Incidental Mutation 'R1862:Nup54'
ID 204009
Institutional Source Beutler Lab
Gene Symbol Nup54
Ensembl Gene ENSMUSG00000034826
Gene Name nucleoporin 54
Synonyms 54kDa, 3110079L04Rik
MMRRC Submission 039885-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.965) question?
Stock # R1862 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 92415540-92435219 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to A at 92419567 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Leucine at position 375 (I375L)
Ref Sequence ENSEMBL: ENSMUSP00000046540 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000038514] [ENSMUST00000113083] [ENSMUST00000117108] [ENSMUST00000118106] [ENSMUST00000119587] [ENSMUST00000120193] [ENSMUST00000120416] [ENSMUST00000121096]
AlphaFold Q8BTS4
Predicted Effect possibly damaging
Transcript: ENSMUST00000038514
AA Change: I375L

PolyPhen 2 Score 0.745 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000046540
Gene: ENSMUSG00000034826
AA Change: I375L

DomainStartEndE-ValueType
low complexity region 5 109 N/A INTRINSIC
Pfam:Nup54 303 441 4.8e-49 PFAM
PDB:3T98|C 445 494 2e-26 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000113083
SMART Domains Protein: ENSMUSP00000108706
Gene: ENSMUSG00000034842

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Pfam:ART 29 251 4.4e-65 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000117108
SMART Domains Protein: ENSMUSP00000113041
Gene: ENSMUSG00000034842

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Pfam:ART 29 251 1.9e-65 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000118106
SMART Domains Protein: ENSMUSP00000114083
Gene: ENSMUSG00000034842

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Pfam:ART 29 251 9e-66 PFAM
low complexity region 298 309 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000119587
SMART Domains Protein: ENSMUSP00000112648
Gene: ENSMUSG00000034842

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Pfam:ART 29 251 4e-65 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000120193
SMART Domains Protein: ENSMUSP00000113074
Gene: ENSMUSG00000034842

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Pfam:ART 29 251 8.4e-66 PFAM
low complexity region 298 309 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000120416
SMART Domains Protein: ENSMUSP00000113493
Gene: ENSMUSG00000034842

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Pfam:ART 29 251 3.1e-65 PFAM
low complexity region 298 309 N/A INTRINSIC
low complexity region 366 373 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000121096
SMART Domains Protein: ENSMUSP00000113510
Gene: ENSMUSG00000034842

DomainStartEndE-ValueType
signal peptide 1 26 N/A INTRINSIC
Pfam:ART 29 251 1.8e-65 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123694
Predicted Effect probably benign
Transcript: ENSMUST00000126281
SMART Domains Protein: ENSMUSP00000116110
Gene: ENSMUSG00000034842

DomainStartEndE-ValueType
Pfam:ART 1 190 3e-53 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129222
Predicted Effect probably benign
Transcript: ENSMUST00000138003
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201228
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.8%
  • 10x: 94.9%
  • 20x: 90.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013]
Allele List at MGI
Other mutations in this stock
Total: 82 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acox2 T A 14: 8,241,416 E565D probably benign Het
Adam30 A T 3: 98,162,113 K421* probably null Het
Atp6v1b1 A G 6: 83,749,852 probably null Het
Cacna1a A T 8: 84,415,930 I96F possibly damaging Het
Card10 G A 15: 78,780,514 R747W probably damaging Het
Cdh8 T A 8: 99,190,394 D363V probably damaging Het
Cecr2 T C 6: 120,757,941 Y685H probably damaging Het
Cmklr1 T C 5: 113,614,407 T178A probably damaging Het
Col16a1 G A 4: 130,092,782 probably null Het
Col4a1 C T 8: 11,226,439 probably benign Het
Coro2a T A 4: 46,548,797 I166F possibly damaging Het
Cry2 T C 2: 92,424,566 H148R probably damaging Het
Crygd T C 1: 65,061,974 Y154C probably benign Het
Cubn T C 2: 13,308,561 Y3066C probably damaging Het
Defb15 C T 8: 21,929,986 E42K possibly damaging Het
Dnah12 A G 14: 26,697,398 D147G probably benign Het
Dnah12 A T 14: 26,709,257 Y340F probably benign Het
Dot1l G T 10: 80,783,539 R193L probably damaging Het
Dupd1 A G 14: 21,686,689 V115A probably benign Het
Esd A C 14: 74,742,074 Y119S probably damaging Het
Esp36 A G 17: 38,419,439 probably benign Het
Etfbkmt T A 6: 149,144,151 M1K probably null Het
Exph5 A G 9: 53,376,248 H1543R probably benign Het
Fam92a C T 4: 12,155,717 V306I possibly damaging Het
Fbxo16 A G 14: 65,270,803 T23A probably damaging Het
Gm11492 A G 11: 87,567,235 H145R possibly damaging Het
Gm6614 T C 6: 142,003,423 M76V possibly damaging Het
Gorasp2 C A 2: 70,679,464 H136Q probably damaging Het
Hdc T A 2: 126,597,933 I367F probably benign Het
Hmcn1 C T 1: 150,638,900 V3574M probably benign Het
Ilvbl A G 10: 78,584,124 D592G probably benign Het
Inmt G A 6: 55,174,883 A34V probably damaging Het
Ints9 A C 14: 65,026,413 H378P probably benign Het
Kcnh7 T A 2: 62,787,754 I464L possibly damaging Het
Kcnt2 T A 1: 140,425,330 V259D probably damaging Het
Lipo1 A G 19: 33,784,692 F135S probably damaging Het
Lrba T C 3: 86,773,203 probably null Het
Mapk1 T A 16: 17,026,429 S22T probably benign Het
Mbd3l2 T C 9: 18,444,921 S181P possibly damaging Het
Mgat5 C T 1: 127,459,969 P554L probably damaging Het
Mki67 T C 7: 135,699,361 T1315A probably benign Het
Mprip C T 11: 59,758,221 T917M possibly damaging Het
Mroh3 T A 1: 136,185,988 I688F probably benign Het
Myo1d A T 11: 80,663,048 Y536N probably damaging Het
Neb C T 2: 52,162,187 probably null Het
Noc2l A G 4: 156,237,708 R161G probably benign Het
Nup93 T C 8: 94,306,102 F539L probably damaging Het
Olfr138 A G 17: 38,275,344 E191G probably damaging Het
Olfr417 T A 1: 174,369,452 H178Q probably damaging Het
Olfr480 A C 7: 108,066,725 Y24* probably null Het
Olfr874 T A 9: 37,746,968 M278K probably benign Het
Panx1 A T 9: 15,007,428 D378E probably damaging Het
Papss1 T A 3: 131,583,184 V170D possibly damaging Het
Pcnx T C 12: 81,918,732 S558P probably damaging Het
Pde3a T A 6: 141,250,353 I255N probably damaging Het
Pde3a G T 6: 141,487,513 A757S probably damaging Het
Pdzph1 A G 17: 58,922,583 Y1027H probably damaging Het
Pkhd1 G T 1: 20,551,020 R805S probably benign Het
Polr1a G A 6: 71,909,203 G14D probably damaging Het
Prg4 T A 1: 150,460,669 D60V probably damaging Het
Ptprc T C 1: 138,112,227 S311G probably benign Het
Rapgefl1 G A 11: 98,842,209 R205K probably benign Het
Rcan2 A T 17: 44,037,089 probably null Het
Rock1 A G 18: 10,079,207 I1087T probably damaging Het
Sectm1b A G 11: 121,054,942 I191T possibly damaging Het
Setd1b T C 5: 123,147,613 S241P unknown Het
Srpk2 T C 5: 23,524,150 K497R probably benign Het
Sspo T C 6: 48,491,006 S4296P probably damaging Het
Syne4 T C 7: 30,316,883 V168A probably benign Het
Tank T C 2: 61,649,912 F264S probably damaging Het
Ticrr T C 7: 79,695,207 S1607P probably damaging Het
Trim30a A G 7: 104,411,198 V457A probably damaging Het
Trim43b T A 9: 89,085,571 K336N probably damaging Het
Trim47 T C 11: 116,106,137 Q598R probably damaging Het
Tspan12 T C 6: 21,851,023 N18S probably damaging Het
Ubap2 A G 4: 41,221,607 S231P probably benign Het
Vit A G 17: 78,622,746 D380G probably damaging Het
Vmn2r2 T C 3: 64,134,521 N258D possibly damaging Het
Vmn2r52 C T 7: 10,173,406 C131Y possibly damaging Het
Zadh2 T C 18: 84,095,318 V373A possibly damaging Het
Zfp58 A T 13: 67,491,188 F395I probably damaging Het
Zfp940 C A 7: 29,845,010 G491C probably damaging Het
Other mutations in Nup54
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00491:Nup54 APN 5 92417485 missense probably benign 0.00
IGL01526:Nup54 APN 5 92417475 missense probably benign 0.12
IGL01924:Nup54 APN 5 92424435 missense probably benign 0.02
IGL02248:Nup54 APN 5 92428329 splice site probably null
IGL02253:Nup54 APN 5 92417451 critical splice donor site probably null
IGL02508:Nup54 APN 5 92417539 nonsense probably null
IGL02721:Nup54 APN 5 92417857 missense possibly damaging 0.96
IGL03150:Nup54 APN 5 92428164 missense probably damaging 1.00
R0189:Nup54 UTSW 5 92422564 missense probably damaging 1.00
R1401:Nup54 UTSW 5 92428221 missense probably damaging 1.00
R3938:Nup54 UTSW 5 92417529 missense probably damaging 1.00
R4171:Nup54 UTSW 5 92417484 missense possibly damaging 0.64
R4574:Nup54 UTSW 5 92425782 missense probably benign 0.17
R5372:Nup54 UTSW 5 92417857 missense probably damaging 1.00
R6003:Nup54 UTSW 5 92422994 missense probably damaging 1.00
R6191:Nup54 UTSW 5 92424294 missense probably damaging 0.99
R6197:Nup54 UTSW 5 92430804 utr 3 prime probably benign
R7861:Nup54 UTSW 5 92431093 missense unknown
R8005:Nup54 UTSW 5 92428147 missense probably benign 0.00
R8016:Nup54 UTSW 5 92434317 missense unknown
R8439:Nup54 UTSW 5 92425746 missense probably benign 0.22
R8709:Nup54 UTSW 5 92422408 intron probably benign
R9711:Nup54 UTSW 5 92434359 missense unknown
Z1177:Nup54 UTSW 5 92434279 missense unknown
Predicted Primers PCR Primer
(F):5'- TACTTTCTGAAACCAGGAATGGG -3'
(R):5'- CTTGGAATTAGGCTTGGACATG -3'

Sequencing Primer
(F):5'- CTGAAACCAGGAATGGGTAATTTTC -3'
(R):5'- ACATGTGGGTGTGCCTATTAAATAG -3'
Posted On 2014-06-23