Incidental Mutation 'R7516:Usp1'
ID 582443
Institutional Source Beutler Lab
Gene Symbol Usp1
Ensembl Gene ENSMUSG00000028560
Gene Name ubiquitin specific peptidase 1
Synonyms
MMRRC Submission 045589-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.901) question?
Stock # R7516 (G1)
Quality Score 225.009
Status Not validated
Chromosome 4
Chromosomal Location 98812047-98823780 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 98822356 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 557 (T557A)
Ref Sequence ENSEMBL: ENSMUSP00000030289 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000030286] [ENSMUST00000030289] [ENSMUST00000075836] [ENSMUST00000091358] [ENSMUST00000125104] [ENSMUST00000127417] [ENSMUST00000205650]
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: T557A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000030289
Gene: ENSMUSG00000028560
AA Change: T557A

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: T557A

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000088917
Gene: ENSMUSG00000028560
AA Change: T557A

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: 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
Predicted Effect probably benign
Transcript: ENSMUST00000205650
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.2%
Validation Efficiency
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam28 T A 14: 68,868,125 (GRCm39) I407F probably damaging Het
Agbl1 A G 7: 76,075,669 (GRCm39) Y437C probably damaging Het
Alkbh5 T C 11: 60,429,979 (GRCm39) V244A probably damaging Het
Arap1 T C 7: 101,058,538 (GRCm39) F1390L probably benign Het
Asph T C 4: 9,630,940 (GRCm39) D136G possibly damaging Het
Atp8a2 A T 14: 60,094,516 (GRCm39) Y841N probably damaging Het
Cald1 A T 6: 34,686,492 (GRCm39) probably benign Het
Capn11 A G 17: 45,949,766 (GRCm39) I400T possibly damaging Het
Cdh18 T A 15: 23,259,684 (GRCm39) probably null Het
Ces2h T A 8: 105,743,458 (GRCm39) L204Q probably damaging Het
Chrna3 G A 9: 54,922,653 (GRCm39) A385V probably benign Het
Clca4a A T 3: 144,672,009 (GRCm39) L311Q probably damaging Het
Clip1 A G 5: 123,721,448 (GRCm39) V1149A probably benign Het
Clip3 T A 7: 29,998,268 (GRCm39) V238D possibly damaging Het
Col12a1 A G 9: 79,520,192 (GRCm39) probably null Het
Coro2a A G 4: 46,562,992 (GRCm39) V54A probably benign Het
Crem T C 18: 3,299,141 (GRCm39) probably null Het
Dennd5b T C 6: 148,969,878 (GRCm39) I192V probably benign Het
Dst A G 1: 34,209,560 (GRCm39) N1209S probably benign Het
Ero1a T A 14: 45,525,480 (GRCm39) M385L probably benign Het
Fam13a A T 6: 58,932,248 (GRCm39) V375D probably damaging Het
Fgfbp3 T A 19: 36,896,324 (GRCm39) Y98F possibly damaging Het
Frem3 T C 8: 81,338,712 (GRCm39) V335A probably damaging Het
Gm19410 T A 8: 36,263,433 (GRCm39) D951E probably benign Het
Gpatch1 T C 7: 35,007,625 (GRCm39) D145G probably benign Het
H60c G T 10: 3,209,746 (GRCm39) C180* probably null Het
Hmcn1 T C 1: 150,498,718 (GRCm39) T4054A probably benign Het
Hrg A G 16: 22,780,048 (GRCm39) Y442C unknown Het
Hspg2 C T 4: 137,269,931 (GRCm39) R2327C possibly damaging Het
Klhl31 G T 9: 77,558,429 (GRCm39) A382S probably damaging Het
Knl1 T C 2: 118,901,179 (GRCm39) V960A probably damaging Het
Lztr1 C T 16: 17,327,525 (GRCm39) A76V possibly damaging Het
Me3 G T 7: 89,497,183 (GRCm39) E395* probably null Het
Morc2b G A 17: 33,356,435 (GRCm39) H446Y probably benign Het
Mroh7 A T 4: 106,548,316 (GRCm39) M1054K probably benign Het
Ms4a6b T C 19: 11,506,907 (GRCm39) V232A probably benign Het
Nmt2 C A 2: 3,313,767 (GRCm39) D224E probably damaging Het
Nox4 C A 7: 86,970,905 (GRCm39) R261S probably benign Het
Obscn T A 11: 59,015,416 (GRCm39) K1019* probably null Het
Or4a15 T A 2: 89,193,719 (GRCm39) N18I probably benign Het
Or4g7 T A 2: 111,309,282 (GRCm39) V51D probably benign Het
Or5p67 G A 7: 107,922,223 (GRCm39) S220F probably damaging Het
Or8k24 C T 2: 86,216,328 (GRCm39) V145I probably benign Het
Pcdha11 A T 18: 37,144,671 (GRCm39) N254I probably damaging Het
Pck2 T A 14: 55,779,913 (GRCm39) I54N probably benign Het
Pkd1l3 T A 8: 110,361,861 (GRCm39) W978R probably damaging Het
Plxna4 T C 6: 32,214,703 (GRCm39) T593A probably benign Het
Podn G A 4: 107,879,321 (GRCm39) R266W probably damaging Het
Ptpn22 A G 3: 103,792,854 (GRCm39) D335G probably benign Het
Pxn A G 5: 115,644,922 (GRCm39) D3G unknown Het
Rapgefl1 T G 11: 98,736,960 (GRCm39) V320G probably benign Het
Rel A G 11: 23,692,785 (GRCm39) I416T probably benign Het
Sema5b A G 16: 35,471,540 (GRCm39) N378D probably benign Het
Sh3bp4 C A 1: 89,073,368 (GRCm39) L739M probably damaging Het
Skint2 A T 4: 112,483,168 (GRCm39) D191V probably damaging Het
Slc3a1 T C 17: 85,371,190 (GRCm39) Y581H probably damaging Het
Smcr8 G T 11: 60,670,814 (GRCm39) C654F probably benign Het
Spta1 A C 1: 174,025,349 (GRCm39) Q738P probably damaging Het
Sptlc3 C A 2: 139,431,438 (GRCm39) A320D probably benign Het
Thnsl2 T A 6: 71,108,990 (GRCm39) K274* probably null Het
Tmed2 T A 5: 124,685,055 (GRCm39) I68K possibly damaging Het
Tmtc4 G A 14: 123,180,735 (GRCm39) A326V possibly damaging Het
Tnks2 T A 19: 36,849,064 (GRCm39) S179T possibly damaging Het
Trim34b G T 7: 103,978,918 (GRCm39) C55F probably damaging Het
Trpm4 T A 7: 44,954,444 (GRCm39) E1129V probably damaging Het
Tvp23b T C 11: 62,782,867 (GRCm39) S188P possibly damaging Het
Vmn2r66 C T 7: 84,661,176 (GRCm39) C18Y possibly damaging Het
Vmn2r85 T A 10: 130,254,852 (GRCm39) T611S probably damaging Het
Vps13c T C 9: 67,862,289 (GRCm39) S2969P possibly damaging Het
Wdr74 T A 19: 8,713,554 (GRCm39) C62* probably null Het
Wfikkn1 A T 17: 26,097,020 (GRCm39) C435S probably damaging Het
Zbtb45 A T 7: 12,740,269 (GRCm39) F449I probably damaging 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
R5141:Usp1 UTSW 4 98,822,446 (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
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'- TGCATTTTCCTCAGAATTGAAGCC -3'
(R):5'- TCATCGTCGTAGTTCCCAGC -3'

Sequencing Primer
(F):5'- CTCAGAATTGAAGCCTTAGTTTGCC -3'
(R):5'- CAGTGGCTCTGGCTTACCTAG -3'
Posted On 2019-10-17