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Gene

SLX4

SLX4 structure-specific endonuclease subunit

Summary

Cytogenetic location
16p13.3
Coordinates
Chromosome 16: 3,581,181–3,611,606 (GRCh38)
Exons
15 exons across 30.4 kb
Protein
1,834 amino acids
Inheritance
Autosomal recessive
Also known as
KIAA1784, KIAA1987, FANCP
Previous symbols
BTBD12
MANE Select transcript
ENST00000294008.4NM_032444.4
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 reports relevant to this gene

  • DNA Repair Disease

    • Autosomal recessive

      A disease that has its basis in the disruption of DNA repair.

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

  • Fanconi Anemia

    • Autosomal recessive

      Fanconi anemia (FA) is a hereditary DNA repair disorder characterized by progressive pancytopenia with bone marrow failure, variable congenital malformations and predisposition to develop hematological or solid tumors.

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

      Hematopoietic stem cell transplantation using FA-specific reduced-intensity conditioning; androgens (oxymetholone) as bridge therapy; cancer surveillance for head/neck and gynecological malignancies; gene therapy in clinical trials

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 SLX4 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 16, with a bracket where SLX4 sits. SLX4 and 22 genes near it on chromosome 16, from 3,096,394 to 4,096,393.Chromosome 1616p13.3p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.33.2 Mb3.4 Mb3.6 Mb3.8 Mb4 MbZSCAN10: 3,088,888–3,099,370, reverse strandZSCAN10ZNF205: 3,112,550–3,120,527, forward strandZNF205ZNF213: 3,129,777–3,142,804, forward strandZNF213OR1F1: 3,188,204–3,224,779, forward strandOR1F1ZNF200: 3,222,324–3,236,221, reverse strandZNF200MEFV: 3,240,392–3,256,954, reverse strandMEFVZNF263: 3,263,800–3,301,705, forward strandZNF263TIGD7: 3,298,390–3,305,729, reverse strandTIGD7ZNF75A: 3,305,385–3,320,003, forward strandZNF75AOR2C1: 3,355,889–3,357,306, forward strandOR2C1: 3,365,099–3,479,550, forward strandZSCAN32: 3,382,081–3,401,483, reverse strandZSCAN32ZNF174: 3,401,194–3,409,478, forward strandZNF174ZNF597: 3,432,414–3,443,539, reverse strandZNF597NAA60: 3,443,623–3,486,961, forward strandNAA60C16orf90: 3,493,484–3,495,489, reverse strandC16orf90IFT38: 3,500,976–3,540,653, forward strandIFT38NLRC3: 3,538,090–3,577,403, reverse strandNLRC3SLX4: 3,581,181–3,611,606, reverse strandSLX4DNASE1: 3,611,678–3,680,143, forward strandDNASE1TRAP1: 3,651,639–3,717,595, reverse strandTRAP1CREBBP: 3,725,054–3,880,734, reverse strandCREBBPADCY9: 3,953,387–4,116,493, reverse strandADCY9Diagram of SLX4: 15 exons on the reverse strand of chromosome 16Exon 15: 3 known disease-causing sitesExon 14: 14 known disease-causing sitesExon 13: 3 known disease-causing sitesExon 12: 60 known disease-causing sitesExon 11: 1 known disease-causing siteExon 10: 4 known disease-causing sitesExon 9: 3 known disease-causing sitesExon 8: 6 known disease-causing sitesExon 7: 5 known disease-causing sitesExon 6: 2 known disease-causing sitesExon 5: 7 known disease-causing sitesExon 4: 3 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 2: 14 known disease-causing sitesExon 15: 3,581,181–3,582,693, 1,513 basesExon 14: 3,583,097–3,583,510, 414 basesExon 13: 3,584,769–3,584,871, 103 basesExon 12: 3,589,002–3,591,310, 2,309 basesExon 11: 3,592,699–3,592,865, 167 basesExon 10: 3,594,453–3,594,599, 147 basesExon 9: 3,595,605–3,595,693, 89 basesExon 8: 3,596,153–3,596,393, 241 basesExon 7: 3,597,379–3,597,695, 317 basesExon 6: 3,597,797–3,597,999, 203 basesExon 5: 3,600,979–3,601,191, 213 basesExon 4: 3,602,118–3,602,307, 190 basesExon 3: 3,606,474–3,606,698, 225 basesExon 2: 3,608,430–3,609,566, 1,137 basesExon 1: 3,611,560–3,611,606, 47 bases15141210864215′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 7.3 kb of the gene's 30.4 kb; 5,505 of those bases code for the protein.

How a genome test reads SLX4

139

positions in SLX4 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 30.4 kb of SLX4, introns included, not only the 7.3 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.). SLX4 gene: SLX4 structure-specific endonuclease subunit. Retrieved 16 October 2026, from https://dantelabs.com/genes/slx4

Vancouver

Dante Labs. SLX4 gene: SLX4 structure-specific endonuclease subunit [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/slx4

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