Incidental Mutation 'R3928:Atrx'
ID |
308397 |
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 |
040823-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.943)
|
Stock # |
R3928 (G1)
|
Quality Score |
222 |
Status
|
Validated
|
Chromosome |
X |
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: 99.3%
- 3x: 98.7%
- 10x: 97.5%
- 20x: 95.6%
|
Validation Efficiency |
100% (48/48) |
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 |
Abr |
A |
T |
11: 76,359,561 (GRCm39) |
H181Q |
probably benign |
Het |
Birc6 |
A |
G |
17: 74,918,170 (GRCm39) |
D1856G |
possibly damaging |
Het |
Birc6 |
A |
G |
17: 74,945,404 (GRCm39) |
T2811A |
probably damaging |
Het |
Brsk2 |
T |
C |
7: 141,552,155 (GRCm39) |
F108S |
probably damaging |
Het |
Clasp2 |
C |
A |
9: 113,735,173 (GRCm39) |
H1004N |
probably benign |
Het |
Cntd1 |
G |
A |
11: 101,178,345 (GRCm39) |
V315I |
probably benign |
Het |
Col13a1 |
A |
G |
10: 61,703,304 (GRCm39) |
|
probably benign |
Het |
Ctps1 |
T |
A |
4: 120,399,093 (GRCm39) |
H553L |
probably benign |
Het |
Dpysl2 |
A |
G |
14: 67,061,880 (GRCm39) |
I242T |
possibly damaging |
Het |
Exoc3l |
C |
T |
8: 106,017,549 (GRCm39) |
|
probably benign |
Het |
Fam229a |
A |
G |
4: 129,385,204 (GRCm39) |
|
probably benign |
Het |
Fshr |
C |
T |
17: 89,292,962 (GRCm39) |
R572H |
probably damaging |
Het |
Gm5501 |
A |
G |
18: 9,917,267 (GRCm39) |
|
noncoding transcript |
Het |
Gmpr |
A |
G |
13: 45,683,223 (GRCm39) |
I165V |
probably benign |
Het |
Gnat3 |
G |
A |
5: 18,208,892 (GRCm39) |
|
probably benign |
Het |
H1f8 |
A |
G |
6: 115,925,757 (GRCm39) |
K185E |
probably benign |
Het |
H2-Q4 |
T |
G |
17: 35,598,666 (GRCm39) |
L16R |
unknown |
Het |
Hs2st1 |
T |
C |
3: 144,140,389 (GRCm39) |
K311E |
possibly damaging |
Het |
Kcnj15 |
A |
G |
16: 95,097,368 (GRCm39) |
E330G |
possibly damaging |
Het |
Kif3a |
A |
G |
11: 53,461,441 (GRCm39) |
K29E |
probably benign |
Het |
Krtap4-1 |
A |
G |
11: 99,518,983 (GRCm39) |
V9A |
unknown |
Het |
Lmntd2 |
C |
T |
7: 140,791,117 (GRCm39) |
G432S |
probably damaging |
Het |
Me3 |
T |
C |
7: 89,482,898 (GRCm39) |
|
probably benign |
Het |
Myo1d |
G |
T |
11: 80,375,087 (GRCm39) |
R996S |
probably benign |
Het |
Myo9a |
T |
A |
9: 59,802,566 (GRCm39) |
W2018R |
probably damaging |
Het |
Nphp3 |
G |
T |
9: 103,888,929 (GRCm39) |
V265F |
probably damaging |
Het |
Or10ak9 |
T |
C |
4: 118,726,179 (GRCm39) |
L66P |
probably damaging |
Het |
Or5p67 |
A |
G |
7: 107,922,232 (GRCm39) |
I217T |
probably benign |
Het |
Or8c16 |
T |
C |
9: 38,130,131 (GRCm39) |
M1T |
probably null |
Het |
Pgp |
A |
G |
17: 24,690,315 (GRCm39) |
E247G |
probably damaging |
Het |
Pirb |
A |
T |
7: 3,720,637 (GRCm39) |
L287Q |
probably benign |
Het |
Plch1 |
G |
A |
3: 63,675,044 (GRCm39) |
A202V |
probably damaging |
Het |
Rbm11 |
G |
A |
16: 75,389,932 (GRCm39) |
|
probably null |
Het |
Scg5 |
T |
C |
2: 113,622,230 (GRCm39) |
K124R |
probably damaging |
Het |
Serpina3j |
A |
T |
12: 104,285,916 (GRCm39) |
H357L |
probably damaging |
Het |
St6gal2 |
A |
G |
17: 55,803,324 (GRCm39) |
D353G |
possibly damaging |
Het |
Tdpoz3 |
T |
C |
3: 93,734,216 (GRCm39) |
I297T |
possibly damaging |
Het |
Tdrd5 |
G |
A |
1: 156,128,348 (GRCm39) |
T136I |
probably benign |
Het |
Tfcp2l1 |
T |
A |
1: 118,597,206 (GRCm39) |
I429K |
possibly damaging |
Het |
Tnrc6c |
C |
T |
11: 117,614,355 (GRCm39) |
R838W |
probably damaging |
Het |
Top1 |
T |
C |
2: 160,529,669 (GRCm39) |
|
probably benign |
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 |
Vmn1r183 |
T |
C |
7: 23,754,997 (GRCm39) |
S267P |
probably damaging |
Het |
Xirp2 |
T |
A |
2: 67,342,013 (GRCm39) |
F1418Y |
possibly damaging |
Het |
Zfp114 |
T |
C |
7: 23,880,467 (GRCm39) |
V271A |
possibly damaging |
Het |
Zfp710 |
A |
G |
7: 79,731,134 (GRCm39) |
R104G |
probably 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 |
R3929: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'- CCCAAGACATTTTCCCACGG -3'
Sequencing Primer
(F):5'- CACTTAACTCAACTAACTCTTACTCG -3'
(R):5'- CCCACGGATTATGAACTCTAGTG -3'
|
Posted On |
2015-04-17 |