Incidental Mutation 'R0645:Smarcd1'
ID 57093
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 038830-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.874) question?
Stock # R0645 (G1)
Quality Score 155
Status Validated
Chromosome 15
Chromosomal Location 99600175-99611872 bp(+) (GRCm39)
Type of Mutation splice site (1702 bp from exon)
DNA Base Change (assembly) A to G at 99605267 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000155619 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000023759] [ENSMUST00000163472] [ENSMUST00000228984] [ENSMUST00000229236] [ENSMUST00000229845] [ENSMUST00000230530]
AlphaFold Q61466
Predicted Effect probably damaging
Transcript: ENSMUST00000023759
AA Change: T283A

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000023759
Gene: ENSMUSG00000023018
AA Change: T283A

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 probably null
Transcript: ENSMUST00000228984
Predicted Effect probably damaging
Transcript: ENSMUST00000229236
AA Change: T242A

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229686
Predicted Effect probably null
Transcript: ENSMUST00000229845
Predicted Effect noncoding transcript
Transcript: ENSMUST00000229968
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230504
Predicted Effect noncoding transcript
Transcript: ENSMUST00000230748
Predicted Effect probably null
Transcript: ENSMUST00000230530
Meta Mutation Damage Score 0.2291 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 99% (94/95)
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: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam18 G T 8: 25,162,136 (GRCm39) Y46* probably null Het
Adam26b A C 8: 43,973,524 (GRCm39) C493G probably damaging Het
Ak5 A T 3: 152,359,252 (GRCm39) L182Q probably damaging Het
Akt1s1 T C 7: 44,498,645 (GRCm39) probably benign Het
Amhr2 G T 15: 102,354,863 (GRCm39) G133C probably damaging Het
Btbd9 A T 17: 30,743,941 (GRCm39) L187Q probably damaging Het
Ccdc117 A T 11: 5,484,385 (GRCm39) probably benign Het
Ccdc138 A T 10: 58,411,542 (GRCm39) I637F probably damaging Het
Ccdc162 A G 10: 41,462,407 (GRCm39) probably benign Het
Cdc25b C A 2: 131,033,533 (GRCm39) H157Q probably benign Het
Cdon A G 9: 35,388,379 (GRCm39) probably null Het
Cdt1 G A 8: 123,298,884 (GRCm39) probably benign Het
Cep350 C T 1: 155,816,458 (GRCm39) probably null Het
Cfb T C 17: 35,078,992 (GRCm39) K831R probably benign Het
Cldn4 C A 5: 134,975,645 (GRCm39) probably benign Het
Cntnap5b T C 1: 99,999,767 (GRCm39) probably benign Het
Cyp27b1 T G 10: 126,884,967 (GRCm39) S77A probably benign Het
Dlc1 T C 8: 37,041,203 (GRCm39) D1342G possibly damaging Het
Dlgap4 A G 2: 156,603,799 (GRCm39) H887R probably damaging Het
Duox2 A G 2: 122,123,139 (GRCm39) I503T probably damaging Het
Eml4 T C 17: 83,770,922 (GRCm39) probably benign Het
Ermap A G 4: 119,042,888 (GRCm39) S212P probably benign Het
Esrrg T A 1: 187,775,538 (GRCm39) C22S probably benign Het
Evx2 T A 2: 74,488,238 (GRCm39) Y194F possibly damaging Het
Fbn2 T G 18: 58,191,461 (GRCm39) D1554A probably damaging Het
Flrt1 G A 19: 7,074,508 (GRCm39) probably benign Het
Fndc5 A G 4: 129,033,630 (GRCm39) probably benign Het
Frem1 A T 4: 82,907,403 (GRCm39) I837N probably damaging Het
Fzd10 G T 5: 128,679,662 (GRCm39) A461S possibly damaging Het
Ganab T A 19: 8,888,477 (GRCm39) Y511N probably damaging Het
Gbp7 A G 3: 142,243,926 (GRCm39) probably null Het
Gm5919 T A 9: 83,765,436 (GRCm39) C91S unknown Het
Gpr31b A T 17: 13,271,093 (GRCm39) C25* probably null Het
Grb10 A G 11: 11,886,755 (GRCm39) S505P probably damaging Het
Grm4 A T 17: 27,654,183 (GRCm39) V542E probably damaging Het
Gsta5 T C 9: 78,206,303 (GRCm39) I75T possibly damaging Het
Hivep3 G A 4: 119,954,531 (GRCm39) R949H possibly damaging Het
Hycc1 C T 5: 24,184,506 (GRCm39) G242D probably damaging Het
Invs A T 4: 48,407,653 (GRCm39) M543L probably benign Het
Kcnk2 T C 1: 188,988,927 (GRCm39) probably null Het
Kdm6b A T 11: 69,295,844 (GRCm39) S808T unknown Het
Klhl30 C T 1: 91,283,228 (GRCm39) R277W probably damaging Het
Lama1 A G 17: 68,080,707 (GRCm39) Q1245R probably benign Het
Lingo3 G T 10: 80,671,169 (GRCm39) H254N probably benign Het
Lzts1 A T 8: 69,588,392 (GRCm39) H521Q possibly damaging Het
Map3k19 A C 1: 127,749,919 (GRCm39) I1144S possibly damaging Het
Mast2 A G 4: 116,165,184 (GRCm39) S1411P probably damaging Het
Mast2 T C 4: 116,170,043 (GRCm39) probably benign Het
Mesp1 G T 7: 79,442,328 (GRCm39) S225R possibly damaging Het
Micu1 A G 10: 59,675,503 (GRCm39) T366A possibly damaging Het
Mideas G T 12: 84,205,077 (GRCm39) N834K possibly damaging Het
Mknk2 T C 10: 80,507,742 (GRCm39) probably null Het
Msh5 A G 17: 35,258,199 (GRCm39) L309P probably damaging Het
Myo7b T C 18: 32,127,962 (GRCm39) I577V probably benign Het
Myom2 T A 8: 15,167,698 (GRCm39) D1094E probably damaging Het
Nedd1 T C 10: 92,527,693 (GRCm39) probably null Het
Neu4 T C 1: 93,950,191 (GRCm39) L50S probably damaging Het
Noa1 T C 5: 77,457,722 (GRCm39) Y61C probably benign Het
Nr1h4 A T 10: 89,342,390 (GRCm39) M30K probably benign Het
Nsd3 A G 8: 26,199,096 (GRCm39) I1219V probably benign Het
Nup188 T A 2: 30,233,478 (GRCm39) probably null Het
Or10ag2 T A 2: 87,248,612 (GRCm39) Y71* probably null Het
Or5al5 A G 2: 85,961,378 (GRCm39) S210P probably damaging Het
Or6c208 T A 10: 129,224,162 (GRCm39) I220N possibly damaging Het
Or6k2 A T 1: 173,986,920 (GRCm39) T194S probably benign Het
Pbk G A 14: 66,051,245 (GRCm39) probably benign Het
Pcnx2 G A 8: 126,487,459 (GRCm39) T1848M possibly damaging Het
Pdzd7 C T 19: 45,033,914 (GRCm39) G57R possibly damaging Het
Pik3r4 C A 9: 105,546,386 (GRCm39) probably benign Het
Plce1 A G 19: 38,766,433 (GRCm39) S2153G probably damaging Het
Potefam1 C T 2: 111,044,928 (GRCm39) probably null Het
Pphln1 G A 15: 93,318,192 (GRCm39) V34M possibly damaging Het
Prrc2a T C 17: 35,375,308 (GRCm39) D1114G probably damaging Het
Prss16 T C 13: 22,193,546 (GRCm39) probably benign Het
Rtp3 T C 9: 110,816,168 (GRCm39) K128E probably damaging Het
Scn3a T A 2: 65,355,194 (GRCm39) I241F possibly damaging Het
Setd1a G A 7: 127,386,382 (GRCm39) V336I probably damaging Het
Sfpq A G 4: 126,916,762 (GRCm39) I320V possibly damaging Het
Skint5 A T 4: 113,620,679 (GRCm39) D678E unknown Het
Slc12a9 G A 5: 137,313,638 (GRCm39) P774S probably benign Het
Slc25a54 C G 3: 109,019,481 (GRCm39) L362V possibly damaging Het
Spata31e5 T A 1: 28,816,011 (GRCm39) N674Y probably damaging Het
Suco A T 1: 161,661,683 (GRCm39) M916K probably damaging Het
Tiam2 T C 17: 3,564,973 (GRCm39) S1404P possibly damaging Het
Topors T C 4: 40,260,333 (GRCm39) T984A unknown Het
Trabd2b A T 4: 114,443,767 (GRCm39) K308M probably damaging Het
Trmo A T 4: 46,377,083 (GRCm39) probably benign Het
Trpc3 A T 3: 36,725,654 (GRCm39) D107E probably benign Het
Ugcg C T 4: 59,207,798 (GRCm39) P46S probably benign Het
Uggt2 A C 14: 119,295,010 (GRCm39) Y539D probably benign Het
Wwc2 T G 8: 48,353,674 (GRCm39) probably benign Het
Zdbf2 T A 1: 63,344,109 (GRCm39) D829E 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
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
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'- ATGTTCTCGTAGGGAGGTCGTCAC -3'
(R):5'- GGCGCTCAGTACAGGAACACATTC -3'

Sequencing Primer
(F):5'- atccacctgcctctgcc -3'
(R):5'- CAATCTAACAAACATTGGCAAATCTG -3'
Posted On 2013-07-11