Incidental Mutation 'R1960:Arid1a'
ID 318018
Institutional Source Beutler Lab
Gene Symbol Arid1a
Ensembl Gene ENSMUSG00000007880
Gene Name AT-rich interaction domain 1A
Synonyms Smarcf1, 1110030E03Rik, Osa1, BAF250a
MMRRC Submission 039974-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1960 (G1)
Quality Score 109
Status Not validated
Chromosome 4
Chromosomal Location 133406319-133484080 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 133480401 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Glutamine at position 174 (H174Q)
Ref Sequence ENSEMBL: ENSMUSP00000122354 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000008024] [ENSMUST00000105897] [ENSMUST00000145664]
AlphaFold A2BH40
Predicted Effect probably benign
Transcript: ENSMUST00000008024
SMART Domains Protein: ENSMUSP00000008024
Gene: ENSMUSG00000007880

DomainStartEndE-ValueType
low complexity region 17 42 N/A INTRINSIC
low complexity region 86 110 N/A INTRINSIC
low complexity region 113 211 N/A INTRINSIC
low complexity region 226 237 N/A INTRINSIC
low complexity region 274 290 N/A INTRINSIC
low complexity region 310 323 N/A INTRINSIC
internal_repeat_3 329 402 4.13e-5 PROSPERO
low complexity region 410 426 N/A INTRINSIC
low complexity region 429 442 N/A INTRINSIC
internal_repeat_1 443 563 4.59e-6 PROSPERO
internal_repeat_2 461 595 1.38e-5 PROSPERO
low complexity region 604 626 N/A INTRINSIC
ARID 630 720 3.56e-25 SMART
BRIGHT 634 725 3.76e-31 SMART
low complexity region 739 751 N/A INTRINSIC
low complexity region 756 770 N/A INTRINSIC
internal_repeat_3 778 872 4.13e-5 PROSPERO
internal_repeat_2 781 928 1.38e-5 PROSPERO
internal_repeat_1 825 940 4.59e-6 PROSPERO
low complexity region 962 987 N/A INTRINSIC
low complexity region 1014 1045 N/A INTRINSIC
low complexity region 1187 1200 N/A INTRINSIC
low complexity region 1380 1404 N/A INTRINSIC
low complexity region 1500 1518 N/A INTRINSIC
Pfam:DUF3518 1592 1848 1.8e-146 PFAM
low complexity region 1849 1859 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000105897
AA Change: H174Q

PolyPhen 2 Score 0.533 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000101517
Gene: ENSMUSG00000007880
AA Change: H174Q

DomainStartEndE-ValueType
low complexity region 2 10 N/A INTRINSIC
low complexity region 24 52 N/A INTRINSIC
low complexity region 74 96 N/A INTRINSIC
low complexity region 118 148 N/A INTRINSIC
low complexity region 161 169 N/A INTRINSIC
low complexity region 233 266 N/A INTRINSIC
low complexity region 273 295 N/A INTRINSIC
low complexity region 308 332 N/A INTRINSIC
low complexity region 367 373 N/A INTRINSIC
low complexity region 402 427 N/A INTRINSIC
low complexity region 471 495 N/A INTRINSIC
low complexity region 498 596 N/A INTRINSIC
low complexity region 611 622 N/A INTRINSIC
low complexity region 659 675 N/A INTRINSIC
low complexity region 695 708 N/A INTRINSIC
low complexity region 795 811 N/A INTRINSIC
low complexity region 814 827 N/A INTRINSIC
internal_repeat_2 828 948 9.26e-7 PROSPERO
internal_repeat_1 831 980 9.26e-7 PROSPERO
low complexity region 989 1011 N/A INTRINSIC
ARID 1015 1105 3.56e-25 SMART
BRIGHT 1019 1110 3.76e-31 SMART
low complexity region 1124 1136 N/A INTRINSIC
low complexity region 1141 1155 N/A INTRINSIC
internal_repeat_1 1159 1314 9.26e-7 PROSPERO
internal_repeat_2 1211 1326 9.26e-7 PROSPERO
low complexity region 1343 1368 N/A INTRINSIC
low complexity region 1395 1426 N/A INTRINSIC
low complexity region 1568 1581 N/A INTRINSIC
low complexity region 1761 1785 N/A INTRINSIC
low complexity region 1881 1899 N/A INTRINSIC
Pfam:DUF3518 1973 2229 1.4e-146 PFAM
low complexity region 2230 2240 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138473
Predicted Effect possibly damaging
Transcript: ENSMUST00000145664
AA Change: H174Q

PolyPhen 2 Score 0.838 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000122354
Gene: ENSMUSG00000007880
AA Change: H174Q

DomainStartEndE-ValueType
low complexity region 2 10 N/A INTRINSIC
low complexity region 24 52 N/A INTRINSIC
low complexity region 74 96 N/A INTRINSIC
low complexity region 118 148 N/A INTRINSIC
low complexity region 161 169 N/A INTRINSIC
low complexity region 233 266 N/A INTRINSIC
low complexity region 273 295 N/A INTRINSIC
low complexity region 308 332 N/A INTRINSIC
low complexity region 367 373 N/A INTRINSIC
low complexity region 402 427 N/A INTRINSIC
low complexity region 471 495 N/A INTRINSIC
low complexity region 498 596 N/A INTRINSIC
low complexity region 611 622 N/A INTRINSIC
low complexity region 659 675 N/A INTRINSIC
low complexity region 695 708 N/A INTRINSIC
internal_repeat_3 714 787 9.49e-6 PROSPERO
low complexity region 795 811 N/A INTRINSIC
low complexity region 814 827 N/A INTRINSIC
internal_repeat_1 828 948 8.73e-7 PROSPERO
internal_repeat_2 846 980 2.88e-6 PROSPERO
low complexity region 989 1011 N/A INTRINSIC
ARID 1015 1105 3.56e-25 SMART
BRIGHT 1019 1110 3.76e-31 SMART
low complexity region 1124 1136 N/A INTRINSIC
low complexity region 1141 1155 N/A INTRINSIC
internal_repeat_3 1163 1257 9.49e-6 PROSPERO
internal_repeat_2 1166 1313 2.88e-6 PROSPERO
internal_repeat_1 1210 1325 8.73e-7 PROSPERO
low complexity region 1347 1372 N/A INTRINSIC
low complexity region 1399 1430 N/A INTRINSIC
low complexity region 1572 1585 N/A INTRINSIC
low complexity region 1765 1789 N/A INTRINSIC
low complexity region 1885 1903 N/A INTRINSIC
Pfam:DUF3518 1978 2233 1.3e-117 PFAM
low complexity region 2234 2244 N/A INTRINSIC
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency 100% (95/95)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the SWI/SNF family, whose members have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. It possesses at least two conserved domains that could be important for its function. First, it has a DNA-binding domain that can specifically bind an AT-rich DNA sequence known to be recognized by a SNF/SWI complex at the beta-globin locus. Second, the C-terminus of the protein can stimulate glucocorticoid receptor-dependent transcriptional activation. It is thought that the protein encoded by this gene confers specificity to the SNF/SWI complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Embryos with homozygous null alleles arrest development at E6.5 with failure to form a mesoderm layer. Mice homozygous for an allele lacking exon 2 and 3 die shortly after birth and exhibit an increase in the hematopoietic stem cell population of the fetal liver at E14.5. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2410004B18Rik C T 3: 145,643,976 (GRCm39) P55S probably damaging Het
Adgre4 T C 17: 56,098,497 (GRCm39) S136P probably benign Het
Aoc1l1 C T 6: 48,952,687 (GRCm39) T204I probably damaging Het
Arap1 C A 7: 101,022,222 (GRCm39) A8E probably damaging Het
Btbd2 A G 10: 80,480,539 (GRCm39) I358T probably benign Het
Camkk2 G A 5: 122,875,575 (GRCm39) R492* probably null Het
Capn3 T C 2: 120,294,421 (GRCm39) V23A probably benign Het
Carm1 T G 9: 21,491,606 (GRCm39) V225G probably benign Het
Ccdc113 T A 8: 96,267,459 (GRCm39) N141K probably benign Het
Ccdc60 C A 5: 116,284,243 (GRCm39) M298I probably benign Het
Celsr3 C T 9: 108,723,016 (GRCm39) P2801L probably benign Het
Clec4n T A 6: 123,207,505 (GRCm39) V23E probably damaging Het
Cmtr2 T G 8: 110,948,382 (GRCm39) L231V probably damaging Het
Csrnp3 T G 2: 65,853,363 (GRCm39) V585G probably null Het
Ctnnd2 T C 15: 30,647,257 (GRCm39) S318P probably damaging Het
Cubn A T 2: 13,344,828 (GRCm39) probably null Het
Dgkd C A 1: 87,857,549 (GRCm39) P754T possibly damaging Het
Dnah7a A G 1: 53,724,142 (GRCm39) S108P probably benign Het
Dnajc24 A G 2: 105,832,268 (GRCm39) probably benign Het
Dner A T 1: 84,423,177 (GRCm39) S475R probably damaging Het
Dtnb T C 12: 3,831,190 (GRCm39) L630P probably benign Het
Dysf T C 6: 84,050,885 (GRCm39) F411L probably benign Het
Fbh1 G A 2: 11,762,339 (GRCm39) A566V probably damaging Het
Fbxw19 G T 9: 109,315,004 (GRCm39) T186K probably benign Het
Flacc1 A T 1: 58,698,437 (GRCm39) V327D possibly damaging Het
Gm4825 A G 15: 85,395,245 (GRCm39) noncoding transcript Het
Grhl2 T A 15: 37,336,558 (GRCm39) V54D probably damaging Het
Hmcn1 T C 1: 150,551,742 (GRCm39) I2621V probably benign Het
Hmcn1 T A 1: 150,553,127 (GRCm39) E2521V possibly damaging Het
Kcng1 A G 2: 168,104,904 (GRCm39) V314A probably benign Het
Kif13a G A 13: 47,018,314 (GRCm39) probably benign Het
Kif21a G A 15: 90,855,051 (GRCm39) A703V probably damaging Het
Kifc1 A G 17: 34,103,561 (GRCm39) probably null Het
Klk13 T A 7: 43,370,431 (GRCm39) N31K possibly damaging Het
Klri1 T A 6: 129,674,347 (GRCm39) H221L probably benign Het
Ltbp4 G A 7: 27,028,443 (GRCm39) P273L unknown Het
Med16 T C 10: 79,742,929 (GRCm39) H14R possibly damaging Het
Mpeg1 G A 19: 12,440,275 (GRCm39) V578M probably damaging Het
Mrgpra2a T A 7: 47,076,983 (GRCm39) I92F probably benign Het
Muc5b T C 7: 141,416,374 (GRCm39) C3107R possibly damaging Het
Myo5a T A 9: 75,055,139 (GRCm39) F441I probably damaging Het
Ndst4 T A 3: 125,232,331 (GRCm39) L300* probably null Het
Nlgn2 G T 11: 69,718,136 (GRCm39) D356E probably damaging Het
Nlrp2 T C 7: 5,330,737 (GRCm39) E553G probably damaging Het
Oas1f G A 5: 120,994,502 (GRCm39) C341Y possibly damaging Het
Olfm5 A T 7: 103,809,619 (GRCm39) C111S possibly damaging Het
Oplah G A 15: 76,181,664 (GRCm39) T1119I probably damaging Het
Or2ag15 T C 7: 106,340,601 (GRCm39) E180G probably damaging Het
Or5d46 T C 2: 88,170,545 (GRCm39) L212P probably damaging Het
Or6c74 C T 10: 129,870,187 (GRCm39) Q231* probably null Het
Or6f2 A T 7: 139,756,596 (GRCm39) I188L probably benign Het
Or8b12c A G 9: 37,715,242 (GRCm39) I12V probably benign Het
Or8g51 T A 9: 38,609,500 (GRCm39) H58L probably benign Het
Pde10a T C 17: 9,161,750 (GRCm39) I477T possibly damaging Het
Pde4b A G 4: 102,454,657 (GRCm39) E108G probably damaging Het
Pdgfrb A T 18: 61,198,855 (GRCm39) T338S probably benign Het
Pgghg A G 7: 140,523,260 (GRCm39) M180V probably benign Het
Phactr4 G A 4: 132,104,559 (GRCm39) T256I probably benign Het
Pot1b A T 17: 55,969,531 (GRCm39) Y546N probably damaging Het
Rangap1 T C 15: 81,590,704 (GRCm39) T463A probably benign Het
Rap1gds1 T C 3: 138,756,317 (GRCm39) I13V probably null Het
Rbak A T 5: 143,160,437 (GRCm39) Y205* probably null Het
Reg3b A T 6: 78,348,797 (GRCm39) K31M probably damaging Het
Rfpl4 A T 7: 5,118,533 (GRCm39) Y12* probably null Het
Rnase6 A G 14: 51,367,889 (GRCm39) N94D possibly damaging Het
Rtn4 T C 11: 29,686,464 (GRCm39) L273P probably damaging Het
Ryr3 A C 2: 112,624,812 (GRCm39) F2203V probably damaging Het
Sae1 A T 7: 16,102,490 (GRCm39) D161E possibly damaging Het
Sema5a T C 15: 32,562,877 (GRCm39) F296S possibly damaging Het
Sh3rf1 C A 8: 61,837,897 (GRCm39) P814Q probably damaging Het
Slc22a29 C A 19: 8,146,557 (GRCm39) R415M probably benign Het
Slc25a25 C T 2: 32,310,663 (GRCm39) probably null Het
Slco4c1 T A 1: 96,795,654 (GRCm39) M135L probably benign Het
Slfn1 A G 11: 83,012,579 (GRCm39) I232V possibly damaging Het
Slitrk1 T A 14: 109,149,622 (GRCm39) N363I probably damaging Het
Srr A G 11: 74,799,542 (GRCm39) V311A probably damaging Het
Tasor T C 14: 27,160,621 (GRCm39) S128P probably damaging Het
Tasor C T 14: 27,201,746 (GRCm39) H1419Y possibly damaging Het
Tenm1 T C X: 41,916,078 (GRCm39) D402G probably benign Het
Topors T C 4: 40,261,044 (GRCm39) R747G unknown Het
Trank1 A T 9: 111,220,696 (GRCm39) I2478F probably damaging Het
Trim69 A G 2: 121,998,165 (GRCm39) N46D probably benign Het
Trpm1 T A 7: 63,879,978 (GRCm39) L661Q probably damaging Het
Ttbk1 A C 17: 46,791,150 (GRCm39) F45V probably damaging Het
Ttn T C 2: 76,644,649 (GRCm39) K4708R probably damaging Het
Unkl A G 17: 25,428,619 (GRCm39) probably benign Het
Uros A T 7: 133,288,735 (GRCm39) N257K probably benign Het
Usp25 A G 16: 76,873,259 (GRCm39) Y439C probably damaging Het
Vgf A G 5: 137,061,029 (GRCm39) probably benign Het
Vmn2r8 A T 5: 108,947,152 (GRCm39) D533E probably damaging Het
Vps13a A T 19: 16,702,995 (GRCm39) Y653N probably damaging Het
Zfp358 T C 8: 3,545,742 (GRCm39) V135A possibly damaging Het
Other mutations in Arid1a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00565:Arid1a APN 4 133,412,793 (GRCm39) missense unknown
IGL01139:Arid1a APN 4 133,421,308 (GRCm39) missense unknown
IGL01392:Arid1a APN 4 133,408,348 (GRCm39) missense unknown
IGL01543:Arid1a APN 4 133,409,033 (GRCm39) missense unknown
IGL01642:Arid1a APN 4 133,409,155 (GRCm39) missense unknown
IGL01843:Arid1a APN 4 133,408,765 (GRCm39) missense unknown
IGL02108:Arid1a APN 4 133,407,827 (GRCm39) missense unknown
IGL02117:Arid1a APN 4 133,420,126 (GRCm39) missense unknown
IGL02150:Arid1a APN 4 133,414,568 (GRCm39) missense unknown
IGL02478:Arid1a APN 4 133,408,585 (GRCm39) missense unknown
IGL02544:Arid1a APN 4 133,409,059 (GRCm39) missense unknown
IGL03070:Arid1a APN 4 133,422,064 (GRCm39) missense unknown
PIT4520001:Arid1a UTSW 4 133,409,227 (GRCm39) missense unknown
R0023:Arid1a UTSW 4 133,418,487 (GRCm39) missense unknown
R0023:Arid1a UTSW 4 133,418,487 (GRCm39) missense unknown
R0419:Arid1a UTSW 4 133,408,435 (GRCm39) missense unknown
R0452:Arid1a UTSW 4 133,416,416 (GRCm39) missense unknown
R0631:Arid1a UTSW 4 133,416,481 (GRCm39) missense unknown
R0648:Arid1a UTSW 4 133,412,515 (GRCm39) missense unknown
R1004:Arid1a UTSW 4 133,414,586 (GRCm39) missense unknown
R1225:Arid1a UTSW 4 133,414,676 (GRCm39) missense unknown
R1229:Arid1a UTSW 4 133,418,548 (GRCm39) missense unknown
R1435:Arid1a UTSW 4 133,408,009 (GRCm39) missense unknown
R1480:Arid1a UTSW 4 133,407,700 (GRCm39) missense unknown
R1491:Arid1a UTSW 4 133,448,237 (GRCm39) missense unknown
R1674:Arid1a UTSW 4 133,416,571 (GRCm39) missense unknown
R1909:Arid1a UTSW 4 133,421,072 (GRCm39) missense unknown
R2018:Arid1a UTSW 4 133,409,145 (GRCm39) missense unknown
R2147:Arid1a UTSW 4 133,408,677 (GRCm39) missense unknown
R2303:Arid1a UTSW 4 133,414,562 (GRCm39) missense unknown
R2320:Arid1a UTSW 4 133,407,840 (GRCm39) missense unknown
R3775:Arid1a UTSW 4 133,414,075 (GRCm39) missense unknown
R3907:Arid1a UTSW 4 133,420,223 (GRCm39) splice site probably benign
R4509:Arid1a UTSW 4 133,423,010 (GRCm39) intron probably benign
R4510:Arid1a UTSW 4 133,423,010 (GRCm39) intron probably benign
R4551:Arid1a UTSW 4 133,423,010 (GRCm39) intron probably benign
R4552:Arid1a UTSW 4 133,423,010 (GRCm39) intron probably benign
R4606:Arid1a UTSW 4 133,414,634 (GRCm39) missense unknown
R4745:Arid1a UTSW 4 133,480,417 (GRCm39) missense probably benign 0.33
R4851:Arid1a UTSW 4 133,408,672 (GRCm39) missense unknown
R4867:Arid1a UTSW 4 133,448,168 (GRCm39) missense probably benign 0.01
R5203:Arid1a UTSW 4 133,409,314 (GRCm39) missense unknown
R5227:Arid1a UTSW 4 133,407,716 (GRCm39) missense unknown
R5294:Arid1a UTSW 4 133,418,366 (GRCm39) splice site probably benign
R5299:Arid1a UTSW 4 133,414,537 (GRCm39) missense unknown
R5412:Arid1a UTSW 4 133,446,913 (GRCm39) unclassified probably benign
R5540:Arid1a UTSW 4 133,407,765 (GRCm39) missense unknown
R5704:Arid1a UTSW 4 133,409,050 (GRCm39) missense unknown
R5870:Arid1a UTSW 4 133,408,387 (GRCm39) missense unknown
R6092:Arid1a UTSW 4 133,421,163 (GRCm39) missense unknown
R6151:Arid1a UTSW 4 133,412,287 (GRCm39) missense unknown
R6240:Arid1a UTSW 4 133,407,997 (GRCm39) missense unknown
R6379:Arid1a UTSW 4 133,408,238 (GRCm39) missense unknown
R6427:Arid1a UTSW 4 133,408,835 (GRCm39) missense unknown
R6739:Arid1a UTSW 4 133,414,937 (GRCm39) missense unknown
R7159:Arid1a UTSW 4 133,480,879 (GRCm39) missense unknown
R7186:Arid1a UTSW 4 133,480,544 (GRCm39)
R7354:Arid1a UTSW 4 133,421,258 (GRCm39) missense unknown
R7408:Arid1a UTSW 4 133,408,391 (GRCm39) missense unknown
R7452:Arid1a UTSW 4 133,480,438 (GRCm39) missense possibly damaging 0.86
R7471:Arid1a UTSW 4 133,408,355 (GRCm39) missense unknown
R7478:Arid1a UTSW 4 133,412,482 (GRCm39) missense unknown
R7581:Arid1a UTSW 4 133,407,662 (GRCm39) missense unknown
R7614:Arid1a UTSW 4 133,418,466 (GRCm39) missense unknown
R7712:Arid1a UTSW 4 133,479,922 (GRCm39) missense probably benign 0.14
R7734:Arid1a UTSW 4 133,408,679 (GRCm39) missense unknown
R7878:Arid1a UTSW 4 133,414,582 (GRCm39) missense unknown
R7973:Arid1a UTSW 4 133,480,381 (GRCm39) missense probably damaging 0.96
R8012:Arid1a UTSW 4 133,420,174 (GRCm39) missense unknown
R8355:Arid1a UTSW 4 133,448,174 (GRCm39) missense unknown
R8396:Arid1a UTSW 4 133,479,973 (GRCm39) missense probably damaging 0.99
R8708:Arid1a UTSW 4 133,409,145 (GRCm39) missense unknown
R8923:Arid1a UTSW 4 133,412,304 (GRCm39) missense unknown
R8997:Arid1a UTSW 4 133,421,343 (GRCm39) missense unknown
R9003:Arid1a UTSW 4 133,411,799 (GRCm39) missense unknown
R9145:Arid1a UTSW 4 133,421,214 (GRCm39) missense unknown
R9224:Arid1a UTSW 4 133,409,167 (GRCm39) missense unknown
R9310:Arid1a UTSW 4 133,413,625 (GRCm39) missense unknown
R9470:Arid1a UTSW 4 133,413,057 (GRCm39) missense unknown
RF012:Arid1a UTSW 4 133,480,131 (GRCm39) small deletion probably benign
RF015:Arid1a UTSW 4 133,480,142 (GRCm39) small deletion probably benign
X0064:Arid1a UTSW 4 133,416,571 (GRCm39) missense unknown
Z1176:Arid1a UTSW 4 133,447,861 (GRCm39) missense probably null
Z1177:Arid1a UTSW 4 133,408,227 (GRCm39) missense unknown
Predicted Primers PCR Primer
(F):5'- CGACGTGAGCAGTTGGTTGA -3'
(R):5'- TAGGCCCGCCCTGAACAATA -3'

Sequencing Primer
(F):5'- ACCTCTCGGGGAGCTCAG -3'
(R):5'- ATAACCTCCCGGAGCCG -3'
Posted On 2015-05-19