Incidental Mutation 'R1799:Atrx'
ID 202995
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 039829-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.943) question?
Stock # R1799 (G1)
Quality Score 222
Status Not validated
Chromosome X
Chromosomal Location 104841221-104972978 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 104891235 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Arginine at position 1536 (Q1536R)
Ref Sequence ENSEMBL: ENSMUSP00000109203 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000113573] [ENSMUST00000198209]
AlphaFold Q61687
Predicted Effect probably damaging
Transcript: ENSMUST00000113573
AA Change: Q1536R

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000109203
Gene: ENSMUSG00000031229
AA Change: Q1536R

DomainStartEndE-ValueType
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: ENSMUST00000116081
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123174
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142235
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146193
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155445
Predicted Effect noncoding transcript
Transcript: ENSMUST00000196998
Predicted Effect probably benign
Transcript: ENSMUST00000198209
SMART Domains Protein: ENSMUSP00000142726
Gene: ENSMUSG00000031229

DomainStartEndE-ValueType
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
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.9%
  • 10x: 95.3%
  • 20x: 92.3%
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: 102 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A930011G23Rik A G 5: 99,382,435 (GRCm39) L271P probably benign Het
Adamts3 A C 5: 89,923,280 (GRCm39) D175E probably benign Het
Adcy4 T C 14: 56,008,929 (GRCm39) T833A probably benign Het
Adgrf5 A T 17: 43,750,958 (GRCm39) I508F probably damaging Het
Arhgap9 G T 10: 127,163,593 (GRCm39) V464L probably damaging Het
Atp10a T A 7: 58,474,182 (GRCm39) D1156E probably damaging Het
Atp2a1 A T 7: 126,049,314 (GRCm39) M576K probably benign Het
Ccdc141 A C 2: 76,842,015 (GRCm39) V1472G possibly damaging Het
Cd84 A G 1: 171,700,317 (GRCm39) T145A possibly damaging Het
Celsr1 G T 15: 85,916,886 (GRCm39) N362K probably damaging Het
Cep290 G A 10: 100,352,058 (GRCm39) A755T probably benign Het
Cfap70 T A 14: 20,445,067 (GRCm39) E1071V probably damaging Het
Cps1 T C 1: 67,248,801 (GRCm39) V1176A probably damaging Het
Csf2rb2 A C 15: 78,181,268 (GRCm39) N41K probably damaging Het
Csn1s2a G A 5: 87,926,052 (GRCm39) V43M probably damaging Het
Cyp26b1 T C 6: 84,561,254 (GRCm39) D136G probably benign Het
Cyp7b1 A G 3: 18,151,616 (GRCm39) L199P probably benign Het
Dapk1 C T 13: 60,867,468 (GRCm39) T225I probably damaging Het
Dio2 T A 12: 90,696,680 (GRCm39) T103S probably benign Het
Dipk1a C A 5: 108,057,713 (GRCm39) V237F probably damaging Het
Dnhd1 T A 7: 105,304,974 (GRCm39) S339T probably benign Het
Drc1 A G 5: 30,523,841 (GRCm39) N737D probably damaging Het
Efhc1 C T 1: 21,049,762 (GRCm39) P541S probably benign Het
Elmo2 A T 2: 165,134,077 (GRCm39) I637N probably damaging Het
Eps15 T A 4: 109,240,034 (GRCm39) D492E probably damaging Het
Ermn G T 2: 57,938,249 (GRCm39) N121K probably benign Het
F5 A G 1: 164,021,100 (GRCm39) T1192A possibly damaging Het
Fbxo22 T C 9: 55,130,771 (GRCm39) F347L probably benign Het
Fbxw15 G A 9: 109,387,314 (GRCm39) S227F probably damaging Het
Foxj3 A G 4: 119,476,548 (GRCm39) N242S probably benign Het
Gjb3 G A 4: 127,220,224 (GRCm39) R103W probably damaging Het
Grm4 A G 17: 27,691,914 (GRCm39) V235A probably damaging Het
Gstm4 T C 3: 107,950,874 (GRCm39) N74S probably damaging Het
Gtf3c3 A G 1: 54,459,583 (GRCm39) V393A possibly damaging Het
Hltf T A 3: 20,159,855 (GRCm39) L702H probably damaging Het
Inpp4a T A 1: 37,432,059 (GRCm39) V153E possibly damaging Het
Kmt5c T C 7: 4,745,729 (GRCm39) probably null Het
Kynu A G 2: 43,494,169 (GRCm39) R201G possibly damaging Het
Lrp2 T A 2: 69,333,874 (GRCm39) T1456S probably benign Het
Lrrc40 G A 3: 157,742,441 (GRCm39) V19I probably benign Het
M1ap T A 6: 82,982,491 (GRCm39) C258* probably null Het
Man2a1 T C 17: 65,059,452 (GRCm39) L1113P probably benign Het
Man2a1 C T 17: 64,976,492 (GRCm39) R427W probably damaging Het
Meikin C A 11: 54,308,613 (GRCm39) Q404K probably benign Het
Mfsd4a T C 1: 131,981,334 (GRCm39) I222V possibly damaging Het
N4bp2 A G 5: 65,964,168 (GRCm39) N739S possibly damaging Het
Ncoa2 A T 1: 13,232,517 (GRCm39) probably null Het
Nisch G T 14: 30,899,228 (GRCm39) probably benign Het
Nmur2 A G 11: 55,920,447 (GRCm39) V266A probably damaging Het
Npcd G A 15: 79,712,987 (GRCm39) R147C probably damaging Het
Or4q3 T A 14: 50,583,537 (GRCm39) M121L probably benign Het
Or5ac25 T A 16: 59,182,243 (GRCm39) I113F probably benign Het
Pals2 T A 6: 50,173,525 (GRCm39) M463K probably damaging Het
Parp4 A T 14: 56,885,589 (GRCm39) H1556L unknown Het
Pcdh9 G T 14: 94,126,107 (GRCm39) A21E probably benign Het
Phtf1 A G 3: 103,903,958 (GRCm39) E436G probably benign Het
Piezo2 C A 18: 63,165,911 (GRCm39) probably null Het
Piezo2 T C 18: 63,241,158 (GRCm39) Y690C probably damaging Het
Pla2g4f T C 2: 120,141,549 (GRCm39) R183G possibly damaging Het
Plxnd1 T C 6: 115,971,018 (GRCm39) D250G probably damaging Het
Ppig A G 2: 69,579,744 (GRCm39) D426G unknown Het
Ppp3cb T C 14: 20,574,540 (GRCm39) E185G possibly damaging Het
Qsox1 A T 1: 155,670,364 (GRCm39) M151K probably null Het
Ralgapa2 T C 2: 146,184,648 (GRCm39) E1453G probably benign Het
Rnf167 G A 11: 70,540,838 (GRCm39) V191I probably benign Het
Rp1 T C 1: 4,419,055 (GRCm39) K686E possibly damaging Het
Ryr1 T G 7: 28,767,046 (GRCm39) Q2979P probably damaging Het
Scaf1 T A 7: 44,657,443 (GRCm39) I479F probably damaging Het
Septin8 A G 11: 53,425,310 (GRCm39) T68A probably benign Het
Sh3rf1 A T 8: 61,825,661 (GRCm39) N552I probably damaging Het
Shoc1 A T 4: 59,099,383 (GRCm39) V103D possibly damaging Het
Slc1a3 A G 15: 8,717,888 (GRCm39) L68P probably damaging Het
Slc39a6 G A 18: 24,718,524 (GRCm39) P511L probably benign Het
Slc9c1 A G 16: 45,374,652 (GRCm39) Y339C probably damaging Het
Smarcal1 G T 1: 72,625,120 (GRCm39) C89F probably damaging Het
Smu1 A T 4: 40,745,537 (GRCm39) M261K probably damaging Het
Spag8 T G 4: 43,653,087 (GRCm39) probably benign Het
Spag8 T C 4: 43,653,345 (GRCm39) probably benign Het
Spata31d1a T C 13: 59,851,216 (GRCm39) D304G probably benign Het
Spdl1 A T 11: 34,711,856 (GRCm39) L298* probably null Het
Stac2 C T 11: 97,930,444 (GRCm39) probably null Het
Stag1 A G 9: 100,835,515 (GRCm39) probably null Het
Stpg2 C T 3: 139,125,542 (GRCm39) P445L probably damaging Het
Sult2a8 A T 7: 14,157,451 (GRCm39) V128E probably damaging Het
Synm A G 7: 67,385,707 (GRCm39) F210L probably damaging Het
Tbck C G 3: 132,480,263 (GRCm39) A714G probably benign Het
Tcerg1 A T 18: 42,694,012 (GRCm39) Y711F possibly damaging Het
Tnfrsf25 A G 4: 152,201,465 (GRCm39) T98A probably benign Het
Togaram2 T C 17: 71,998,450 (GRCm39) S218P probably damaging Het
Tpp1 A T 7: 105,399,515 (GRCm39) D84E probably benign Het
Trim30d G T 7: 104,132,682 (GRCm39) Q202K probably damaging Het
Trim37 T A 11: 87,068,845 (GRCm39) V397E probably damaging Het
Triml1 A T 8: 43,583,512 (GRCm39) I363N probably damaging Het
Trpm6 T A 19: 18,869,363 (GRCm39) probably null Het
Tsc2 T C 17: 24,823,382 (GRCm39) S1055G probably benign Het
Ubr5 T C 15: 37,989,621 (GRCm39) D2065G probably damaging Het
Uggt2 G T 14: 119,269,688 (GRCm39) P948Q probably benign Het
Vps13c A T 9: 67,851,399 (GRCm39) S2345C probably damaging Het
Wtap G T 17: 13,199,771 (GRCm39) R48S possibly damaging Het
Zbtb38 A G 9: 96,570,934 (GRCm39) V50A probably damaging Het
Zcchc2 T A 1: 105,958,017 (GRCm39) S829R probably benign Het
Zfp385b T C 2: 77,246,316 (GRCm39) D237G probably benign Het
Other mutations in Atrx
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
Predicted Primers PCR Primer
(F):5'- GCTTGCAGACACCCAACTTG -3'
(R):5'- GTTAAGGTTGCTATACCACCATTGC -3'

Sequencing Primer
(F):5'- CCTTGTAAGATCTGTAACAGCTGG -3'
(R):5'- GCTTCACCTACTAAGTGTCC -3'
Posted On 2014-06-23