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Gene

NT5C2

5'-nucleotidase, cytosolic II

Summary

Cytogenetic location
10q24.32-q24.33
Coordinates
Chromosome 10: 103,088,038–103,193,272 (GRCh38)
Exons
19 exons across 105.2 kb
Protein
561 amino acids
Also known as
PNT5, GMP, cN-II, SPG65
Previous symbols
NT5B, SPG45
MANE Select transcript
ENST00000404739.8NM_001351169.2
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

    • Hereditary Spastic Paraplegia

      • Hereditary Spastic Paraplegia (All Types)

        One of 66 genes linked to it

        Umbrella term covering all hereditary spastic paraplegias, including SPG4 (SPAST), the most common dominant form, and SPG5A, SPG6, SPG10, SPG18, SPG30 and SPG31.

        • ClinGen rates the link definitive
        • 3 GenCC submitters rate it definitive or strong

    How NT5C2 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 10, with a bracket where NT5C2 sits. NT5C2 and 20 genes near it on chromosome 10, from 102,640,655 to 103,640,654.Chromosome 1010q24.32-q24.33p15.3p15.2p15.1p14p13p12.33p12.32p12.31p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.31q23.32q23.33q24.1q24.2q24.31q24.32q24.33q25.1q25.2q25.3q26.11q26.12q26.13q26.2q26.3102.8 Mb103 Mb103.2 Mb103.4 Mb103.6 MbTRIM8: 102,642,394–102,662,789, forward strandTRIM8ARL3: 102,673,731–102,714,527, reverse strandARL3SFXN2: 102,714,476–102,743,492, forward strandSFXN2WBP1L: 102,743,923–102,834,613, forward strandWBP1LCYP17A1: 102,830,460–102,837,506, reverse strandCYP17A1BORCS7: 102,854,224–102,864,979, forward strandBORCS7BORCS7-ASMT: 102,854,272–102,901,899, forward strandBORCS7-ASMTAS3MT: 102,869,296–102,901,911, forward strandAS3MTCNNM2: 102,918,123–103,090,222, forward strandCNNM2NT5C2: 103,088,038–103,193,272, reverse strandNT5C2RPEL1: 103,245,887–103,248,016, forward strandRPEL1INA: 103,277,082–103,290,351, forward strandINAPCGF6: 103,302,796–103,351,150, reverse strandPCGF6TAF5: 103,367,948–103,389,323, forward strandTAF5ATP5MK: 103,388,974–103,396,492, reverse strandATP5MKPDCD11: 103,396,602–103,446,297, forward strandPDCD11CALHM2: 103,446,777–103,452,780, reverse strandCALHM2CALHM1: 103,453,240–103,458,900, reverse strandCALHM1CALHM3: 103,472,804–103,479,240, reverse strandCALHM3NEURL1: 103,493,592–103,595,168, forward strandNEURL1SH3PXD2A: 103,594,027–103,855,773, reverse strandSH3PXD2ADiagram of NT5C2: 19 exons on the reverse strand of chromosome 10Exon 19: 2 known disease-causing sitesExon 18: 2 known disease-causing sitesExon 16: 1 known disease-causing siteExon 15: 3 known disease-causing sitesExon 10: 1 known disease-causing siteExon 9: 2 known disease-causing sitesExon 8: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 19: 103,088,038–103,089,908, 1,871 basesExon 18: 103,090,611–103,090,787, 177 basesExon 17: 103,090,936–103,090,996, 61 basesExon 16: 103,091,564–103,091,615, 52 basesExon 15: 103,093,139–103,093,309, 171 basesExon 14: 103,093,972–103,094,038, 67 basesExon 13: 103,094,348–103,094,455, 108 basesExon 12: 103,095,939–103,095,980, 42 basesExon 11: 103,097,291–103,097,374, 84 basesExon 10: 103,098,931–103,098,984, 54 basesExon 9: 103,099,926–103,100,019, 94 basesExon 8: 103,101,045–103,101,102, 58 basesExon 7: 103,101,235–103,101,326, 92 basesExon 6: 103,105,706–103,105,801, 96 basesExon 5: 103,106,589–103,106,706, 118 basesExon 4: 103,139,406–103,139,479, 74 basesExon 3: 103,174,858–103,174,982, 125 basesExon 2: 103,181,185–103,181,328, 144 basesExon 1: 103,193,236–103,193,272, 37 bases191510515′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 3.5 kb of the gene's 105.2 kb; 1,686 of those bases code for the protein.

    How a genome test reads NT5C2

    22

    positions in NT5C2 where ClinVar classes a change as pathogenic or likely pathogenic

    None of them falls in a region short reads find hard.

    A whole genome covers all 105.2 kb of NT5C2, introns included, not only the 3.5 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.). NT5C2 gene: 5'-nucleotidase, cytosolic II. Retrieved 16 October 2026, from https://dantelabs.com/genes/nt5c2

    Vancouver

    Dante Labs. NT5C2 gene: 5'-nucleotidase, cytosolic II [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/nt5c2

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