Incidental Mutation 'IGL01293:Atrx'
| ID |
72967 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| 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 |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.948)
|
| Stock # |
IGL01293
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
X |
| Chromosomal Location |
104841221-104972978 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 104919801 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 641
(S641P)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000121416
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000113573]
[ENSMUST00000128968]
[ENSMUST00000134381]
[ENSMUST00000134507]
[ENSMUST00000197302]
[ENSMUST00000198441]
[ENSMUST00000198448]
[ENSMUST00000199233]
[ENSMUST00000198209]
[ENSMUST00000154866]
[ENSMUST00000150914]
|
| AlphaFold |
Q61687 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000113573
AA Change: S680P
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000109203
Gene: ENSMUSG00000031229
AA Change: S680P
| 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: ENSMUST00000122626
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000123174
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000128968
AA Change: S641P
PolyPhen 2
Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
|
| SMART Domains |
Protein: ENSMUSP00000121416
Gene: ENSMUSG00000031229
AA Change: S641P
| 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
|
| SMART Domains |
Protein: ENSMUSP00000122875
Gene: ENSMUSG00000031229
| 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
|
| SMART Domains |
Protein: ENSMUSP00000123085
Gene: ENSMUSG00000031229
| 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: ENSMUST00000197302
|
| SMART Domains |
Protein: ENSMUSP00000143163
Gene: ENSMUSG00000031229
| Domain | Start | End | E-Value | Type |
|---|
|
PDB:2JM1|A
|
72 |
134 |
6e-42 |
PDB |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000198441
|
| SMART Domains |
Protein: ENSMUSP00000143565
Gene: ENSMUSG00000031229
| 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: ENSMUST00000200471
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000198448
|
| SMART Domains |
Protein: ENSMUSP00000143090
Gene: ENSMUSG00000031229
| 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
|
| SMART Domains |
Protein: ENSMUSP00000143015
Gene: ENSMUSG00000031229
| 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: 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: ENSMUST00000154866
|
| SMART Domains |
Protein: ENSMUSP00000121291
Gene: ENSMUSG00000031229
| 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 |
probably benign
Transcript: ENSMUST00000150914
|
| SMART Domains |
Protein: ENSMUSP00000122034
Gene: ENSMUSG00000031229
| 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 |
|
| Coding Region Coverage |
|
| 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: 44 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl3 |
A |
G |
4: 144,190,226 (GRCm39) |
V25A |
probably benign |
Het |
| Aadacl4fm5 |
G |
T |
4: 144,504,159 (GRCm39) |
H331N |
probably benign |
Het |
| Aagab |
T |
C |
9: 63,543,751 (GRCm39) |
V235A |
probably benign |
Het |
| Ash1l |
T |
C |
3: 88,890,836 (GRCm39) |
V905A |
probably benign |
Het |
| Bnc1 |
T |
C |
7: 81,624,237 (GRCm39) |
E330G |
probably damaging |
Het |
| Cenpq |
A |
T |
17: 41,244,067 (GRCm39) |
S4T |
possibly damaging |
Het |
| Clvs1 |
T |
A |
4: 9,281,559 (GRCm39) |
M1K |
probably null |
Het |
| Cul2 |
A |
G |
18: 3,419,426 (GRCm39) |
K196E |
probably damaging |
Het |
| Cyp2d10 |
A |
T |
15: 82,287,210 (GRCm39) |
V471E |
possibly damaging |
Het |
| Efhc2 |
T |
A |
X: 17,073,934 (GRCm39) |
I469L |
probably benign |
Het |
| Fhod3 |
C |
T |
18: 25,153,709 (GRCm39) |
|
probably benign |
Het |
| Gm1968 |
A |
G |
16: 29,777,632 (GRCm39) |
|
noncoding transcript |
Het |
| Hpdl |
T |
A |
4: 116,678,141 (GRCm39) |
T107S |
possibly damaging |
Het |
| Il1rl1 |
G |
A |
1: 40,485,376 (GRCm39) |
G276D |
possibly damaging |
Het |
| Irgq |
A |
G |
7: 24,233,149 (GRCm39) |
D330G |
probably damaging |
Het |
| Kdm4b |
A |
G |
17: 56,660,019 (GRCm39) |
D62G |
probably benign |
Het |
| Lama2 |
T |
C |
10: 27,107,632 (GRCm39) |
T793A |
probably benign |
Het |
| Lrrk2 |
T |
C |
15: 91,610,340 (GRCm39) |
F691L |
probably benign |
Het |
| Macf1 |
C |
T |
4: 123,365,104 (GRCm39) |
G1654E |
probably benign |
Het |
| Mgat4c |
A |
T |
10: 102,224,086 (GRCm39) |
Y100F |
probably benign |
Het |
| Ncapg |
A |
G |
5: 45,839,196 (GRCm39) |
N532S |
probably benign |
Het |
| Nfkb1 |
T |
C |
3: 135,296,600 (GRCm39) |
D782G |
probably damaging |
Het |
| Nthl1 |
G |
T |
17: 24,857,683 (GRCm39) |
C294F |
probably damaging |
Het |
| Obp2b |
A |
G |
2: 25,627,719 (GRCm39) |
H45R |
probably benign |
Het |
| Olfm1 |
A |
G |
2: 28,104,715 (GRCm39) |
E156G |
probably damaging |
Het |
| Or14j2 |
A |
G |
17: 37,886,308 (GRCm39) |
I2T |
probably benign |
Het |
| Or7g29 |
C |
A |
9: 19,286,632 (GRCm39) |
A182S |
probably benign |
Het |
| Otud6b |
A |
G |
4: 14,822,682 (GRCm39) |
|
probably benign |
Het |
| Patl2 |
T |
C |
2: 121,954,291 (GRCm39) |
T427A |
probably benign |
Het |
| Pdzd8 |
T |
A |
19: 59,288,218 (GRCm39) |
R1061W |
probably damaging |
Het |
| Plk3 |
A |
T |
4: 116,990,194 (GRCm39) |
L137* |
probably null |
Het |
| Rps6ka6 |
T |
C |
X: 110,360,059 (GRCm39) |
|
probably benign |
Het |
| Shank1 |
T |
C |
7: 44,003,660 (GRCm39) |
V1784A |
possibly damaging |
Het |
| Smc1b |
A |
T |
15: 85,016,099 (GRCm39) |
S14T |
probably damaging |
Het |
| Sox4 |
C |
A |
13: 29,136,664 (GRCm39) |
R114L |
probably damaging |
Het |
| Speg |
C |
T |
1: 75,364,746 (GRCm39) |
R221W |
probably damaging |
Het |
| Tram1l1 |
T |
C |
3: 124,115,788 (GRCm39) |
V316A |
probably benign |
Het |
| Virma |
G |
T |
4: 11,521,114 (GRCm39) |
K840N |
probably damaging |
Het |
| Vmn1r49 |
A |
T |
6: 90,049,394 (GRCm39) |
S203T |
probably damaging |
Het |
| Wdr1 |
T |
C |
5: 38,686,886 (GRCm39) |
T293A |
probably benign |
Het |
| Xirp2 |
C |
T |
2: 67,345,528 (GRCm39) |
P2590S |
possibly damaging |
Het |
| Zfp106 |
T |
C |
2: 120,365,516 (GRCm39) |
Y297C |
possibly damaging |
Het |
| Zfp128 |
A |
G |
7: 12,625,351 (GRCm39) |
*573W |
probably null |
Het |
| Zfp575 |
G |
A |
7: 24,285,182 (GRCm39) |
P153L |
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 |
|
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 |
|
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 |
|
| Posted On |
2013-10-07 |
Incidental Mutation