089S	probably damaging	Het
St6gal2	A	G	17: 55,803,324 (GRCm39)	D353G	possibly damaging	Het
Stap2	A	C	17: 56,310,156 (GRCm39)	F50V	probably damaging	Het
Stkld1	T	A	2: 26,830,059 (GRCm39)		probably null	Het
Tars3	A	G	7: 65,333,791 (GRCm39)		probably null	Het
Tbl1xr1	G	C	3: 22,243,932 (GRCm39)	D69H	probably damaging	Het
Tnrc6c	C	T	11: 117,614,355 (GRCm39)	R838W	probably damaging	Het
Trim61	A	G	8: 65,465,969 (GRCm39)	F431L	probably benign	Het
Trmo	C	T	4: 46,382,647 (GRCm39)	G150S	probably damaging	Het
Vmn1r61	A	G	7: 5,614,176 (GRCm39)	I46T	probably benign	Het
Vmn2r19	T	C	6: 123,292,587 (GRCm39)	Y210H	probably benign	Het
Xrn1	T	C	9: 95,870,926 (GRCm39)	S584P	possibly damaging	Het

Other mutations in Atrx

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00508:Atrx	APN	X	104,867,405 (GRCm39)	missense	probably damaging	0.99
IGL01293:Atrx	APN	X	104,919,801 (GRCm39)	missense	probably benign	0.02
IGL01383:Atrx	APN	X	104,845,681 (GRCm39)	missense	probably damaging	0.98
IGL01701:Atrx	APN	X	104,874,526 (GRCm39)	missense	probably damaging	1.00
IGL02252:Atrx	APN	X	104,889,429 (GRCm39)	missense	possibly damaging	0.89
IGL02411:Atrx	APN	X	104,874,587 (GRCm39)	missense	possibly damaging	0.82
IGL02929:Atrx	APN	X	104,923,512 (GRCm39)	splice site	probably null
IGL03004:Atrx	APN	X	104,876,115 (GRCm39)	nonsense	probably null
R1799:Atrx	UTSW	X	104,891,235 (GRCm39)	missense	probably damaging	1.00
R2920:Atrx	UTSW	X	104,874,474 (GRCm39)	missense	probably benign	0.22
R3928:Atrx	UTSW	X	104,923,523 (GRCm39)	missense	possibly damaging	0.91
X0028:Atrx	UTSW	X	104,921,018 (GRCm39)	missense	probably damaging	0.99
X0060:Atrx	UTSW	X	104,891,293 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTAAATACAGTAAGTCTCCCCTCCC -3'
(R):5'- GCCCAAGACATTTTCCCACG -3'

Sequencing Primer
(F):5'- CACTTAACTCAACTAACTCTTACTCG -3'
(R):5'- CCCACGGATTATGAACTCTAGTG -3'

Posted On

2015-04-17