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Gene

SIL1

SIL1 nucleotide exchange factor

Summary

Cytogenetic location
5q31.2
Coordinates
Chromosome 5: 138,946,724–139,198,368 (GRCh38)
Exons
10 exons across 251.6 kb
Protein
461 amino acids
Inheritance
Autosomal recessive
Also known as
BAP, ULG5
Previous symbols
MSS
MANE Select transcript
ENST00000394817.7NM_022464.5
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

    • Autosomal Recessive Cerebellar Ataxias (incl. CANVAS and AVED)

      • Autosomal Recessive Cerebellar AtaxiaAutosomal recessive

        One of 57 genes linked to it

        A group of recessively inherited ataxias caused by biallelic variants in genes such as RFC1, FXN, SACS, TTPA, SETX, APTX, PNKP, ANO10 and SYNE1.

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

        Ataxia with vitamin E deficiency (TTPA) is treatable with vitamin E supplements; other forms are managed with physiotherapy and symptom care, and relatives can be offered carrier testing.

    Inheritance

    Autosomal recessive
    It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

    How SIL1 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 SIL1 sits. SIL1 and 15 genes near it on chromosome 5, from 138,572,546 to 139,572,545.Chromosome 55q31.2p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.3138.6 Mb138.8 Mb139 Mb139.2 Mb139.4 MbHSPA9: 138,553,756–138,575,675, reverse strandHSPA9CTNNA1: 138,610,967–138,935,039, forward strandCTNNA1LRRTM2: 138,868,921–138,875,383, reverse strandLRRTM2SIL1: 138,946,724–139,198,368, reverse strandSIL1MATR3: 139,273,752–139,332,518, forward strandMATR3PAIP2: 139,341,587–139,369,733, forward strandPAIP2SLC23A1: 139,366,642–139,385,495, reverse strandSLC23A1MZB1: 139,387,467–139,390,081, reverse strandMZB1PROB1: 139,390,592–139,395,104, reverse strandPROB1SPATA24: 139,396,563–139,404,094, reverse strandDNAJC18: 139,408,588–139,444,491, reverse strand: 139,442,316–139,462,707, reverse strandECSCR: 139,446,541–139,462,751, reverse strandECSCRSMIM33: 139,471,004–139,474,650, forward strandSMIM33STING1: 139,475,528–139,482,935, reverse strandUBE2D2: 139,526,431–139,633,291, forward strandUBE2D2Diagram of SIL1: 10 exons on the reverse strand of chromosome 5Exon 10: 7 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 8: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 6: 2 known disease-causing sitesExon 4: 1 known disease-causing siteExon 3: 5 known disease-causing sitesExon 2: 1 known disease-causing siteExon 10: 138,946,724–138,947,473, 750 basesExon 9: 138,951,171–138,951,335, 165 basesExon 8: 138,951,788–138,951,884, 97 basesExon 7: 139,021,171–139,021,292, 122 basesExon 6: 139,026,801–139,026,992, 192 basesExon 5: 139,042,620–139,042,719, 100 basesExon 4: 139,050,938–139,051,046, 109 basesExon 3: 139,121,035–139,121,173, 139 basesExon 2: 139,127,739–139,127,853, 115 basesExon 1: 139,198,269–139,198,368, 100 bases10515′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 1.9 kb of the gene's 251.6 kb; 1,386 of those bases code for the protein.

    How a genome test reads SIL1

    27

    positions in SIL1 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 251.6 kb of SIL1, introns included, not only the 1.9 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.). SIL1 gene: SIL1 nucleotide exchange factor. Retrieved 16 October 2026, from https://dantelabs.com/genes/sil1

    Vancouver

    Dante Labs. SIL1 gene: SIL1 nucleotide exchange factor [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/sil1

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