Incidental Mutation 'R5141:Usp1'
ID 396450
Institutional Source Beutler Lab
Gene Symbol Usp1
Ensembl Gene ENSMUSG00000028560
Gene Name ubiquitin specific peptidase 1
Synonyms
MMRRC Submission 042727-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.901) question?
Stock # R5141 (G1)
Quality Score 225
Status Validated
Chromosome 4
Chromosomal Location 98812047-98823780 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 98822446 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 587 (T587A)
Ref Sequence ENSEMBL: ENSMUSP00000088917 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030286] [ENSMUST00000030289] [ENSMUST00000075836] [ENSMUST00000091358] [ENSMUST00000125104] [ENSMUST00000205650] [ENSMUST00000127417]
AlphaFold Q8BJQ2
Predicted Effect probably benign
Transcript: ENSMUST00000030286
SMART Domains Protein: ENSMUSP00000030286
Gene: ENSMUSG00000028556

DomainStartEndE-ValueType
Pfam:DUF3398 67 159 6.5e-30 PFAM
coiled coil region 367 394 N/A INTRINSIC
low complexity region 493 504 N/A INTRINSIC
Pfam:DOCK-C2 557 736 1.8e-51 PFAM
low complexity region 789 799 N/A INTRINSIC
low complexity region 862 873 N/A INTRINSIC
low complexity region 888 901 N/A INTRINSIC
low complexity region 1135 1163 N/A INTRINSIC
low complexity region 1350 1364 N/A INTRINSIC
low complexity region 1543 1565 N/A INTRINSIC
Pfam:DHR-2 1571 2095 1.4e-217 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000030289
AA Change: T587A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000030289
Gene: ENSMUSG00000028560
AA Change: T587A

DomainStartEndE-ValueType
Pfam:UCH 80 616 9.2e-35 PFAM
Pfam:UCH_1 415 618 1.3e-11 PFAM
Pfam:UCH 723 781 3.9e-6 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000075836
SMART Domains Protein: ENSMUSP00000075233
Gene: ENSMUSG00000028556

DomainStartEndE-ValueType
Pfam:DUF3398 65 159 5.8e-34 PFAM
coiled coil region 367 394 N/A INTRINSIC
low complexity region 493 504 N/A INTRINSIC
Pfam:DOCK-C2 556 737 3.3e-58 PFAM
low complexity region 789 799 N/A INTRINSIC
low complexity region 862 873 N/A INTRINSIC
low complexity region 888 901 N/A INTRINSIC
low complexity region 1105 1133 N/A INTRINSIC
low complexity region 1320 1334 N/A INTRINSIC
low complexity region 1513 1535 N/A INTRINSIC
Pfam:Ded_cyto 1888 2065 6.5e-80 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000091358
AA Change: T587A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000088917
Gene: ENSMUSG00000028560
AA Change: T587A

DomainStartEndE-ValueType
Pfam:UCH 80 622 5e-39 PFAM
Pfam:UCH_1 346 613 2.8e-11 PFAM
low complexity region 765 779 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000124466
Predicted Effect probably benign
Transcript: ENSMUST00000125104
SMART Domains Protein: ENSMUSP00000135496
Gene: ENSMUSG00000028560

DomainStartEndE-ValueType
Pfam:UCH 37 150 4.1e-14 PFAM
Pfam:UCH_1 38 80 1.2e-7 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000205650
Predicted Effect noncoding transcript
Transcript: ENSMUST00000206128
Predicted Effect probably benign
Transcript: ENSMUST00000127417
SMART Domains Protein: ENSMUSP00000117797
Gene: ENSMUSG00000028556

DomainStartEndE-ValueType
low complexity region 140 162 N/A INTRINSIC
Pfam:Ded_cyto 517 694 3e-80 PFAM
Meta Mutation Damage Score 0.3879 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.6%
Validation Efficiency 96% (76/79)
MGI Phenotype FUNCTION: This gene encodes a member of the ubiquitin-specific peptidase family. The encoded protein acts as a catalytic subunit in a heterodimeric deubiquitinating enzyme complex that deubiquitinates Fanconi anemia, complementation group D2, and plays a role in homologous recombination-mediated DNA repair. Disruption of this gene is associated with a Fanconi anemia-like phenotype and genomic instability. Alternative splicing results in multiple transcript variants. Pseudogenes of this gene have been defined on chromosomes 3, 12, and 15. [provided by RefSeq, Aug 2014]
PHENOTYPE: Homozygous null mice have a high rate of postnatal lethality related to cyanosis. Male survivors are infertile while female survivors have reduced fertility. Both sexes have reduced number of gametes, are sensitive to ionizing radiation, and have decreased numbers of bone marrow cells. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 75 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamdec1 A G 14: 68,810,577 (GRCm39) V193A probably benign Het
Adamts18 T A 8: 114,501,902 (GRCm39) T320S probably damaging Het
Adamtsl1 G T 4: 86,075,087 (GRCm39) M151I possibly damaging Het
Adgrv1 A T 13: 81,419,037 (GRCm39) V5986E probably damaging Het
Aifm3 A G 16: 17,317,586 (GRCm39) E69G probably damaging Het
Akap13 C A 7: 75,259,362 (GRCm39) T662K probably benign Het
Alms1 A G 6: 85,598,414 (GRCm39) D1080G probably benign Het
Als2 T C 1: 59,209,611 (GRCm39) E1457G possibly damaging Het
Apobec4 A G 1: 152,631,964 (GRCm39) probably benign Het
Apoo-ps C T 13: 107,550,895 (GRCm39) noncoding transcript Het
Aspscr1 G A 11: 120,580,003 (GRCm39) V181I probably benign Het
Atrn T C 2: 130,841,050 (GRCm39) probably benign Het
C3 T A 17: 57,526,570 (GRCm39) I804F probably damaging Het
Cbfa2t3 C T 8: 123,361,760 (GRCm39) G421R probably benign Het
Chmp4c A G 3: 10,432,213 (GRCm39) E41G probably damaging Het
Clk4 T A 11: 51,166,598 (GRCm39) F96L possibly damaging Het
Ctsg G A 14: 56,339,184 (GRCm39) R25* probably null Het
Cul1 A G 6: 47,497,773 (GRCm39) D618G probably benign Het
Cylc2 T C 4: 51,228,587 (GRCm39) probably benign Het
Dip2a G A 10: 76,106,287 (GRCm39) T1326I probably damaging Het
Etnk2 A G 1: 133,296,600 (GRCm39) I210V probably benign Het
Gm5773 T A 3: 93,681,034 (GRCm39) D235E probably benign Het
Gm7353 T C 7: 3,161,001 (GRCm39) noncoding transcript Het
Gpi1 G A 7: 33,926,521 (GRCm39) probably benign Het
Ing4 T C 6: 125,016,837 (GRCm39) M5T probably benign Het
Inpp4a A G 1: 37,419,168 (GRCm39) I583V probably benign Het
Isyna1 T C 8: 71,047,543 (GRCm39) V64A probably damaging Het
Katnal2 T A 18: 77,085,337 (GRCm39) D310V probably damaging Het
Kbtbd8 A G 6: 95,098,820 (GRCm39) T126A probably damaging Het
Kif13a T C 13: 46,906,197 (GRCm39) D582G probably benign Het
Lmf2 G A 15: 89,235,810 (GRCm39) probably null Het
Lrp2 T C 2: 69,382,693 (GRCm39) probably null Het
Lrp4 T C 2: 91,309,023 (GRCm39) probably benign Het
Lyzl1 A C 18: 4,169,209 (GRCm39) D71A possibly damaging Het
Mak C T 13: 41,186,039 (GRCm39) C543Y possibly damaging Het
Mapk8ip1 T C 2: 92,217,110 (GRCm39) D404G probably damaging Het
Mdga1 C T 17: 30,071,467 (GRCm39) E385K probably benign Het
Mst1r T A 9: 107,789,440 (GRCm39) I573N probably damaging Het
Muc5ac T A 7: 141,368,479 (GRCm39) N2365K possibly damaging Het
Ncan T C 8: 70,565,487 (GRCm39) E179G probably damaging Het
Nlgn2 C T 11: 69,716,216 (GRCm39) R775H probably damaging Het
Or10d5 T G 9: 39,861,170 (GRCm39) K299T probably benign Het
Or4c122 A C 2: 89,079,473 (GRCm39) Y176* probably null Het
Or8g20 A G 9: 39,395,827 (GRCm39) F238L probably damaging Het
Pcolce G T 5: 137,604,012 (GRCm39) Q352K probably benign Het
Peg3 G T 7: 6,712,381 (GRCm39) T947N probably benign Het
Pld3 C T 7: 27,233,220 (GRCm39) D344N probably damaging Het
Plec A C 15: 76,074,733 (GRCm39) D411E probably damaging Het
Pmp2 C T 3: 10,247,474 (GRCm39) D72N probably benign Het
Ptpn9 T C 9: 56,943,960 (GRCm39) V278A possibly damaging Het
Rbm33 A G 5: 28,557,687 (GRCm39) H300R probably damaging Het
Rpgrip1l T C 8: 91,987,546 (GRCm39) Q837R probably benign Het
Rwdd4a T C 8: 48,003,709 (GRCm39) probably benign Het
Sema6a T C 18: 47,381,455 (GRCm39) T1048A probably damaging Het
Senp1 G A 15: 97,974,488 (GRCm39) A108V probably benign Het
Serpine2 G T 1: 79,780,580 (GRCm39) Q290K possibly damaging Het
Sesn1 A G 10: 41,687,097 (GRCm39) N27S probably benign Het
Shroom1 T A 11: 53,354,809 (GRCm39) L243* probably null Het
Slc17a5 A G 9: 78,448,270 (GRCm39) Y395H probably damaging Het
Slc5a8 T C 10: 88,755,422 (GRCm39) probably null Het
Sptbn5 G A 2: 119,892,212 (GRCm39) S1083F probably benign Het
Stx4a T A 7: 127,445,787 (GRCm39) V231E probably damaging Het
Swt1 A T 1: 151,287,145 (GRCm39) S116T probably benign Het
Syt9 C T 7: 107,103,426 (GRCm39) T408I probably damaging Het
Tgm7 T C 2: 120,931,480 (GRCm39) T228A probably benign Het
Tmem115 A G 9: 107,415,141 (GRCm39) D310G probably benign Het
Trcg1 G A 9: 57,148,587 (GRCm39) G53D probably damaging Het
Tsfm T C 10: 126,865,482 (GRCm39) K100E probably damaging Het
Vcpip1 G T 1: 9,818,302 (GRCm39) A27E unknown Het
Vmn2r49 T C 7: 9,720,300 (GRCm39) N397S probably benign Het
Vmn2r8 A G 5: 108,956,572 (GRCm39) S17P probably damaging Het
Vwa3b A G 1: 37,226,102 (GRCm39) probably benign Het
Ythdc2 T A 18: 44,998,114 (GRCm39) S1094T probably benign Het
Zbtb22 C G 17: 34,137,610 (GRCm39) S585C possibly damaging Het
Zhx2 A G 15: 57,685,182 (GRCm39) T184A probably benign Het
Other mutations in Usp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00715:Usp1 APN 4 98,822,818 (GRCm39) splice site probably null
IGL02692:Usp1 APN 4 98,817,197 (GRCm39) missense probably benign 0.00
R1782:Usp1 UTSW 4 98,822,435 (GRCm39) missense probably damaging 1.00
R1991:Usp1 UTSW 4 98,822,531 (GRCm39) missense probably benign 0.00
R1992:Usp1 UTSW 4 98,822,531 (GRCm39) missense probably benign 0.00
R2273:Usp1 UTSW 4 98,818,079 (GRCm39) missense probably damaging 1.00
R2274:Usp1 UTSW 4 98,818,079 (GRCm39) missense probably damaging 1.00
R2275:Usp1 UTSW 4 98,818,079 (GRCm39) missense probably damaging 1.00
R3750:Usp1 UTSW 4 98,822,357 (GRCm39) splice site probably null
R3886:Usp1 UTSW 4 98,817,973 (GRCm39) missense probably damaging 1.00
R4014:Usp1 UTSW 4 98,822,939 (GRCm39) missense probably damaging 1.00
R5304:Usp1 UTSW 4 98,822,855 (GRCm39) missense probably benign
R5388:Usp1 UTSW 4 98,819,294 (GRCm39) missense probably benign
R5709:Usp1 UTSW 4 98,819,360 (GRCm39) missense probably damaging 0.99
R6035:Usp1 UTSW 4 98,818,082 (GRCm39) missense probably damaging 1.00
R6035:Usp1 UTSW 4 98,818,082 (GRCm39) missense probably damaging 1.00
R6592:Usp1 UTSW 4 98,814,756 (GRCm39) missense possibly damaging 0.86
R6956:Usp1 UTSW 4 98,819,243 (GRCm39) missense probably damaging 0.96
R7117:Usp1 UTSW 4 98,817,127 (GRCm39) missense possibly damaging 0.59
R7396:Usp1 UTSW 4 98,814,688 (GRCm39) intron probably benign
R7516:Usp1 UTSW 4 98,822,356 (GRCm39) missense probably damaging 1.00
R7590:Usp1 UTSW 4 98,822,489 (GRCm39) missense possibly damaging 0.67
R7828:Usp1 UTSW 4 98,820,544 (GRCm39) missense probably damaging 1.00
R8050:Usp1 UTSW 4 98,817,150 (GRCm39) missense probably benign 0.10
R8085:Usp1 UTSW 4 98,816,578 (GRCm39) missense probably damaging 1.00
R8298:Usp1 UTSW 4 98,819,136 (GRCm39) missense probably damaging 1.00
R8736:Usp1 UTSW 4 98,821,105 (GRCm39) missense probably damaging 1.00
R8801:Usp1 UTSW 4 98,822,848 (GRCm39) missense probably benign
R8844:Usp1 UTSW 4 98,823,017 (GRCm39) missense probably damaging 1.00
R8887:Usp1 UTSW 4 98,819,185 (GRCm39) missense probably benign 0.43
R8899:Usp1 UTSW 4 98,819,347 (GRCm39) missense probably damaging 1.00
R9063:Usp1 UTSW 4 98,819,389 (GRCm39) missense probably benign 0.00
R9275:Usp1 UTSW 4 98,819,578 (GRCm39) missense probably damaging 0.98
R9738:Usp1 UTSW 4 98,819,672 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- AGGACTTACTACTTGGCTTCAC -3'
(R):5'- GGCATTTCCACCAACTCTAATTG -3'

Sequencing Primer
(F):5'- GACTTACTACTTGGCTTCACATTGTG -3'
(R):5'- GATACTTCATCGTCGTAGTTCCCAG -3'
Posted On 2016-06-21