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Gene

NPM1

nucleophosmin 1

Summary

Cytogenetic location
5q35.1
Coordinates
Chromosome 5: 171,387,849–171,410,900 (GRCh38)
Exons
11 exons across 23.1 kb
Protein
294 amino acids
Also known as
B23, NPM
MANE Select transcript
ENST00000296930.10NM_002520.7
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Dyskeratosis Congenita

    • Dyskeratosis congenita (DC) is a rare ectodermal dysplasia that often presents with the classic triad of nail dysplasia, skin pigmentary changes, and oral leukoplakia associated with a high risk of bone marrow failure (BMF) and cancer.

      • 2 GenCC submitters rate it definitive or strong

How NPM1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 5, with a bracket where NPM1 sits. NPM1 and 5 genes near it on chromosome 5, from 170,899,375 to 171,899,374.Chromosome 55q35.1p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.3171 Mb171.2 Mb171.4 Mb171.6 Mb171.8 MbRANBP17: 170,861,855–171,300,015, forward strandRANBP17TLX3: 171,309,191–171,312,139, forward strandTLX3NPM1: 171,387,849–171,410,900, forward strandNPM1FGF18: 171,419,637–171,457,626, forward strandFGF18SMIM23: 171,782,432–171,796,126, forward strandSMIM23FBXW11: 171,844,094–172,006,907, reverse strandFBXW11Diagram of NPM1: 11 exons on the forward strand of chromosome 5Exon 11: 1 known disease-causing siteExon 1: 171,387,849–171,388,006, 158 basesExon 2: 171,390,051–171,390,130, 80 basesExon 3: 171,391,305–171,391,424, 120 basesExon 4: 171,391,706–171,391,799, 94 basesExon 5: 171,392,710–171,392,816, 107 basesExon 6: 171,392,914–171,392,978, 65 basesExon 7: 171,400,153–171,400,210, 58 basesExon 8: 171,400,839–171,400,925, 87 basesExon 9: 171,405,302–171,405,403, 102 basesExon 10: 171,407,700–171,407,774, 75 basesExon 11: 171,410,527–171,410,900, 374 bases1246810115′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 1.3 kb of the gene's 23.1 kb; 885 of those bases code for the protein.

How a genome test reads NPM1

1

position in NPM1 where ClinVar classes a change as pathogenic or likely pathogenic

1 of them (100%) falls in a region short reads find hard.

  • Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 23.1 kb of NPM1, introns included, not only the 1.3 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). NPM1 gene: nucleophosmin 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/npm1

Vancouver

Dante Labs. NPM1 gene: nucleophosmin 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/npm1

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