Incidental Mutation 'R2871:Psmd13'
ID 253736
Institutional Source Beutler Lab
Gene Symbol Psmd13
Ensembl Gene ENSMUSG00000025487
Gene Name proteasome (prosome, macropain) 26S subunit, non-ATPase, 13
Synonyms 26S proteasome subunit p40.5, S11
MMRRC Submission 040459-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.964) question?
Stock # R2871 (G1)
Quality Score 225
Status Not validated
Chromosome 7
Chromosomal Location 140881968-140898643 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to T at 140887055 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 116 (T116S)
Ref Sequence ENSEMBL: ENSMUSP00000130580 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026559] [ENSMUST00000026560] [ENSMUST00000163610] [ENSMUST00000164681] [ENSMUST00000166889] [ENSMUST00000211179] [ENSMUST00000210296]
AlphaFold Q9WVJ2
Predicted Effect probably benign
Transcript: ENSMUST00000026559
SMART Domains Protein: ENSMUSP00000026559
Gene: ENSMUSG00000025486

DomainStartEndE-ValueType
Pfam:SIR2 3 184 5.3e-57 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000026560
AA Change: T116S

PolyPhen 2 Score 0.094 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000026560
Gene: ENSMUSG00000025487
AA Change: T116S

DomainStartEndE-ValueType
low complexity region 9 14 N/A INTRINSIC
PINT 263 356 2.26e-21 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000121585
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125668
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129683
Predicted Effect probably benign
Transcript: ENSMUST00000130462
SMART Domains Protein: ENSMUSP00000126160
Gene: ENSMUSG00000025487

DomainStartEndE-ValueType
PINT 100 189 6.59e-14 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000140411
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146875
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151644
Predicted Effect probably damaging
Transcript: ENSMUST00000163610
AA Change: T116S

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000130580
Gene: ENSMUSG00000025487
AA Change: T116S

DomainStartEndE-ValueType
low complexity region 9 14 N/A INTRINSIC
PDB:4CR4|O 16 347 7e-44 PDB
Blast:PINT 245 329 9e-26 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000164681
AA Change: T116S

PolyPhen 2 Score 0.393 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000132405
Gene: ENSMUSG00000025487
AA Change: T116S

DomainStartEndE-ValueType
low complexity region 9 14 N/A INTRINSIC
PDB:4CR4|O 16 184 1e-12 PDB
low complexity region 217 232 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000166889
SMART Domains Protein: ENSMUSP00000126532
Gene: ENSMUSG00000025487

DomainStartEndE-ValueType
low complexity region 9 14 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000211179
Predicted Effect noncoding transcript
Transcript: ENSMUST00000210398
Predicted Effect probably benign
Transcript: ENSMUST00000210296
Coding Region Coverage
  • 1x: 99.5%
  • 3x: 98.2%
  • 10x: 92.4%
  • 20x: 72.0%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a non-ATPase subunit of the 19S regulator. Two transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca8b A G 11: 109,955,176 C811R possibly damaging Het
AI481877 A C 4: 59,093,850 L226R probably damaging Het
Akap8l G A 17: 32,338,442 T65I possibly damaging Het
Arid4a T A 12: 71,022,260 probably null Het
Armc2 C T 10: 41,966,700 probably null Het
Atp6v1g1 A G 4: 63,550,021 Y87C probably benign Het
Cfap54 A T 10: 92,921,419 F273I possibly damaging Het
Clasrp C A 7: 19,585,240 probably benign Het
Csmd2 T C 4: 128,557,718 F113S unknown Het
Cyp4a14 C A 4: 115,487,301 G456W probably damaging Het
Cyp4a30b A G 4: 115,458,362 H260R possibly damaging Het
Ddrgk1 T A 2: 130,664,644 probably benign Het
Dhx57 A T 17: 80,251,376 D1051E probably benign Het
Eef2 GCCC GCCCC 10: 81,178,767 probably null Het
Eif4enif1 C T 11: 3,242,586 P805S probably damaging Het
Eml5 C T 12: 98,865,401 D433N probably damaging Het
Fan1 A G 7: 64,363,190 I668T probably benign Het
Frmpd4 A T X: 167,477,247 D1166E probably benign Het
Gm813 A T 16: 58,613,979 I125K probably benign Het
Gria2 G A 3: 80,702,492 T670I probably damaging Het
Grid2ip C A 5: 143,357,929 Q127K probably benign Het
Hdhd2 T C 18: 76,955,006 F44L probably damaging Het
Hjurp GT GTT 1: 88,266,524 probably null Het
Hmcn1 A T 1: 150,738,716 V1313D possibly damaging Het
Ift172 C T 5: 31,257,861 V1335I probably benign Het
Ighv2-2 G A 12: 113,588,498 T40I possibly damaging Het
Kcnk10 T A 12: 98,434,813 R520S probably benign Het
Kif1c A G 11: 70,724,081 E567G probably damaging Het
Klf8 A T X: 153,382,682 E82D probably damaging Het
Kpna7 T C 5: 144,993,935 T367A probably benign Het
Lpo A G 11: 87,816,524 I221T possibly damaging Het
Lrrn3 T C 12: 41,452,723 I532V probably benign Het
Matr3 T A 18: 35,572,296 S91R probably benign Het
Mki67 G A 7: 135,708,149 P191L probably benign Het
Mlxip A G 5: 123,452,667 M878V probably benign Het
Mpp7 G A 18: 7,461,678 P65L possibly damaging Het
Mroh2a C A 1: 88,255,565 L1292I probably damaging Het
Msh2 C A 17: 87,685,584 Q314K possibly damaging Het
Mtor T A 4: 148,540,030 M2089K probably benign Het
Myo9b G A 8: 71,334,337 R721Q probably benign Het
Nlrp4b C T 7: 10,710,243 Q40* probably null Het
Nomo1 C A 7: 46,046,937 T293N probably damaging Het
Notum A G 11: 120,660,196 V48A probably benign Het
Npas3 C T 12: 54,068,013 R542* probably null Het
Olfr1101 A T 2: 86,988,848 C109* probably null Het
Olfr419 T C 1: 174,250,526 S134G probably benign Het
Olfr45 A G 7: 140,691,285 I127V possibly damaging Het
Olfr71 C A 4: 43,706,458 V37L probably benign Het
Ostc T C 3: 130,703,508 N80S probably damaging Het
Palmd T C 3: 116,923,751 R366G possibly damaging Het
Parp1 A G 1: 180,573,665 D45G probably damaging Het
Pcdhga9 T A 18: 37,737,471 Y118N possibly damaging Het
Pes1 C A 11: 3,976,834 T372K probably benign Het
Pkp4 C A 2: 59,308,156 T250K probably benign Het
Plekhg5 T A 4: 152,107,503 C433S probably benign Het
Plin2 A G 4: 86,668,678 M1T probably null Het
Prdx4 A G X: 155,340,464 V15A probably benign Het
Psmb8 T C 17: 34,200,170 I146T probably damaging Het
Rel T C 11: 23,761,129 I13V probably benign Het
Reln C T 5: 22,049,791 V527I possibly damaging Het
Rnf6 T C 5: 146,210,405 Y601C probably benign Het
Rps6kc1 T C 1: 190,899,569 I48M probably damaging Het
Sfi1 CCTCTC CCTCTCTC 11: 3,177,419 probably benign Het
Slc39a8 T A 3: 135,886,793 probably null Het
Sppl2c C T 11: 104,187,315 P314S probably benign Het
St5 A T 7: 109,557,430 Y38N probably benign Het
Tnni3k C T 3: 154,938,750 probably null Het
Ugt1a1 AT A 1: 88,212,371 probably null Het
Vmn2r68 A C 7: 85,233,626 M306R probably benign Het
Vmn2r70 T A 7: 85,559,019 Y750F probably damaging Het
Vwa7 G A 17: 35,021,242 M395I probably damaging Het
Zfp53 A T 17: 21,508,078 E124D probably benign Het
Other mutations in Psmd13
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00233:Psmd13 APN 7 140897621 missense probably damaging 0.97
IGL02265:Psmd13 APN 7 140882518 missense probably damaging 1.00
R0326:Psmd13 UTSW 7 140897711 missense probably damaging 1.00
R1163:Psmd13 UTSW 7 140897454 missense probably damaging 0.97
R1667:Psmd13 UTSW 7 140890609 missense probably damaging 1.00
R1721:Psmd13 UTSW 7 140883517 missense probably damaging 1.00
R1867:Psmd13 UTSW 7 140883517 missense probably damaging 1.00
R1993:Psmd13 UTSW 7 140898194 missense probably damaging 1.00
R2070:Psmd13 UTSW 7 140897648 missense probably damaging 0.99
R2844:Psmd13 UTSW 7 140897740 intron probably benign
R2845:Psmd13 UTSW 7 140897740 intron probably benign
R2846:Psmd13 UTSW 7 140897740 intron probably benign
R2869:Psmd13 UTSW 7 140887055 missense probably damaging 0.99
R2869:Psmd13 UTSW 7 140887055 missense probably damaging 0.99
R2871:Psmd13 UTSW 7 140887055 missense probably damaging 0.99
R4358:Psmd13 UTSW 7 140889505 intron probably benign
R4973:Psmd13 UTSW 7 140886853 nonsense probably null
R5197:Psmd13 UTSW 7 140894461 splice site probably null
R6700:Psmd13 UTSW 7 140890609 missense probably damaging 1.00
R8239:Psmd13 UTSW 7 140886537 missense probably damaging 1.00
R8798:Psmd13 UTSW 7 140897750 nonsense probably null
R9516:Psmd13 UTSW 7 140898542 missense
Z1176:Psmd13 UTSW 7 140882426 unclassified probably benign
Predicted Primers PCR Primer
(F):5'- TTTCTGGAAAAGACTCGTGAGAAG -3'
(R):5'- AAGTAACAGCGGGGACATCTC -3'

Sequencing Primer
(F):5'- GCATTTTCTAGTATTTACGTGATTCG -3'
(R):5'- CATCTCGGTTAGAATACGAGAGTGC -3'
Posted On 2014-12-04