Incidental Mutation 'R4592:Smarcd3'
ID 386394
Institutional Source Beutler Lab
Gene Symbol Smarcd3
Ensembl Gene ENSMUSG00000028949
Gene Name SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3
Synonyms 2210409C08Rik, BAF60C, 1500001J14Rik
MMRRC Submission 041808-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4592 (G1)
Quality Score 225
Status Validated
Chromosome 5
Chromosomal Location 24797620-24829649 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 24797802 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 467 (I467V)
Ref Sequence ENSEMBL: ENSMUSP00000030791 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030791] [ENSMUST00000088295] [ENSMUST00000121863] [ENSMUST00000195943] [ENSMUST00000197318]
AlphaFold Q6P9Z1
Predicted Effect probably benign
Transcript: ENSMUST00000030791
AA Change: I467V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000030791
Gene: ENSMUSG00000028949
AA Change: I467V

DomainStartEndE-ValueType
low complexity region 40 55 N/A INTRINSIC
low complexity region 72 89 N/A INTRINSIC
low complexity region 93 102 N/A INTRINSIC
Blast:KISc 103 239 5e-41 BLAST
SWIB 259 338 3.6e-29 SMART
Blast:MYSc 420 466 1e-11 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000088295
SMART Domains Protein: ENSMUSP00000085633
Gene: ENSMUSG00000038181

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
Pfam:Fringe 143 298 3.2e-11 PFAM
Pfam:CHGN 242 755 1.7e-144 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000102432
Predicted Effect probably benign
Transcript: ENSMUST00000121863
SMART Domains Protein: ENSMUSP00000112804
Gene: ENSMUSG00000038181

DomainStartEndE-ValueType
signal peptide 1 19 N/A INTRINSIC
Pfam:Fringe 143 298 3.2e-11 PFAM
Pfam:CHGN 242 755 3e-176 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140744
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143501
Predicted Effect probably benign
Transcript: ENSMUST00000195943
AA Change: I438V

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000143437
Gene: ENSMUSG00000028949
AA Change: I438V

DomainStartEndE-ValueType
low complexity region 11 26 N/A INTRINSIC
low complexity region 43 60 N/A INTRINSIC
low complexity region 64 73 N/A INTRINSIC
Blast:KISc 74 210 2e-41 BLAST
SWIB 230 309 2.3e-31 SMART
Blast:MYSc 391 437 8e-12 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197933
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197566
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144518
Predicted Effect noncoding transcript
Transcript: ENSMUST00000198521
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145565
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147857
Predicted Effect noncoding transcript
Transcript: ENSMUST00000144995
Predicted Effect probably benign
Transcript: ENSMUST00000197318
SMART Domains Protein: ENSMUSP00000143185
Gene: ENSMUSG00000038181

DomainStartEndE-ValueType
Pfam:CHGN 1 74 7.5e-22 PFAM
Meta Mutation Damage Score 0.0596 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.8%
Validation Efficiency 98% (64/65)
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, whose members display helicase and ATPase activities and which 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 and has sequence similarity to the yeast Swp73 protein. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933430I17Rik T A 4: 62,457,164 (GRCm39) V161E possibly damaging Het
Arhgap40 T C 2: 158,388,629 (GRCm39) V521A possibly damaging Het
Atrn T C 2: 130,841,050 (GRCm39) probably benign Het
Casp12 T C 9: 5,352,923 (GRCm39) probably benign Het
Cenpf G A 1: 189,411,230 (GRCm39) T318M probably damaging Het
Cfap119 C T 7: 127,184,663 (GRCm39) R172H probably benign Het
Clcn2 T C 16: 20,527,892 (GRCm39) K525E probably damaging Het
Cntln A G 4: 84,889,419 (GRCm39) T301A probably benign Het
Crat T C 2: 30,305,378 (GRCm39) probably benign Het
Cul5 A G 9: 53,545,027 (GRCm39) probably benign Het
Cxcl14 A T 13: 56,443,708 (GRCm39) I34N probably damaging Het
Cyp2b19 A G 7: 26,470,819 (GRCm39) I487V probably benign Het
Cyp4a10 T A 4: 115,386,690 (GRCm39) F446I probably damaging Het
D430041D05Rik T A 2: 104,063,824 (GRCm39) M659L possibly damaging Het
Dclk3 T C 9: 111,296,963 (GRCm39) F169S probably damaging Het
Ddx52 T C 11: 83,848,306 (GRCm39) I532T probably damaging Het
Dnm1 T C 2: 32,226,023 (GRCm39) D352G probably damaging Het
Eif4g2 T C 7: 110,677,509 (GRCm39) E174G probably damaging Het
Enpp6 G T 8: 47,546,067 (GRCm39) V386L probably damaging Het
Entr1 C A 2: 26,278,909 (GRCm39) probably benign Het
Eps15l1 T C 8: 73,095,238 (GRCm39) D904G probably damaging Het
Esrrb A G 12: 86,565,604 (GRCm39) Y356C probably damaging Het
Flt3 A T 5: 147,291,509 (GRCm39) S619T possibly damaging Het
Fndc7 A T 3: 108,766,218 (GRCm39) C716S probably damaging Het
Gm26996 T A 6: 130,556,448 (GRCm39) noncoding transcript Het
Grik2 A T 10: 49,298,711 (GRCm39) F50I possibly damaging Het
Guf1 T C 5: 69,723,786 (GRCm39) V367A possibly damaging Het
Hspg2 C T 4: 137,246,251 (GRCm39) R1010C probably damaging Het
Ifnar2 T C 16: 91,188,684 (GRCm39) V55A probably benign Het
Impg1 T A 9: 80,322,907 (GRCm39) I33F probably benign Het
Ltbp4 A C 7: 27,024,608 (GRCm39) V674G probably damaging Het
Mroh2b T A 15: 4,947,772 (GRCm39) L529H probably damaging Het
Negr1 T C 3: 156,914,023 (GRCm39) probably benign Het
Neurog3 A G 10: 61,969,599 (GRCm39) T25A probably damaging Het
Or10v1 T C 19: 11,874,126 (GRCm39) V247A probably benign Het
Or4a69 T A 2: 89,313,100 (GRCm39) K126N probably damaging Het
Or51h1 A C 7: 102,308,685 (GRCm39) Y219S probably damaging Het
Or5k17 T C 16: 58,746,455 (GRCm39) T160A probably benign Het
Pax8 T A 2: 24,333,201 (GRCm39) probably benign Het
Pcsk6 A C 7: 65,581,480 (GRCm39) I254L possibly damaging Het
Pde3a A G 6: 141,404,942 (GRCm39) K389R probably benign Het
Rab3gap1 C A 1: 127,852,996 (GRCm39) probably benign Het
Rbck1 G A 2: 152,160,653 (GRCm39) Q428* probably null Het
Rptor A G 11: 119,689,666 (GRCm39) D321G probably null Het
Sall2 C A 14: 52,551,260 (GRCm39) R643L probably damaging Het
Skp1 T C 11: 52,134,446 (GRCm39) I59T possibly damaging Het
Slc23a3 T G 1: 75,105,200 (GRCm39) N456T probably damaging Het
Slc4a7 G A 14: 14,778,850 (GRCm38) G920S probably damaging Het
Spata31d1c C T 13: 65,183,874 (GRCm39) A472V probably damaging Het
Spmap1 A G 11: 97,662,441 (GRCm39) S144P probably damaging Het
Srsf6 T C 2: 162,773,643 (GRCm39) I18T probably damaging Het
Stom C T 2: 35,213,758 (GRCm39) G80D probably damaging Het
Svep1 A T 4: 58,084,028 (GRCm39) Y1915N possibly damaging Het
Tmf1 C T 6: 97,150,361 (GRCm39) V449I probably benign Het
Triobp C T 15: 78,851,295 (GRCm39) A483V probably benign Het
Vdac1 G A 11: 52,265,799 (GRCm39) probably null Het
Vmn2r75 T G 7: 85,815,494 (GRCm39) E123D probably benign Het
Vmn2r79 T A 7: 86,653,319 (GRCm39) V528D possibly damaging Het
Zdbf2 T G 1: 63,345,750 (GRCm39) N1376K possibly damaging Het
Zeb1os1 T C 18: 5,525,375 (GRCm39) noncoding transcript Het
Other mutations in Smarcd3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02401:Smarcd3 APN 5 24,798,717 (GRCm39) missense probably damaging 1.00
R0135:Smarcd3 UTSW 5 24,800,497 (GRCm39) unclassified probably benign
R1614:Smarcd3 UTSW 5 24,799,874 (GRCm39) missense possibly damaging 0.93
R1617:Smarcd3 UTSW 5 24,800,192 (GRCm39) missense probably damaging 1.00
R1753:Smarcd3 UTSW 5 24,800,820 (GRCm39) nonsense probably null
R1879:Smarcd3 UTSW 5 24,798,019 (GRCm39) missense probably damaging 0.99
R2307:Smarcd3 UTSW 5 24,800,746 (GRCm39) missense probably damaging 1.00
R3800:Smarcd3 UTSW 5 24,798,225 (GRCm39) nonsense probably null
R6369:Smarcd3 UTSW 5 24,799,982 (GRCm39) missense probably damaging 0.99
R6388:Smarcd3 UTSW 5 24,801,024 (GRCm39) missense possibly damaging 0.94
R7077:Smarcd3 UTSW 5 24,799,960 (GRCm39) missense probably damaging 1.00
R7078:Smarcd3 UTSW 5 24,798,067 (GRCm39) missense probably damaging 0.98
R7341:Smarcd3 UTSW 5 24,800,435 (GRCm39) missense possibly damaging 0.95
R7426:Smarcd3 UTSW 5 24,800,810 (GRCm39) missense probably benign 0.30
R7806:Smarcd3 UTSW 5 24,798,260 (GRCm39) missense probably benign 0.45
R7935:Smarcd3 UTSW 5 24,801,024 (GRCm39) missense probably damaging 0.98
R8685:Smarcd3 UTSW 5 24,800,988 (GRCm39) missense probably damaging 1.00
R8769:Smarcd3 UTSW 5 24,803,792 (GRCm39) missense probably benign
R8877:Smarcd3 UTSW 5 24,798,990 (GRCm39) missense possibly damaging 0.93
R8984:Smarcd3 UTSW 5 24,798,986 (GRCm39) missense probably null 0.99
R9240:Smarcd3 UTSW 5 24,801,831 (GRCm39) missense probably benign 0.21
RF007:Smarcd3 UTSW 5 24,801,068 (GRCm39) missense probably damaging 0.98
Predicted Primers PCR Primer
(F):5'- ACGTGACCTTTAATCCATCCAGC -3'
(R):5'- AGCCGCTACTTCTACTGTAAGG -3'

Sequencing Primer
(F):5'- GACCTTTAATCCATCCAGCCCTCC -3'
(R):5'- ACTTCTACTGTAAGGTAATGGAGGCC -3'
Posted On 2016-05-24