Incidental Mutation 'R5116:Smarcd1'
ID 394216
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 042704-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.874) question?
Stock # R5116 (G1)
Quality Score 105
Status Validated
Chromosome 15
Chromosomal Location 99600175-99611872 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 99600369 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Valine at position 56 (A56V)
Ref Sequence ENSEMBL: ENSMUSP00000155750 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023758] [ENSMUST00000023759] [ENSMUST00000163472] [ENSMUST00000228185] [ENSMUST00000228984] [ENSMUST00000229236] [ENSMUST00000230530] [ENSMUST00000229845]
AlphaFold Q61466
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 benign
Transcript: ENSMUST00000023759
AA Change: A56V

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000023759
Gene: ENSMUSG00000023018
AA Change: A56V

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: ENSMUST00000228185
Predicted Effect noncoding transcript
Transcript: ENSMUST00000228610
Predicted Effect probably benign
Transcript: ENSMUST00000228984
Predicted Effect probably benign
Transcript: ENSMUST00000229236
AA Change: A56V

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230504
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229968
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229686
Predicted Effect probably benign
Transcript: ENSMUST00000230530
Predicted Effect probably benign
Transcript: ENSMUST00000229845
Meta Mutation Damage Score 0.0726 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.2%
  • 10x: 95.8%
  • 20x: 90.5%
Validation Efficiency 97% (59/61)
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: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb9 T C 5: 124,216,930 (GRCm39) H429R probably damaging Het
Adam39 G T 8: 41,278,038 (GRCm39) C143F probably damaging Het
Adamts19 T C 18: 59,036,066 (GRCm39) V417A possibly damaging Het
Adcy10 C A 1: 165,347,069 (GRCm39) A362E probably damaging Het
Akap6 A G 12: 53,188,298 (GRCm39) E1904G probably benign Het
Aldh18a1 A G 19: 40,541,949 (GRCm39) M89T probably benign Het
Alyref G T 11: 120,488,554 (GRCm39) F91L probably benign Het
Capn3 G T 2: 120,315,773 (GRCm39) M248I probably benign Het
Catsper4 A T 4: 133,953,991 (GRCm39) I56N probably damaging Het
Cckbr T A 7: 105,082,862 (GRCm39) I75N probably damaging Het
Ccr8 T C 9: 119,923,095 (GRCm39) I70T probably benign Het
Cdh24 T C 14: 54,873,870 (GRCm39) D428G probably benign Het
Cdk5rap2 G T 4: 70,225,475 (GRCm39) Q557K possibly damaging Het
Clip1 C T 5: 123,768,770 (GRCm39) A610T probably benign Het
Dnajc16 A T 4: 141,495,280 (GRCm39) Y479* probably null Het
Fpr-rs3 A G 17: 20,844,562 (GRCm39) V193A probably benign Het
Gm29125 T C 1: 80,361,690 (GRCm39) noncoding transcript Het
H1f4 A G 13: 23,806,270 (GRCm39) Y71H probably damaging Het
Ifi208 A G 1: 173,505,549 (GRCm39) probably benign Het
Immp1l G A 2: 105,795,640 (GRCm39) R155H probably benign Het
Itgad C A 7: 127,803,065 (GRCm39) T7K probably damaging Het
Itgb3 T C 11: 104,531,903 (GRCm39) V370A probably benign Het
Jak1 A G 4: 101,012,310 (GRCm39) I1053T probably benign Het
Kif21b A G 1: 136,080,521 (GRCm39) R572G probably damaging Het
Lama2 A T 10: 26,994,556 (GRCm39) D1784E probably benign Het
Ltbp2 A T 12: 84,856,511 (GRCm39) V651D probably damaging Het
Mrpl47 A G 3: 32,787,750 (GRCm39) L100S probably damaging Het
Mx1 T G 16: 97,258,679 (GRCm39) N6T possibly damaging Het
Nde1 T A 16: 14,001,351 (GRCm39) M133K probably benign Het
Nlrc5 T C 8: 95,208,488 (GRCm39) L778P probably damaging Het
Odad3 A G 9: 21,901,424 (GRCm39) *595Q probably null Het
Or52e19b G A 7: 103,033,071 (GRCm39) T46I probably benign Het
Or5l13 G A 2: 87,779,873 (GRCm39) R235C probably benign Het
Or6c3b A G 10: 129,527,266 (GRCm39) S215P probably damaging Het
Or7g32 A G 9: 19,389,094 (GRCm39) S151P possibly damaging Het
Or8b38 T C 9: 37,972,634 (GRCm39) V6A probably benign Het
Otog T C 7: 45,923,191 (GRCm39) V1022A probably benign Het
Pcdhac1 G A 18: 37,224,500 (GRCm39) V438M probably damaging Het
Pcsk5 G A 19: 17,440,798 (GRCm39) S1264F possibly damaging Het
Pfas T C 11: 68,881,816 (GRCm39) probably benign Het
Pigr T A 1: 130,776,768 (GRCm39) F648I probably benign Het
Pla2r1 A C 2: 60,279,250 (GRCm39) Y777D probably damaging Het
Pnpla7 G T 2: 24,911,982 (GRCm39) G716V probably damaging Het
Rab11fip5 C T 6: 85,325,789 (GRCm39) E206K probably damaging Het
S100a10 A G 3: 93,468,247 (GRCm39) probably null Het
Slc35f1 T C 10: 52,897,991 (GRCm39) I134T probably benign Het
Snrk A G 9: 121,989,396 (GRCm39) T247A probably benign Het
Srgap1 A G 10: 121,628,284 (GRCm39) L896P possibly damaging Het
Tmem19 A T 10: 115,179,651 (GRCm39) F167I probably benign Het
Tmprss11f T C 5: 86,687,555 (GRCm39) S118G probably benign Het
Tnc A G 4: 63,885,452 (GRCm39) probably null Het
Trem3 T C 17: 48,556,580 (GRCm39) L17P probably benign Het
Upp2 A G 2: 58,661,554 (GRCm39) Y67C probably damaging Het
Zfp276 A G 8: 123,991,716 (GRCm39) probably benign Het
Zfp932 T A 5: 110,157,242 (GRCm39) D280E probably benign 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
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
R6026:Smarcd1 UTSW 15 99,603,619 (GRCm39) missense probably damaging 1.00
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'- ACACCGCTTCTCTATGGTGC -3'
(R):5'- GGTAAGGATGCTAACCTCCTC -3'

Sequencing Primer
(F):5'- AGTGGTCAGCACGCCTTTC -3'
(R):5'- AGGGAGTCCCTCCCACTTC -3'
Posted On 2016-06-15