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Gene

SCP2

sterol carrier protein 2

Summary

Cytogenetic location
1p32.3
Coordinates
Chromosome 1: 52,927,276–53,051,698 (GRCh38)
Exons
16 exons across 124.4 kb
Protein
547 amino acids
Also known as
nsLTP, SCPx, SCP-X
MANE Select transcript
ENST00000371514.8NM_002979.5
Locus type
gene with protein product

Reference genomeGRCh38

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

Curated report relevant to this gene

    • Other Inherited Leukodystrophies

      • Leukodystrophy (other and unspecified types)

        One of 80 genes linked to it

        Inherited conditions that damage or prevent the normal formation of myelin, the white matter of the brain and spinal cord. Different types follow autosomal recessive, autosomal dominant or X-linked inheritance depending on the gene involved.

        • ClinGen rates the link definitive
        • 2 GenCC submitters rate it definitive or strong
        What knowing changes

        Knowing the specific genetic cause can end a diagnostic search, guide supportive care and surveillance, show whether a specific treatment exists, and allow testing of relatives.

    How SCP2 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 1, with a bracket where SCP2 sits. SCP2 and 15 genes near it on chromosome 1, from 52,489,487 to 53,489,486.Chromosome 11p32.3p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q4452.6 Mb52.8 Mb53 Mb53.2 Mb53.4 MbTUT4: 52,408,282–52,553,504, reverse strandTUT4GPX7: 52,602,280–52,609,143, forward strandGPX7SHISAL2A: 52,633,168–52,670,143, forward strandSHISAL2ACOA7: 52,662,885–52,698,369, reverse strandCOA7ZYG11B: 52,726,390–52,827,336, forward strandZYG11BZYG11A: 52,842,511–52,894,998, forward strandZYG11AECHDC2: 52,895,910–52,927,212, reverse strandECHDC2SCP2: 52,927,276–53,051,698, forward strandSCP2PODN: 53,061,293–53,093,681, forward strandPODNSLC1A7: 53,087,179–53,142,638, reverse strandSLC1A7CPT2: 53,196,770–53,214,197, forward strandCPT2CZIB: 53,214,099–53,220,657, reverse strandCZIBMAGOH: 53,226,638–53,238,626, reverse strandMAGOHLRP8: 53,242,364–53,328,469, reverse strandLRP8: 53,413,149–53,440,018, reverse strandDMRTB1: 53,459,391–53,467,488, forward strandDMRTB1Diagram of SCP2: 16 exons on the forward strand of chromosome 1Exon 8: 1 known disease-causing siteExon 12: 1 known disease-causing siteExon 1: 52,927,276–52,927,465, 190 basesExon 2: 52,941,796–52,941,853, 58 basesExon 3: 52,948,009–52,948,080, 72 basesExon 4: 52,950,755–52,950,886, 132 basesExon 5: 52,954,740–52,954,804, 65 basesExon 6: 52,961,503–52,961,629, 127 basesExon 7: 52,974,769–52,974,832, 64 basesExon 8: 52,976,683–52,976,769, 87 basesExon 9: 52,978,217–52,978,367, 151 basesExon 10: 52,980,396–52,980,543, 148 basesExon 11: 52,988,029–52,988,136, 108 basesExon 12: 53,014,890–53,015,043, 154 basesExon 13: 53,027,969–53,028,071, 103 basesExon 14: 53,038,917–53,039,046, 130 basesExon 15: 53,047,858–53,047,937, 80 basesExon 16: 53,050,609–53,051,698, 1,090 bases12468101214165′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 2.8 kb of the gene's 124.4 kb; 1,644 of those bases code for the protein.

    How a genome test reads SCP2

    5

    positions in SCP2 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 124.4 kb of SCP2, introns included, not only the 2.8 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.). SCP2 gene: sterol carrier protein 2. Retrieved 16 October 2026, from https://dantelabs.com/genes/scp2

    Vancouver

    Dante Labs. SCP2 gene: sterol carrier protein 2 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/scp2

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