Incidental Mutation 'R5844:Smarca4'
ID 450600
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 044062-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5844 (G1)
Quality Score 140
Status Validated
Chromosome 9
Chromosomal Location 21527465-21615526 bp(+) (GRCm39)
Type of Mutation intron
DNA Base Change (assembly) T to A at 21589238 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000133922 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034707] [ENSMUST00000098948] [ENSMUST00000174008]
AlphaFold Q3TKT4
Predicted Effect probably benign
Transcript: ENSMUST00000034707
SMART Domains Protein: ENSMUSP00000034707
Gene: ENSMUSG00000032187

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 benign
Transcript: ENSMUST00000098948
SMART Domains Protein: ENSMUSP00000096547
Gene: ENSMUSG00000032187

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 probably benign
Transcript: ENSMUST00000172996
SMART Domains Protein: ENSMUSP00000133535
Gene: ENSMUSG00000032187

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 benign
Transcript: ENSMUST00000174008
SMART Domains Protein: ENSMUSP00000133922
Gene: ENSMUSG00000032187

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: 99.9%
  • 3x: 99.7%
  • 10x: 98.5%
  • 20x: 95.9%
Validation Efficiency 98% (55/56)
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930407I10Rik A T 15: 81,950,065 (GRCm39) M1321L probably benign Het
Adra1a C T 14: 66,965,183 (GRCm39) T391I probably benign Het
Atf7ip C A 6: 136,583,812 (GRCm39) A1281D probably damaging Het
BC005624 T C 2: 30,866,023 (GRCm39) N141S probably benign Het
Catsperg2 A T 7: 29,397,257 (GRCm39) L1082Q possibly damaging Het
Cavin2 C T 1: 51,328,998 (GRCm39) R152C probably damaging Het
Ccdc33 C T 9: 57,940,489 (GRCm39) probably benign Het
Cfap43 T C 19: 47,784,135 (GRCm39) D466G probably benign Het
Cfap46 C A 7: 139,230,858 (GRCm39) M923I probably damaging Het
Chd1l T A 3: 97,479,883 (GRCm39) K621N probably benign Het
Cnksr1 A G 4: 133,955,575 (GRCm39) probably benign Het
Cym T C 3: 107,127,080 (GRCm39) H25R probably benign Het
Dagla T A 19: 10,248,489 (GRCm39) D57V probably damaging Het
Dnah3 TTCCTC TTC 7: 119,550,244 (GRCm39) probably benign Het
Dse T A 10: 34,029,038 (GRCm39) D684V probably damaging Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Fbxo10 A T 4: 45,058,760 (GRCm39) S326T probably benign Het
Galntl5 G T 5: 25,391,091 (GRCm39) probably benign Het
Grm5 A G 7: 87,453,232 (GRCm39) R290G possibly damaging Het
Gtpbp3 A G 8: 71,945,199 (GRCm39) T425A probably benign Het
Hepacam2 A G 6: 3,476,073 (GRCm39) I284T probably damaging Het
Ifi205 A C 1: 173,854,258 (GRCm39) probably null Het
Irs3 T C 5: 137,642,548 (GRCm39) T297A probably benign Het
Kmt2d G A 15: 98,749,990 (GRCm39) probably benign Het
Map4k4 T A 1: 40,039,036 (GRCm39) probably benign Het
Mfsd6 T C 1: 52,697,542 (GRCm39) S782G probably benign Het
Mis18a G A 16: 90,523,969 (GRCm39) silent Het
Mtpn C T 6: 35,489,225 (GRCm39) D100N probably benign Het
Myom2 G A 8: 15,181,182 (GRCm39) probably null Het
Ntaq1 A G 15: 58,017,056 (GRCm39) N157S probably benign Het
Or13a1 A T 6: 116,470,900 (GRCm39) E110V probably damaging Het
Or5g25 A G 2: 85,478,239 (GRCm39) V142A probably benign Het
Pde3b C T 7: 114,108,106 (GRCm39) T568I probably benign Het
Pip4p1 T C 14: 51,166,499 (GRCm39) T160A probably benign Het
Pkhd1 G T 1: 20,451,685 (GRCm39) D2203E probably benign Het
Ppp1r36 A G 12: 76,473,566 (GRCm39) K66E possibly damaging Het
Rfc1 C A 5: 65,451,130 (GRCm39) M319I probably benign Het
Rnd2 C T 11: 101,359,825 (GRCm39) L57F probably damaging Het
Runx1t1 T C 4: 13,881,068 (GRCm39) V456A probably damaging Het
Rxfp2 A G 5: 149,966,589 (GRCm39) K109R probably benign Het
Sgo2a T G 1: 58,055,556 (GRCm39) V580G probably damaging Het
Skint9 T C 4: 112,271,080 (GRCm39) Q110R probably benign Het
Slc38a9 A G 13: 112,868,035 (GRCm39) Y507C probably damaging Het
Tmem88 C G 11: 69,288,504 (GRCm39) Q138H probably benign Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Tns3 A C 11: 8,384,580 (GRCm39) F1413V probably damaging Het
Trpm8 T C 1: 88,312,433 (GRCm39) *1105Q probably null Het
Zfp853 C T 5: 143,274,424 (GRCm39) V399M unknown Het
Zim1 T C 7: 6,681,115 (GRCm39) R183G probably benign Het
Zmiz1 T C 14: 25,657,354 (GRCm39) S871P 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
R2004:Smarca4 UTSW 9 21,588,776 (GRCm39) missense probably damaging 1.00
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
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'- AGAAGTCGTCCAGCCATGAG -3'
(R):5'- CGTCCGAAGATGAGCTGATG -3'

Sequencing Primer
(F):5'- TGAGCATGGTGCCAAGC -3'
(R):5'- TGATGAGCTGGAGGTCCC -3'
Posted On 2016-12-20