Incidental Mutation 'R2004:Smarca4'
ID 223406
Institutional Source Beutler Lab
Gene Symbol Smarca4
Ensembl Gene ENSMUSG00000032187
Gene Name SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
Synonyms SW1/SNF, Brg1, SNF2beta, b2b692Clo, b2b508.1Clo
MMRRC Submission 040013-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2004 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 21527465-21615526 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 21588776 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 1193 (I1193F)
Ref Sequence ENSEMBL: ENSMUSP00000133922 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034707] [ENSMUST00000098948] [ENSMUST00000174008]
AlphaFold Q3TKT4
Predicted Effect probably damaging
Transcript: ENSMUST00000034707
AA Change: I1193F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000034707
Gene: ENSMUSG00000032187
AA Change: I1193F

DomainStartEndE-ValueType
low complexity region 6 58 N/A INTRINSIC
low complexity region 130 153 N/A INTRINSIC
QLQ 170 206 3.98e-14 SMART
low complexity region 221 247 N/A INTRINSIC
low complexity region 252 289 N/A INTRINSIC
low complexity region 304 330 N/A INTRINSIC
low complexity region 407 418 N/A INTRINSIC
HSA 460 532 2e-27 SMART
coiled coil region 563 595 N/A INTRINSIC
BRK 612 656 5.17e-21 SMART
low complexity region 657 672 N/A INTRINSIC
low complexity region 691 702 N/A INTRINSIC
DEXDc 750 942 5.17e-38 SMART
Blast:DEXDc 953 985 7e-10 BLAST
low complexity region 1019 1034 N/A INTRINSIC
HELICc 1110 1194 7.27e-24 SMART
low complexity region 1252 1267 N/A INTRINSIC
SnAC 1288 1356 2.8e-29 SMART
low complexity region 1360 1385 N/A INTRINSIC
low complexity region 1388 1398 N/A INTRINSIC
BROMO 1422 1533 4.19e-42 SMART
low complexity region 1534 1557 N/A INTRINSIC
low complexity region 1578 1588 N/A INTRINSIC
low complexity region 1594 1614 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000098948
AA Change: I1193F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000096547
Gene: ENSMUSG00000032187
AA Change: I1193F

DomainStartEndE-ValueType
low complexity region 6 58 N/A INTRINSIC
low complexity region 130 153 N/A INTRINSIC
QLQ 170 206 3.98e-14 SMART
low complexity region 221 247 N/A INTRINSIC
low complexity region 252 289 N/A INTRINSIC
low complexity region 304 330 N/A INTRINSIC
low complexity region 407 418 N/A INTRINSIC
HSA 460 532 2e-27 SMART
coiled coil region 563 595 N/A INTRINSIC
BRK 612 656 5.17e-21 SMART
low complexity region 657 672 N/A INTRINSIC
low complexity region 691 702 N/A INTRINSIC
DEXDc 750 942 5.17e-38 SMART
Blast:DEXDc 953 985 7e-10 BLAST
low complexity region 1019 1034 N/A INTRINSIC
HELICc 1110 1194 7.27e-24 SMART
low complexity region 1252 1267 N/A INTRINSIC
SnAC 1288 1356 2.8e-29 SMART
low complexity region 1363 1388 N/A INTRINSIC
low complexity region 1391 1401 N/A INTRINSIC
BROMO 1425 1536 4.19e-42 SMART
low complexity region 1537 1560 N/A INTRINSIC
low complexity region 1581 1591 N/A INTRINSIC
low complexity region 1597 1617 N/A INTRINSIC
Predicted Effect unknown
Transcript: ENSMUST00000172996
AA Change: I997F
SMART Domains Protein: ENSMUSP00000133535
Gene: ENSMUSG00000032187
AA Change: I997F

DomainStartEndE-ValueType
low complexity region 26 52 N/A INTRINSIC
low complexity region 57 94 N/A INTRINSIC
low complexity region 109 135 N/A INTRINSIC
low complexity region 212 223 N/A INTRINSIC
HSA 265 337 2e-27 SMART
coiled coil region 367 399 N/A INTRINSIC
BRK 417 461 5.17e-21 SMART
low complexity region 462 477 N/A INTRINSIC
low complexity region 496 507 N/A INTRINSIC
DEXDc 555 747 5.17e-38 SMART
Blast:DEXDc 758 790 6e-10 BLAST
low complexity region 824 839 N/A INTRINSIC
HELICc 915 999 7.27e-24 SMART
low complexity region 1088 1105 N/A INTRINSIC
SnAC 1126 1194 2.8e-29 SMART
low complexity region 1201 1226 N/A INTRINSIC
low complexity region 1229 1239 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000174008
AA Change: I1193F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000133922
Gene: ENSMUSG00000032187
AA Change: I1193F

DomainStartEndE-ValueType
low complexity region 6 58 N/A INTRINSIC
low complexity region 130 153 N/A INTRINSIC
QLQ 170 206 3.98e-14 SMART
low complexity region 221 247 N/A INTRINSIC
low complexity region 252 289 N/A INTRINSIC
low complexity region 304 330 N/A INTRINSIC
low complexity region 407 418 N/A INTRINSIC
HSA 460 532 2e-27 SMART
coiled coil region 563 595 N/A INTRINSIC
BRK 612 656 5.17e-21 SMART
low complexity region 657 672 N/A INTRINSIC
low complexity region 691 702 N/A INTRINSIC
DEXDc 750 942 5.17e-38 SMART
Blast:DEXDc 953 985 7e-10 BLAST
low complexity region 1019 1034 N/A INTRINSIC
HELICc 1110 1194 7.27e-24 SMART
low complexity region 1252 1267 N/A INTRINSIC
SnAC 1288 1356 2.8e-29 SMART
low complexity region 1360 1385 N/A INTRINSIC
low complexity region 1388 1398 N/A INTRINSIC
BROMO 1422 1532 1.36e-41 SMART
low complexity region 1533 1556 N/A INTRINSIC
low complexity region 1577 1587 N/A INTRINSIC
low complexity region 1593 1613 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184017
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 94.9%
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 is a member of the SWI/SNF family of proteins and is similar to the brahma protein of Drosophila. Members of this family 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. In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Mutations in this gene cause rhabdoid tumor predisposition syndrome type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]
PHENOTYPE: Homozygotes for a null allele die in utero before implantation. Embryos heterozygous for this null allele and an ENU-induced allele show impaired definitive erythropoiesis, anemia and lethality during organogenesis. Heterozygotes for a different null allele show cyanosis and cardiovascular defects. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aass A T 6: 23,092,561 (GRCm39) Y146* probably null Het
Adcy2 A G 13: 68,944,722 (GRCm39) L220P probably damaging Het
Agl T C 3: 116,574,914 (GRCm39) Y660C probably damaging Het
Ak1 A G 2: 32,519,622 (GRCm39) T17A probably benign Het
Amph G A 13: 19,326,198 (GRCm39) V643M probably damaging Het
Ankrd11 A T 8: 123,629,161 (GRCm39) probably null Het
Ap5b1 T C 19: 5,620,502 (GRCm39) S641P possibly damaging Het
Apoc4 A G 7: 19,415,304 (GRCm39) M1T probably null Het
Arhgap5 T C 12: 52,564,817 (GRCm39) V596A probably benign Het
Ascc3 A G 10: 50,493,838 (GRCm39) E91G probably damaging Het
Bach2 T A 4: 32,580,055 (GRCm39) V637E probably benign Het
Bicd2 T G 13: 49,532,881 (GRCm39) L489R possibly damaging Het
Bltp1 C T 3: 36,949,527 (GRCm39) T2I possibly damaging Het
Boc A T 16: 44,322,007 (GRCm39) probably null Het
Cbln2 T A 18: 86,734,791 (GRCm39) V188D probably damaging Het
Ccl11 A C 11: 81,953,123 (GRCm39) T94P probably damaging Het
Cd109 A T 9: 78,611,044 (GRCm39) H1220L probably benign Het
Cd226 A G 18: 89,265,435 (GRCm39) I125V probably benign Het
Cep135 T A 5: 76,780,176 (GRCm39) probably null Het
Cgnl1 T G 9: 71,537,821 (GRCm39) E1233A probably damaging Het
Ckap5 T A 2: 91,437,891 (GRCm39) D1597E possibly damaging Het
Clptm1 A G 7: 19,380,762 (GRCm39) I63T possibly damaging Het
Cpsf7 C T 19: 10,518,073 (GRCm39) P428S probably damaging Het
Cuedc1 C T 11: 88,068,216 (GRCm39) P155S probably damaging Het
Dgkb T C 12: 38,134,228 (GRCm39) Y45H probably damaging Het
Dglucy T C 12: 100,823,181 (GRCm39) F459L probably damaging Het
Dmp1 T A 5: 104,359,790 (GRCm39) D155E possibly damaging Het
Dnah1 T A 14: 31,023,813 (GRCm39) I960F possibly damaging Het
Drosha G T 15: 12,915,467 (GRCm39) M795I probably damaging Het
Dsg1b A G 18: 20,529,532 (GRCm39) T326A probably damaging Het
Dusp16 T G 6: 134,695,802 (GRCm39) N343T probably benign Het
Faim2 T C 15: 99,398,127 (GRCm39) S274G possibly damaging Het
Fhip2a G T 19: 57,370,324 (GRCm39) V523L probably benign Het
Fndc1 T C 17: 8,023,761 (GRCm39) R65G probably damaging Het
Fnip2 A T 3: 79,419,632 (GRCm39) probably benign Het
Grm3 T C 5: 9,639,793 (GRCm39) Y84C possibly damaging Het
Herc2 T C 7: 55,787,607 (GRCm39) F1755L probably damaging Het
Hivep1 C T 13: 42,313,625 (GRCm39) T1955I possibly damaging Het
Ift20 T C 11: 78,431,797 (GRCm39) I97T probably damaging Het
Il36rn T C 2: 24,171,376 (GRCm39) C155R probably damaging Het
Lca5l T A 16: 95,963,849 (GRCm39) K358N probably damaging Het
Lca5l T C 16: 95,977,218 (GRCm39) N196S possibly damaging Het
Maf1 G A 15: 76,237,563 (GRCm39) D175N probably damaging Het
Mical3 T C 6: 120,928,283 (GRCm39) K996E probably damaging Het
Midn A G 10: 79,990,983 (GRCm39) N331S probably benign Het
Mki67 T A 7: 135,300,238 (GRCm39) K1599* probably null Het
Mlx A G 11: 100,979,805 (GRCm39) Q162R possibly damaging Het
Nalf1 A G 8: 9,820,607 (GRCm39) S138P probably benign Het
Ngp T C 9: 110,249,929 (GRCm39) C76R probably damaging Het
Nin C T 12: 70,072,251 (GRCm39) G1210D probably benign Het
Nlgn1 A G 3: 25,488,034 (GRCm39) I738T probably benign Het
Nop53 A C 7: 15,672,153 (GRCm39) F465C probably damaging Het
Npas3 A G 12: 54,114,680 (GRCm39) D503G possibly damaging Het
Npbwr1 T A 1: 5,986,570 (GRCm39) S315C probably damaging Het
Nup42 G T 5: 24,386,989 (GRCm39) G260* probably null Het
Ogdh G C 11: 6,284,626 (GRCm39) R200P possibly damaging Het
Or4b13 T A 2: 90,083,036 (GRCm39) I99L probably benign Het
Or52n20 A G 7: 104,320,808 (GRCm39) T300A possibly damaging Het
Or5m13b T G 2: 85,753,939 (GRCm39) probably null Het
Or6ae1 C T 7: 139,742,729 (GRCm39) V45I probably damaging Het
Or7g16 G A 9: 18,726,801 (GRCm39) S263L probably benign Het
Or7g33 A T 9: 19,448,688 (GRCm39) C179* probably null Het
Ovgp1 T A 3: 105,894,309 (GRCm39) probably benign Het
Papln T A 12: 83,819,992 (GRCm39) C150S probably damaging Het
Pde1c A T 6: 56,135,996 (GRCm39) L316Q probably damaging Het
Pdlim2 C T 14: 70,402,228 (GRCm39) R296H probably damaging Het
Piezo2 G T 18: 63,277,997 (GRCm39) D302E probably damaging Het
Pirb A T 7: 3,720,637 (GRCm39) L287Q probably benign Het
Plin1 A G 7: 79,375,378 (GRCm39) probably benign Het
Plxnc1 A G 10: 94,688,484 (GRCm39) I698T probably damaging Het
Ppp1r12c G T 7: 4,485,974 (GRCm39) C572* probably null Het
Ptgis T C 2: 167,056,769 (GRCm39) M273V possibly damaging Het
Samd14 C A 11: 94,914,110 (GRCm39) T283K probably damaging Het
Scnn1g A T 7: 121,337,411 (GRCm39) K91* probably null Het
Slc24a4 A G 12: 102,180,166 (GRCm39) Q95R probably damaging Het
Slfn9 T G 11: 82,879,027 (GRCm39) D34A probably benign Het
Spata31e5 A G 1: 28,816,260 (GRCm39) W591R probably damaging Het
Sphkap T C 1: 83,255,632 (GRCm39) M706V probably benign Het
Stard9 C A 2: 120,504,117 (GRCm39) S221R probably damaging Het
Stxbp1 T C 2: 32,688,201 (GRCm39) D488G probably damaging Het
Sugp2 C T 8: 70,695,306 (GRCm39) probably null Het
Tekt5 T C 16: 10,213,070 (GRCm39) I72V probably benign Het
Themis T A 10: 28,658,720 (GRCm39) N582K probably benign Het
Tmed11 C A 5: 108,934,000 (GRCm39) M65I possibly damaging Het
Top3a G T 11: 60,633,315 (GRCm39) P927Q probably damaging Het
Trpa1 A T 1: 14,976,207 (GRCm39) N165K possibly damaging Het
Tsfm A G 10: 126,866,663 (GRCm39) S2P probably damaging Het
Wdr47 C A 3: 108,534,758 (GRCm39) S559* probably null Het
Wnt2b T C 3: 104,860,331 (GRCm39) Y192C probably damaging Het
Zfp280b A G 10: 75,874,370 (GRCm39) D83G probably benign Het
Zfp345 T C 2: 150,314,038 (GRCm39) T500A possibly damaging Het
Zfp78 T A 7: 6,382,074 (GRCm39) C343S probably damaging Het
Other mutations in Smarca4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01380:Smarca4 APN 9 21,590,369 (GRCm39) missense probably benign 0.30
IGL01694:Smarca4 APN 9 21,577,166 (GRCm39) missense probably damaging 1.00
IGL02147:Smarca4 APN 9 21,546,999 (GRCm39) missense probably damaging 0.98
IGL02417:Smarca4 APN 9 21,612,386 (GRCm39) missense probably damaging 1.00
IGL02421:Smarca4 APN 9 21,550,535 (GRCm39) missense probably damaging 1.00
IGL02550:Smarca4 APN 9 21,597,418 (GRCm39) missense probably benign 0.25
IGL02794:Smarca4 APN 9 21,584,638 (GRCm39) splice site probably benign
IGL03030:Smarca4 APN 9 21,547,132 (GRCm39) missense probably benign 0.14
IGL03037:Smarca4 APN 9 21,544,231 (GRCm39) unclassified probably benign
IGL03069:Smarca4 APN 9 21,547,132 (GRCm39) missense probably benign 0.14
IGL03355:Smarca4 APN 9 21,547,132 (GRCm39) missense probably benign 0.14
R0123:Smarca4 UTSW 9 21,548,620 (GRCm39) missense probably damaging 1.00
R0134:Smarca4 UTSW 9 21,548,620 (GRCm39) missense probably damaging 1.00
R0230:Smarca4 UTSW 9 21,612,168 (GRCm39) missense probably damaging 0.99
R0269:Smarca4 UTSW 9 21,547,497 (GRCm39) missense probably benign 0.09
R0631:Smarca4 UTSW 9 21,570,280 (GRCm39) splice site probably benign
R0665:Smarca4 UTSW 9 21,612,239 (GRCm39) small deletion probably benign
R0726:Smarca4 UTSW 9 21,611,435 (GRCm39) critical splice donor site probably null
R0801:Smarca4 UTSW 9 21,553,850 (GRCm39) missense possibly damaging 0.81
R0918:Smarca4 UTSW 9 21,547,511 (GRCm39) missense probably benign 0.16
R1411:Smarca4 UTSW 9 21,570,251 (GRCm39) missense probably damaging 1.00
R1604:Smarca4 UTSW 9 21,612,239 (GRCm39) small deletion probably benign
R1768:Smarca4 UTSW 9 21,612,479 (GRCm39) missense possibly damaging 0.56
R2031:Smarca4 UTSW 9 21,597,358 (GRCm39) missense possibly damaging 0.68
R2211:Smarca4 UTSW 9 21,597,325 (GRCm39) missense probably damaging 1.00
R2512:Smarca4 UTSW 9 21,546,994 (GRCm39) missense possibly damaging 0.95
R2875:Smarca4 UTSW 9 21,553,876 (GRCm39) missense possibly damaging 0.55
R3786:Smarca4 UTSW 9 21,583,355 (GRCm39) missense possibly damaging 0.94
R4829:Smarca4 UTSW 9 21,550,623 (GRCm39) missense probably damaging 0.97
R5084:Smarca4 UTSW 9 21,572,059 (GRCm39) missense probably damaging 1.00
R5222:Smarca4 UTSW 9 21,567,002 (GRCm39) missense probably benign 0.01
R5785:Smarca4 UTSW 9 21,597,322 (GRCm39) missense probably damaging 0.99
R5844:Smarca4 UTSW 9 21,589,238 (GRCm39) intron probably benign
R5964:Smarca4 UTSW 9 21,558,726 (GRCm39) missense probably benign 0.00
R6001:Smarca4 UTSW 9 21,544,205 (GRCm39) unclassified probably benign
R6072:Smarca4 UTSW 9 21,611,417 (GRCm39) missense probably damaging 1.00
R6254:Smarca4 UTSW 9 21,611,173 (GRCm39) missense probably damaging 1.00
R6320:Smarca4 UTSW 9 21,548,671 (GRCm39) missense probably damaging 1.00
R6353:Smarca4 UTSW 9 21,590,445 (GRCm39) critical splice donor site probably null
R6461:Smarca4 UTSW 9 21,590,316 (GRCm39) missense probably damaging 1.00
R6886:Smarca4 UTSW 9 21,570,127 (GRCm39) missense probably damaging 1.00
R7098:Smarca4 UTSW 9 21,546,116 (GRCm39) missense probably benign 0.10
R7253:Smarca4 UTSW 9 21,570,256 (GRCm39) missense probably benign 0.01
R7307:Smarca4 UTSW 9 21,550,096 (GRCm39) missense probably damaging 1.00
R7382:Smarca4 UTSW 9 21,570,229 (GRCm39) missense probably damaging 0.98
R7445:Smarca4 UTSW 9 21,597,543 (GRCm39) missense probably damaging 1.00
R7535:Smarca4 UTSW 9 21,558,921 (GRCm39) missense possibly damaging 0.82
R7573:Smarca4 UTSW 9 21,550,371 (GRCm39) splice site probably null
R7644:Smarca4 UTSW 9 21,566,950 (GRCm39) missense probably benign 0.00
R7734:Smarca4 UTSW 9 21,578,658 (GRCm39) missense possibly damaging 0.65
R7833:Smarca4 UTSW 9 21,558,655 (GRCm39) missense possibly damaging 0.86
R8085:Smarca4 UTSW 9 21,570,108 (GRCm39) splice site probably null
R8119:Smarca4 UTSW 9 21,558,922 (GRCm39) missense possibly damaging 0.61
R8320:Smarca4 UTSW 9 21,588,798 (GRCm39) missense probably benign 0.10
R8445:Smarca4 UTSW 9 21,612,239 (GRCm39) small deletion probably benign
R8493:Smarca4 UTSW 9 21,570,144 (GRCm39) missense probably damaging 1.00
R8748:Smarca4 UTSW 9 21,546,164 (GRCm39) missense possibly damaging 0.85
R8788:Smarca4 UTSW 9 21,550,024 (GRCm39) missense probably damaging 1.00
R8817:Smarca4 UTSW 9 21,547,497 (GRCm39) missense probably benign 0.04
R9241:Smarca4 UTSW 9 21,550,604 (GRCm39) missense possibly damaging 0.72
R9446:Smarca4 UTSW 9 21,547,155 (GRCm39) missense unknown
R9570:Smarca4 UTSW 9 21,580,849 (GRCm39) missense probably damaging 1.00
R9727:Smarca4 UTSW 9 21,611,160 (GRCm39) missense probably damaging 1.00
R9801:Smarca4 UTSW 9 21,586,397 (GRCm39) missense probably damaging 1.00
Z1176:Smarca4 UTSW 9 21,614,253 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- TTGTTGGGTCCCAGGAAAGC -3'
(R):5'- GCAAGTGCGCATCCTCTTTC -3'

Sequencing Primer
(F):5'- CAGACATCTGCTATGGGTACAAGGTC -3'
(R):5'- AGGCTTGGCACCATGCTC -3'
Posted On 2014-08-25