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Gene

KPNA3

karyopherin subunit alpha 3

Summary

Cytogenetic location
13q14.2
Coordinates
Chromosome 13: 49,699,320–49,792,682 (GRCh38)
Exons
17 exons across 93.4 kb
Protein
521 amino acids
Also known as
SRP1gamma, SRP4, hSRP1, IPOA4
MANE Select transcript
ENST00000261667.8NM_002267.4
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.

        • 2 GenCC submitters rate it definitive or strong

    How KPNA3 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 13, with a bracket where KPNA3 sits. KPNA3 and 10 genes near it on chromosome 13, from 49,246,001 to 50,246,000.Chromosome 1313q14.2p13p12p11.2p11.1q11q12.11q12.12q12.13q12.2q12.3q13.1q13.2q13.3q14.11q14.12q14.13q14.2q14.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q3449.4 Mb49.6 Mb49.8 Mb50 Mb50.2 MbCDADC1: 49,247,863–49,293,490, forward strandCDADC1CAB39L: 49,308,629–49,444,342, reverse strandCAB39LSETDB2: 49,443,794–49,495,003, forward strandSETDB2PHF11: 49,495,095–49,528,989, forward strandPHF11RCBTB1: 49,531,939–49,586,740, reverse strandRCBTB1ARL11: 49,628,464–49,634,842, forward strandARL11EBPL: 49,660,674–49,691,613, reverse strandEBPLKPNA3: 49,699,320–49,792,682, reverse strandKPNA3SPRYD7: 49,912,702–49,936,513, reverse strandSPRYD7TRIM13: 49,935,920–50,020,481, forward strandTRIM13KCNRG: 50,015,254–50,022,365, forward strandKCNRGDiagram of KPNA3: 17 exons on the reverse strand of chromosome 13Exon 13: 1 known disease-causing siteExon 17: 49,699,320–49,701,898, 2,579 basesExon 16: 49,702,386–49,702,480, 95 basesExon 15: 49,705,621–49,705,783, 163 basesExon 14: 49,706,098–49,706,169, 72 basesExon 13: 49,706,268–49,706,372, 105 basesExon 12: 49,709,572–49,709,700, 129 basesExon 11: 49,710,891–49,711,022, 132 basesExon 10: 49,719,775–49,719,819, 45 basesExon 9: 49,721,955–49,722,124, 170 basesExon 8: 49,722,477–49,722,563, 87 basesExon 7: 49,725,416–49,725,501, 86 basesExon 6: 49,732,371–49,732,466, 96 basesExon 5: 49,732,605–49,732,657, 53 basesExon 4: 49,732,747–49,732,776, 30 basesExon 3: 49,732,957–49,733,046, 90 basesExon 2: 49,746,949–49,746,993, 45 basesExon 1: 49,792,438–49,792,682, 245 bases171510515′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 4.2 kb of the gene's 93.4 kb; 1,566 of those bases code for the protein.

    How a genome test reads KPNA3

    1

    position in KPNA3 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 93.4 kb of KPNA3, introns included, not only the 4.2 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.). KPNA3 gene: karyopherin subunit alpha 3. Retrieved 16 October 2026, from https://dantelabs.com/genes/kpna3

    Vancouver

    Dante Labs. KPNA3 gene: karyopherin subunit alpha 3 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/kpna3

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