Incidental Mutation 'R5089:Smarcb1'
ID 387645
Institutional Source Beutler Lab
Gene Symbol Smarcb1
Ensembl Gene ENSMUSG00000000902
Gene Name SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
Synonyms Ini1, SNF5/INI1, Baf47, Snf5, integrase interactor 1
MMRRC Submission 042678-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5089 (G1)
Quality Score 203
Status Validated
Chromosome 10
Chromosomal Location 75732603-75757448 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 75751013 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 74 (T74A)
Ref Sequence ENSEMBL: ENSMUSP00000112463 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000925] [ENSMUST00000121304] [ENSMUST00000140388] [ENSMUST00000146555]
AlphaFold Q9Z0H3
Predicted Effect probably benign
Transcript: ENSMUST00000000925
AA Change: T83A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000000925
Gene: ENSMUSG00000000902
AA Change: T83A

DomainStartEndE-ValueType
Blast:HX 31 52 9e-8 BLAST
Pfam:SNF5 179 254 1.1e-27 PFAM
Pfam:SNF5 249 373 3.1e-33 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000121304
AA Change: T74A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000112463
Gene: ENSMUSG00000000902
AA Change: T74A

DomainStartEndE-ValueType
Blast:HX 31 52 9e-8 BLAST
Pfam:SNF5 169 364 1.7e-66 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133189
Predicted Effect probably benign
Transcript: ENSMUST00000140388
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140408
Predicted Effect probably benign
Transcript: ENSMUST00000146555
Meta Mutation Damage Score 0.0612 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.0%
  • 20x: 91.3%
Validation Efficiency 98% (65/66)
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 part of a complex that relieves repressive chromatin structures, allowing the transcriptional machinery to access its targets more effectively. The encoded nuclear protein may also bind to and enhance the DNA joining activity of HIV-1 integrase. This gene has been found to be a tumor suppressor, and mutations in it have been associated with malignant rhabdoid tumors. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2015]
PHENOTYPE: Homozygous inactivation of this gene leads to peri-implantation lethality, likely due to an inability of the blastocysts to hatch and implant in the uterus. A subset of heterozygous null mice develop a variety of tumors in the soft tissues of the head and neck. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700030J22Rik T C 8: 117,698,672 (GRCm39) N145S possibly damaging Het
Acp2 T C 2: 91,042,267 (GRCm39) probably benign Het
Adgrf2 G A 17: 43,020,988 (GRCm39) A612V probably benign Het
Bltp1 T A 3: 37,041,651 (GRCm39) D2676E probably benign Het
Cct3 T G 3: 88,208,150 (GRCm39) M46R probably damaging Het
Cdc123 T C 2: 5,809,811 (GRCm39) D200G probably benign Het
Cdh9 T A 15: 16,778,362 (GRCm39) F59Y probably damaging Het
Cluh A G 11: 74,551,198 (GRCm39) E349G probably damaging Het
Col16a1 C T 4: 129,972,988 (GRCm39) T643M probably benign Het
Col5a1 G A 2: 27,908,614 (GRCm39) W67* probably null Het
Crbn T C 6: 106,758,679 (GRCm39) H381R possibly damaging Het
Crim1 A G 17: 78,681,519 (GRCm39) D991G probably damaging Het
Dhx16 A T 17: 36,194,981 (GRCm39) M503L probably damaging Het
Dthd1 A G 5: 63,007,248 (GRCm39) T650A probably benign Het
Etfa T A 9: 55,396,150 (GRCm39) K139* probably null Het
Flnc T C 6: 29,447,812 (GRCm39) I1205T probably damaging Het
Fzd6 T A 15: 38,870,875 (GRCm39) C32S probably damaging Het
Gm1110 T A 9: 26,793,683 (GRCm39) D515V probably damaging Het
Gm7676 T C 8: 13,946,401 (GRCm39) noncoding transcript Het
Gpr157 T C 4: 150,186,750 (GRCm39) S293P possibly damaging Het
Hc T C 2: 34,914,902 (GRCm39) D810G probably benign Het
Helz2 T C 2: 180,876,942 (GRCm39) H1184R probably benign Het
Hoxc5 A T 15: 102,922,487 (GRCm39) probably benign Het
Iah1 C T 12: 21,373,309 (GRCm39) S196L possibly damaging Het
Il5 C T 11: 53,612,655 (GRCm39) T55I possibly damaging Het
Kras T C 6: 145,170,869 (GRCm39) K169E probably benign Het
Larp1 C A 11: 57,938,693 (GRCm39) T492K possibly damaging Het
Lgr5 T C 10: 115,314,328 (GRCm39) D203G probably damaging Het
Lpcat2 G A 8: 93,606,071 (GRCm39) V241M probably damaging Het
Mpeg1 G A 19: 12,440,361 (GRCm39) M606I probably benign Het
Ms4a1 G A 19: 11,236,176 (GRCm39) P4S probably benign Het
Nat10 A T 2: 103,587,488 (GRCm39) probably benign Het
Ncaph2 T A 15: 89,240,148 (GRCm39) probably null Het
Nfat5 T A 8: 108,078,070 (GRCm39) V403D probably damaging Het
Or2y10 T A 11: 49,455,240 (GRCm39) M164K possibly damaging Het
Or4c109 A G 2: 88,818,516 (GRCm39) F10S probably damaging Het
Pax7 T C 4: 139,557,576 (GRCm39) H65R probably damaging Het
Phf20 C A 2: 156,144,782 (GRCm39) H797N probably benign Het
Pkhd1l1 T A 15: 44,455,283 (GRCm39) S4015T probably benign Het
Prdm5 C T 6: 65,833,074 (GRCm39) H148Y probably benign Het
Prpf8 A G 11: 75,400,054 (GRCm39) probably null Het
Rangap1 A C 15: 81,594,664 (GRCm39) D388E probably benign Het
Sardh A G 2: 27,129,625 (GRCm39) probably null Het
Serpinb6b G A 13: 33,162,133 (GRCm39) E192K probably benign Het
Shfl A T 9: 20,780,212 (GRCm39) M1L probably benign Het
Skor1 A G 9: 63,053,205 (GRCm39) S216P probably damaging Het
Slc51a A G 16: 32,296,364 (GRCm39) probably null Het
Spg11 A T 2: 121,945,198 (GRCm39) Y107* probably null Het
Spmip5 A T 19: 58,774,678 (GRCm39) L176H probably damaging Het
Stk25 T A 1: 93,552,330 (GRCm39) K350M probably benign Het
Syne1 C T 10: 5,355,444 (GRCm39) W379* probably null Het
Taco1 A T 11: 105,960,437 (GRCm39) E126V probably benign Het
Tbc1d12 T A 19: 38,905,232 (GRCm39) L649* probably null Het
Trpm3 G A 19: 22,744,120 (GRCm39) G238R probably damaging Het
Yy1 C A 12: 108,759,663 (GRCm39) Q109K probably damaging Het
Other mutations in Smarcb1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01533:Smarcb1 APN 10 75,752,602 (GRCm39) splice site probably null
IGL02399:Smarcb1 APN 10 75,733,328 (GRCm39) missense probably damaging 1.00
IGL02457:Smarcb1 APN 10 75,757,205 (GRCm39) missense probably benign 0.01
R0505:Smarcb1 UTSW 10 75,732,900 (GRCm39) missense probably damaging 1.00
R1120:Smarcb1 UTSW 10 75,757,157 (GRCm39) missense probably benign
R2846:Smarcb1 UTSW 10 75,733,375 (GRCm39) missense probably damaging 1.00
R3725:Smarcb1 UTSW 10 75,752,620 (GRCm39) missense probably benign 0.00
R5157:Smarcb1 UTSW 10 75,747,628 (GRCm39) intron probably benign
R5632:Smarcb1 UTSW 10 75,740,252 (GRCm39) nonsense probably null
R5662:Smarcb1 UTSW 10 75,740,404 (GRCm39) missense possibly damaging 0.95
R7472:Smarcb1 UTSW 10 75,733,373 (GRCm39) missense probably damaging 1.00
R8112:Smarcb1 UTSW 10 75,745,986 (GRCm39) critical splice donor site probably null
R9151:Smarcb1 UTSW 10 75,750,916 (GRCm39) missense probably benign 0.01
Z1176:Smarcb1 UTSW 10 75,741,911 (GRCm39) missense probably benign 0.00
Z1177:Smarcb1 UTSW 10 75,740,345 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- GCTCTTCAGTGTGAGAAACTCC -3'
(R):5'- CAGTTGCCCTTTTGGAAGACG -3'

Sequencing Primer
(F):5'- TGCACATGTCCCTGAAGC -3'
(R):5'- TTTGGAAGACGCTAGCACTC -3'
Posted On 2016-06-06