Incidental Mutation 'R6026:Smarcd1'
ID 480072
Institutional Source Beutler Lab
Gene Symbol Smarcd1
Ensembl Gene ENSMUSG00000023018
Gene Name SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
Synonyms D15Kz1, Baf60a
MMRRC Submission 044198-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.874) question?
Stock # R6026 (G1)
Quality Score 225.009
Status Validated
Chromosome 15
Chromosomal Location 99600175-99611872 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 99603619 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Leucine at position 256 (V256L)
Ref Sequence ENSEMBL: ENSMUSP00000023759 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023758] [ENSMUST00000023759] [ENSMUST00000163472] [ENSMUST00000228984] [ENSMUST00000229236] [ENSMUST00000229845] [ENSMUST00000230530]
AlphaFold Q61466
PDB Structure Solution structure of the SWIB domain of mouse BRG1-associated factor 60a [SOLUTION NMR]
Predicted Effect probably benign
Transcript: ENSMUST00000023758
SMART Domains Protein: ENSMUSP00000023758
Gene: ENSMUSG00000023017

DomainStartEndE-ValueType
Pfam:ASC 21 454 9.9e-95 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000023759
AA Change: V256L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000023759
Gene: ENSMUSG00000023018
AA Change: V256L

DomainStartEndE-ValueType
low complexity region 9 38 N/A INTRINSIC
low complexity region 103 117 N/A INTRINSIC
Blast:KISc 124 271 2e-43 BLAST
SWIB 291 370 1.97e-35 SMART
Blast:MYSc 452 498 2e-17 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000163472
SMART Domains Protein: ENSMUSP00000128823
Gene: ENSMUSG00000091604

DomainStartEndE-ValueType
low complexity region 18 42 N/A INTRINSIC
low complexity region 44 78 N/A INTRINSIC
low complexity region 85 93 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000227670
Predicted Effect probably benign
Transcript: ENSMUST00000228984
Predicted Effect possibly damaging
Transcript: ENSMUST00000229236
AA Change: V215L

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)
Predicted Effect probably benign
Transcript: ENSMUST00000229845
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229686
Predicted Effect probably benign
Transcript: ENSMUST00000230530
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230504
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229968
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230748
Meta Mutation Damage Score 0.4050 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 97.9%
  • 20x: 93.5%
Validation Efficiency 97% (73/75)
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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1810065E05Rik A G 11: 58,316,581 (GRCm39) D187G probably benign Het
4933421I07Rik A T 7: 42,095,708 (GRCm39) M180K probably benign Het
Aatk T C 11: 119,903,190 (GRCm39) H345R possibly damaging Het
Abcc8 T C 7: 45,816,424 (GRCm39) T239A probably benign Het
Abcf3 A G 16: 20,369,320 (GRCm39) E234G probably damaging Het
Actrt2 T C 4: 154,751,047 (GRCm39) D363G possibly damaging Het
Adam1a A T 5: 121,657,425 (GRCm39) C623S probably damaging Het
Afg3l2 G T 18: 67,554,329 (GRCm39) L458M probably damaging Het
Ash1l T C 3: 88,892,326 (GRCm39) Y1402H probably damaging Het
Barhl2 T A 5: 106,603,474 (GRCm39) K228N probably benign Het
Blvrb A G 7: 27,162,115 (GRCm39) H153R probably damaging Het
Capn9 A G 8: 125,332,601 (GRCm39) D480G probably damaging Het
Cct3 T C 3: 88,219,029 (GRCm39) I182T possibly damaging Het
Clasp2 A G 9: 113,740,646 (GRCm39) N1208D probably benign Het
Col26a1 A G 5: 136,876,354 (GRCm39) C89R probably damaging Het
Cops4 T A 5: 100,690,194 (GRCm39) probably benign Het
Cpox T A 16: 58,491,298 (GRCm39) W170R probably damaging Het
Ddx27 A G 2: 166,875,560 (GRCm39) K656E probably benign Het
Eif4e T C 3: 138,256,661 (GRCm39) I66T probably damaging Het
Ercc3 T C 18: 32,378,974 (GRCm39) probably null Het
Esp38 G A 17: 40,266,032 (GRCm39) C47Y probably damaging Het
Fancd2 T C 6: 113,528,731 (GRCm39) V380A possibly damaging Het
Fbxw7 T A 3: 84,859,948 (GRCm39) probably null Het
Fryl T G 5: 73,257,340 (GRCm39) R736S probably benign Het
Gad2 G A 2: 22,513,748 (GRCm39) V62M probably benign Het
Gigyf2 A G 1: 87,368,454 (GRCm39) T1045A probably damaging Het
Gm13090 T A 4: 151,175,157 (GRCm39) L78* probably null Het
Gm19410 G A 8: 36,279,580 (GRCm39) S1815N probably benign Het
Gm28051 A T 12: 102,686,444 (GRCm39) L72Q unknown Het
Gm44511 T C 6: 128,797,240 (GRCm39) T83A possibly damaging Het
Grk2 C T 19: 4,340,811 (GRCm39) V246I probably damaging Het
Grm7 C T 6: 111,478,500 (GRCm39) Q62* probably null Het
Gsdmc3 T A 15: 63,738,600 (GRCm39) E154V probably damaging Het
Gstz1 A C 12: 87,206,948 (GRCm39) Q114P probably damaging Het
Hax1 GTCATCATCATCATCATC GTCATCATCATCATCATCATC 3: 89,905,247 (GRCm39) probably benign Het
Hhip A T 8: 80,699,069 (GRCm39) C666S probably damaging Het
Hif1a A C 12: 73,979,055 (GRCm39) H193P probably damaging Het
Hyal2 A G 9: 107,449,398 (GRCm39) T385A probably benign Het
Ihh T C 1: 74,985,886 (GRCm39) T200A probably benign Het
Iqgap3 T A 3: 87,997,478 (GRCm39) V218E probably damaging Het
Lct A G 1: 128,227,755 (GRCm39) I1246T probably benign Het
Lmo7 T C 14: 102,118,426 (GRCm39) V217A probably benign Het
Lrp1 C T 10: 127,409,272 (GRCm39) D1616N probably damaging Het
Lrrfip2 A T 9: 111,043,239 (GRCm39) T165S probably damaging Het
Morc2b A G 17: 33,356,957 (GRCm39) Y272H possibly damaging Het
Muc16 A G 9: 18,571,154 (GRCm39) M455T unknown Het
Ncapg2 A T 12: 116,406,641 (GRCm39) D939V possibly damaging Het
Ncbp3 T C 11: 72,958,548 (GRCm39) V236A probably benign Het
Obscn T A 11: 58,957,916 (GRCm39) T3595S probably damaging Het
Odf2l T C 3: 144,854,797 (GRCm39) S545P possibly damaging Het
Or3a1 T A 11: 74,225,914 (GRCm39) I48F probably damaging Het
Or8b36 ATTGCTGTTT ATTGCTGTTTGCTGTTT 9: 37,937,836 (GRCm39) probably null Het
Pdzrn3 A C 6: 101,339,105 (GRCm39) C269G probably benign Het
Pear1 T A 3: 87,664,220 (GRCm39) N278Y probably damaging Het
Phb1 C T 11: 95,562,245 (GRCm39) R41* probably null Het
Pikfyve T C 1: 65,311,856 (GRCm39) V2031A probably damaging Het
Plxna2 A G 1: 194,482,122 (GRCm39) I1465V probably damaging Het
Ppp6r2 A G 15: 89,167,113 (GRCm39) N776S probably benign Het
Prkce A T 17: 86,800,658 (GRCm39) E358V probably benign Het
Prl5a1 A T 13: 28,335,247 (GRCm39) I219F probably benign Het
Prss3 T C 6: 41,354,488 (GRCm39) probably null Het
Ptprc A T 1: 137,998,987 (GRCm39) M858K probably damaging Het
Retreg3 T C 11: 100,997,226 (GRCm39) T85A probably damaging Het
Rfc2 T A 5: 134,624,185 (GRCm39) C265S probably damaging Het
Stat5a T C 11: 100,771,142 (GRCm39) F574L probably damaging Het
Tcirg1 T C 19: 3,947,487 (GRCm39) H624R probably benign Het
Tcstv1a C A 13: 120,355,987 (GRCm39) probably benign Het
Tenm2 C T 11: 35,963,556 (GRCm39) probably null Het
Tomm40 A G 7: 19,444,889 (GRCm39) V164A probably benign Het
Txnl4a T C 18: 80,250,482 (GRCm39) V26A probably damaging Het
Ugt2a3 A T 5: 87,484,336 (GRCm39) F229L probably benign Het
Utp20 T C 10: 88,604,541 (GRCm39) T1785A probably benign Het
Vmn1r22 T A 6: 57,877,390 (GRCm39) I196L probably benign Het
Zfp652 T G 11: 95,640,788 (GRCm39) C238G possibly damaging Het
Other mutations in Smarcd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01516:Smarcd1 APN 15 99,610,094 (GRCm39) missense probably benign 0.10
IGL01714:Smarcd1 APN 15 99,610,302 (GRCm39) missense probably damaging 1.00
IGL02488:Smarcd1 APN 15 99,609,082 (GRCm39) missense possibly damaging 0.83
P0021:Smarcd1 UTSW 15 99,610,242 (GRCm39) splice site probably benign
R0597:Smarcd1 UTSW 15 99,608,975 (GRCm39) missense probably damaging 1.00
R0645:Smarcd1 UTSW 15 99,605,267 (GRCm39) splice site probably null
R1531:Smarcd1 UTSW 15 99,605,264 (GRCm39) missense probably damaging 1.00
R1661:Smarcd1 UTSW 15 99,605,519 (GRCm39) critical splice acceptor site probably null
R1857:Smarcd1 UTSW 15 99,607,295 (GRCm39) missense probably damaging 0.97
R3003:Smarcd1 UTSW 15 99,610,065 (GRCm39) missense probably damaging 1.00
R4170:Smarcd1 UTSW 15 99,605,812 (GRCm39) missense probably damaging 1.00
R4964:Smarcd1 UTSW 15 99,605,862 (GRCm39) missense possibly damaging 0.79
R5116:Smarcd1 UTSW 15 99,600,369 (GRCm39) missense probably benign 0.00
R5358:Smarcd1 UTSW 15 99,601,128 (GRCm39) nonsense probably null
R5559:Smarcd1 UTSW 15 99,601,176 (GRCm39) critical splice donor site probably null
R6424:Smarcd1 UTSW 15 99,602,248 (GRCm39) missense probably damaging 1.00
R6450:Smarcd1 UTSW 15 99,605,766 (GRCm39) missense possibly damaging 0.85
R7126:Smarcd1 UTSW 15 99,607,206 (GRCm39) missense probably damaging 1.00
R8476:Smarcd1 UTSW 15 99,600,305 (GRCm39) missense probably damaging 0.99
R8487:Smarcd1 UTSW 15 99,605,657 (GRCm39) missense probably damaging 0.96
R8872:Smarcd1 UTSW 15 99,608,975 (GRCm39) missense probably damaging 1.00
X0026:Smarcd1 UTSW 15 99,600,330 (GRCm39) missense probably benign 0.13
Predicted Primers PCR Primer
(F):5'- CATCCTGGGGACTTCTTTCTGG -3'
(R):5'- CGTCAGTTACTACAGCCCAC -3'

Sequencing Primer
(F):5'- CTGGCCTTGTGTAACAACAC -3'
(R):5'- CAGTTGAAAGTGTAAGGACTCCACTC -3'
Posted On 2017-06-26