Incidental Mutation 'R4258:Smarcd2'
ID 321912
Institutional Source Beutler Lab
Gene Symbol Smarcd2
Ensembl Gene ENSMUSG00000078619
Gene Name SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2
Synonyms Baf60b
MMRRC Submission 041071-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.955) question?
Stock # R4258 (G1)
Quality Score 202
Status Validated
Chromosome 11
Chromosomal Location 106154005-106163798 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 106156076 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Asparagine at position 292 (I292N)
Ref Sequence ENSEMBL: ENSMUSP00000102456 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021049] [ENSMUST00000021052] [ENSMUST00000106843] [ENSMUST00000140255] [ENSMUST00000133131]
AlphaFold Q99JR8
Predicted Effect probably benign
Transcript: ENSMUST00000021049
SMART Domains Protein: ENSMUSP00000021049
Gene: ENSMUSG00000020708

DomainStartEndE-ValueType
low complexity region 57 69 N/A INTRINSIC
low complexity region 96 108 N/A INTRINSIC
AAA 182 321 6.96e-25 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000021052
AA Change: I339N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000021052
Gene: ENSMUSG00000078619
AA Change: I339N

DomainStartEndE-ValueType
low complexity region 5 42 N/A INTRINSIC
low complexity region 44 58 N/A INTRINSIC
low complexity region 122 131 N/A INTRINSIC
Blast:KISc 136 287 2e-36 BLAST
SWIB 307 386 1.3e-21 SMART
Blast:MYSc 468 514 5e-11 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000083228
Predicted Effect noncoding transcript
Transcript: ENSMUST00000106841
Predicted Effect probably damaging
Transcript: ENSMUST00000106843
AA Change: I292N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000102456
Gene: ENSMUSG00000078619
AA Change: I292N

DomainStartEndE-ValueType
low complexity region 75 84 N/A INTRINSIC
Blast:KISc 89 240 1e-36 BLAST
SWIB 260 339 1.3e-21 SMART
Blast:MYSc 421 467 5e-11 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132278
Predicted Effect probably damaging
Transcript: ENSMUST00000140255
AA Change: I61N

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000133629
Gene: ENSMUSG00000078619
AA Change: I61N

DomainStartEndE-ValueType
SWIB 29 108 1.3e-21 SMART
Blast:MYSc 190 236 6e-12 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155514
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155243
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174253
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174017
Predicted Effect probably benign
Transcript: ENSMUST00000133131
SMART Domains Protein: ENSMUSP00000138057
Gene: ENSMUSG00000020708

DomainStartEndE-ValueType
low complexity region 57 69 N/A INTRINSIC
low complexity region 96 108 N/A INTRINSIC
AAA 182 321 6.96e-25 SMART
Meta Mutation Damage Score 0.8868 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 95% (60/63)
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. Alternatively spliced 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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4932415M13Rik T A 17: 54,031,441 (GRCm39) noncoding transcript Het
Ank3 T C 10: 69,840,592 (GRCm39) I984T probably benign Het
Arnt2 T C 7: 83,960,163 (GRCm39) T204A probably damaging Het
Arsi T C 18: 61,050,388 (GRCm39) W424R probably damaging Het
Aspg A T 12: 112,087,687 (GRCm39) N346I probably benign Het
Brdt A G 5: 107,507,775 (GRCm39) S668G probably damaging Het
Ccdc178 C T 18: 22,150,392 (GRCm39) probably null Het
Cfap58 A T 19: 47,937,923 (GRCm39) probably null Het
Chaf1a C A 17: 56,363,474 (GRCm39) H319Q unknown Het
Colec12 T C 18: 9,720,950 (GRCm39) S13P probably damaging Het
Cpne9 C T 6: 113,259,984 (GRCm39) probably benign Het
Cyp2c65 A C 19: 39,081,872 (GRCm39) D466A probably benign Het
Cyp3a25 T C 5: 145,928,248 (GRCm39) K266E probably damaging Het
Dennd1b G T 1: 138,990,678 (GRCm39) R214L probably damaging Het
Dock9 T C 14: 121,818,854 (GRCm39) I1533V probably benign Het
Dynlt1a C T 17: 6,361,184 (GRCm39) M102I probably benign Het
Edil3 G T 13: 89,325,272 (GRCm39) L220F probably damaging Het
Eml5 A G 12: 98,831,693 (GRCm39) Y383H probably benign Het
Epc1 T A 18: 6,450,130 (GRCm39) T393S probably benign Het
Fbxo8 A T 8: 57,041,076 (GRCm39) D164V probably benign Het
Gbp4 T A 5: 105,284,841 (GRCm39) N16I probably damaging Het
Gdf6 G A 4: 9,844,877 (GRCm39) V134I probably damaging Het
Gm5475 A G 15: 100,322,117 (GRCm39) probably benign Het
Gm6430 T G 1: 96,952,561 (GRCm39) noncoding transcript Het
Ighv9-4 A T 12: 114,263,765 (GRCm39) V56E probably damaging Het
Il3ra A T 14: 14,347,961 (GRCm38) N36Y probably damaging Het
Kif7 G T 7: 79,360,261 (GRCm39) C325* probably null Het
Lipo2 A T 19: 33,708,328 (GRCm39) F229I possibly damaging Het
Lrba A G 3: 86,352,656 (GRCm39) K1935E probably damaging Het
Mki67 A T 7: 135,297,017 (GRCm39) D2672E possibly damaging Het
Mtf1 A G 4: 124,732,576 (GRCm39) T545A probably benign Het
Mup6 A T 4: 60,004,812 (GRCm39) probably null Het
Myo9b T C 8: 71,808,409 (GRCm39) V1672A probably damaging Het
Nudt16l2 T C 9: 105,020,767 (GRCm39) I165V probably damaging Het
Or10al6 C A 17: 38,082,949 (GRCm39) P135Q probably damaging Het
Or10j5 C T 1: 172,785,205 (GRCm39) T281I possibly damaging Het
Or4k36 A T 2: 111,145,983 (GRCm39) H53L probably benign Het
Or5d37 T A 2: 87,923,362 (GRCm39) N306I probably damaging Het
Pcdhgb2 A T 18: 37,825,102 (GRCm39) I698F probably damaging Het
Pkn3 C T 2: 29,978,572 (GRCm39) H665Y probably damaging Het
Ppil6 T A 10: 41,383,531 (GRCm39) L99* probably null Het
Psg22 T A 7: 18,458,554 (GRCm39) V376E probably damaging Het
Pum1 G A 4: 130,457,591 (GRCm39) R201H probably damaging Het
Rasa2 A T 9: 96,439,433 (GRCm39) probably benign Het
Schip1 T A 3: 68,525,963 (GRCm39) M379K possibly damaging Het
Scn9a A T 2: 66,395,398 (GRCm39) probably benign Het
Sh3tc1 C T 5: 35,864,322 (GRCm39) A622T probably benign Het
Ssxb17 C T X: 21,041,167 (GRCm39) S45N probably damaging Het
Stab1 G A 14: 30,876,629 (GRCm39) R862C possibly damaging Het
Tdrd5 T A 1: 156,087,312 (GRCm39) H870L probably benign Het
Tnfaip8 A G 18: 50,223,443 (GRCm39) R60G possibly damaging Het
Traf3ip3 C T 1: 192,880,254 (GRCm39) R25Q probably damaging Het
Unc5b T C 10: 60,601,150 (GRCm39) Y892C probably damaging Het
Vmn2r2 T G 3: 64,042,118 (GRCm39) D199A probably damaging Het
Washc2 C A 6: 116,185,202 (GRCm39) P12Q probably damaging Het
Zfp286 T C 11: 62,671,896 (GRCm39) I121V probably benign Het
Zfp606 T A 7: 12,228,267 (GRCm39) probably null Het
Other mutations in Smarcd2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00392:Smarcd2 APN 11 106,156,730 (GRCm39) missense probably damaging 1.00
IGL01880:Smarcd2 APN 11 106,157,503 (GRCm39) missense probably damaging 1.00
R0357:Smarcd2 UTSW 11 106,158,158 (GRCm39) critical splice donor site probably null
R0626:Smarcd2 UTSW 11 106,158,241 (GRCm39) missense probably benign 0.10
R1524:Smarcd2 UTSW 11 106,157,978 (GRCm39) missense probably benign 0.01
R1822:Smarcd2 UTSW 11 106,158,222 (GRCm39) missense probably benign 0.00
R2072:Smarcd2 UTSW 11 106,156,133 (GRCm39) nonsense probably null
R2074:Smarcd2 UTSW 11 106,156,133 (GRCm39) nonsense probably null
R2359:Smarcd2 UTSW 11 106,157,990 (GRCm39) missense probably benign 0.01
R3960:Smarcd2 UTSW 11 106,157,401 (GRCm39) missense probably damaging 1.00
R4211:Smarcd2 UTSW 11 106,157,731 (GRCm39) nonsense probably null
R4822:Smarcd2 UTSW 11 106,157,357 (GRCm39) splice site probably null
R5174:Smarcd2 UTSW 11 106,157,871 (GRCm39) unclassified probably benign
R6035:Smarcd2 UTSW 11 106,157,715 (GRCm39) critical splice donor site probably null
R6035:Smarcd2 UTSW 11 106,157,715 (GRCm39) critical splice donor site probably null
R7383:Smarcd2 UTSW 11 106,155,602 (GRCm39) missense probably damaging 1.00
R7530:Smarcd2 UTSW 11 106,156,587 (GRCm39) missense probably damaging 1.00
R7855:Smarcd2 UTSW 11 106,158,392 (GRCm39) missense probably benign 0.17
R9469:Smarcd2 UTSW 11 106,163,332 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- CAAAGGCACGGTGATATCAGC -3'
(R):5'- GGGTGCAGGGTCCTTTTAAC -3'

Sequencing Primer
(F):5'- CACGGTGATATCAGCCTGAG -3'
(R):5'- AACTCAGCAGTTCTTAACCTGTGGG -3'
Posted On 2015-06-20