Incidental Mutation 'R3966:Npm1'
ID 312358
Institutional Source Beutler Lab
Gene Symbol Npm1
Ensembl Gene ENSMUSG00000057113
Gene Name nucleophosmin 1
Synonyms B23, nucleolar protein NO38, NO38
MMRRC Submission 040935-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R3966 (G1)
Quality Score 184
Status Validated
Chromosome 11
Chromosomal Location 33102287-33113206 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 33110350 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glycine to Aspartic acid at position 148 (G148D)
Ref Sequence ENSEMBL: ENSMUSP00000098926 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000075641] [ENSMUST00000093201] [ENSMUST00000101375] [ENSMUST00000109354]
AlphaFold Q61937
Predicted Effect probably benign
Transcript: ENSMUST00000075641
AA Change: G148D

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000075067
Gene: ENSMUSG00000057113
AA Change: G148D

DomainStartEndE-ValueType
Pfam:Nucleoplasmin 15 193 8.7e-73 PFAM
Pfam:NPM1-C 243 291 1.8e-37 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000093201
AA Change: G148D

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000090891
Gene: ENSMUSG00000057113
AA Change: G148D

DomainStartEndE-ValueType
Pfam:Nucleoplasmin 13 195 6.1e-58 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000101375
AA Change: G148D

PolyPhen 2 Score 0.271 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000098926
Gene: ENSMUSG00000057113
AA Change: G148D

DomainStartEndE-ValueType
Pfam:Nucleoplasmin 15 193 1e-72 PFAM
PDB:2LLH|A 223 255 2e-13 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000109354
AA Change: G148D

PolyPhen 2 Score 0.029 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000104978
Gene: ENSMUSG00000057113
AA Change: G148D

DomainStartEndE-ValueType
Pfam:Nucleoplasmin 13 195 5e-58 PFAM
PDB:2LLH|A 223 255 1e-13 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146759
Meta Mutation Damage Score 0.0638 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.1%
Validation Efficiency 96% (47/49)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a phosphoprotein which moves between the nucleus and the cytoplasm. The gene product is thought to be involved in several processes including regulation of the ARF/p53 pathway. A number of genes are fusion partners have been characterized, in particular the anaplastic lymphoma kinase gene on chromosome 2. Mutations in this gene are associated with acute myeloid leukemia. More than a dozen pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Nov 2009]
PHENOTYPE: Homozygous mutation of this gene results in embryonic lethality, anemia, defects in primitive hematopoeisis and abnormal brain development. Heterozygous mutation results in hematopoeisis defects and chromosomal instability. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agap1 T C 1: 89,762,183 (GRCm39) I371T probably damaging Het
Brwd1 G A 16: 95,845,730 (GRCm39) T731I probably damaging Het
C1galt1c1 A T X: 37,720,453 (GRCm39) V181E probably benign Het
C3 A G 17: 57,525,664 (GRCm39) V864A probably damaging Het
Cadps A T 14: 12,522,161 (GRCm38) probably null Het
Cemip T A 7: 83,600,717 (GRCm39) Y968F probably benign Het
Ces1g C A 8: 94,055,139 (GRCm39) R186L possibly damaging Het
Chd2 A G 7: 73,114,143 (GRCm39) probably benign Het
Clptm1l T C 13: 73,764,091 (GRCm39) Y404H probably damaging Het
CN725425 T A 15: 91,126,890 (GRCm39) probably null Het
Ctc1 T A 11: 68,921,954 (GRCm39) V800D probably damaging Het
Cyp1a1 T A 9: 57,607,432 (GRCm39) V20D probably benign Het
E330034G19Rik G T 14: 24,356,939 (GRCm39) M158I unknown Het
Ehbp1l1 C T 19: 5,760,601 (GRCm39) probably null Het
Gm14137 T A 2: 119,005,497 (GRCm39) S19T probably benign Het
Gpr141b A G 13: 19,913,614 (GRCm39) noncoding transcript Het
Gprc6a CAAA CA 10: 51,491,776 (GRCm39) probably null Het
Inhbb C A 1: 119,345,291 (GRCm39) G333W probably damaging Het
Kcnb1 C T 2: 166,946,412 (GRCm39) C812Y probably damaging Het
Kdm4c A G 4: 74,216,820 (GRCm39) D193G probably damaging Het
Mbd5 A T 2: 49,162,082 (GRCm39) I855L possibly damaging Het
Mcpt1 G A 14: 56,256,503 (GRCm39) V80M probably benign Het
Med31 C T 11: 72,102,755 (GRCm39) A118T probably benign Het
Megf10 A G 18: 57,313,646 (GRCm39) D30G probably damaging Het
Ms4a6b T C 19: 11,499,098 (GRCm39) S71P probably benign Het
Muc2 G A 7: 141,286,233 (GRCm39) R120H probably benign Het
Mycbp2 A G 14: 103,376,161 (GRCm39) probably benign Het
Myrf T C 19: 10,196,979 (GRCm39) E267G probably benign Het
Ncor1 T C 11: 62,235,583 (GRCm39) T624A probably damaging Het
Nfat5 G T 8: 108,093,921 (GRCm39) A721S possibly damaging Het
Nfatc2 C T 2: 168,346,469 (GRCm39) S875N probably benign Het
Nrap T C 19: 56,330,576 (GRCm39) S1126G probably damaging Het
Nucb2 A G 7: 116,128,110 (GRCm39) E273G probably damaging Het
Prkd1 C T 12: 50,439,724 (GRCm39) E368K probably benign Het
Ptgs2 T A 1: 149,981,226 (GRCm39) I503N probably damaging Het
Qrfpr A G 3: 36,235,149 (GRCm39) S243P possibly damaging Het
Safb2 T C 17: 56,882,356 (GRCm39) S426G probably null Het
Sos1 C T 17: 80,762,608 (GRCm39) R73H probably damaging Het
Spink10 T C 18: 62,790,975 (GRCm39) I87T probably damaging Het
Tet2 A G 3: 133,193,418 (GRCm39) S339P possibly damaging Het
Timd5 T A 11: 46,426,340 (GRCm39) V149D possibly damaging Het
Tmx4 T C 2: 134,441,981 (GRCm39) I206V possibly damaging Het
Tom1 A G 8: 75,785,867 (GRCm39) K360E probably benign Het
Trp73 A G 4: 154,146,493 (GRCm39) V422A probably benign Het
Vmn2r33 T C 7: 7,557,168 (GRCm39) M511V probably benign Het
Zfp628 T C 7: 4,924,744 (GRCm39) S989P probably benign Het
Other mutations in Npm1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03233:Npm1 APN 11 33,106,717 (GRCm39) missense probably benign 0.24
R3959:Npm1 UTSW 11 33,104,012 (GRCm39) missense probably damaging 1.00
R7895:Npm1 UTSW 11 33,106,001 (GRCm39) critical splice donor site probably null
V5622:Npm1 UTSW 11 33,111,186 (GRCm39) missense probably benign 0.39
Z1176:Npm1 UTSW 11 33,110,831 (GRCm39) missense probably benign 0.03
Predicted Primers PCR Primer
(F):5'- TGGTGATTAGCCAAAGTAAATGCC -3'
(R):5'- GGACTGTCGTAGTTCTACAAAGACC -3'

Sequencing Primer
(F):5'- TGGAACTCACTTTGTAGACCAC -3'
(R):5'- GTTCTACAAAGACCTGATTTCTGTC -3'
Posted On 2015-04-29