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Gene

SMARCAL1

SNF2 related chromatin remodeling annealing helicase 1

Summary

Cytogenetic location
2q35
Coordinates
Chromosome 2: 216,412,484–216,483,053 (GRCh38)
Exons
18 exons across 70.6 kb
Protein
954 amino acids
Inheritance
Autosomal recessive
Also known as
HHARP, HARP
MANE Select transcript
ENST00000357276.9NM_014140.4
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

  • Immuno-Osseous Dysplasias

    • Immuno-osseous dysplasiaAutosomal recessive

      A group of conditions, including cartilage-hair hypoplasia (RMRP) and Schimke immuno-osseous dysplasia (SMARCAL1), that combine skeletal dysplasia with immune deficiency.

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

      Knowing the diagnosis guides avoidance of live vaccines, infection prevention and monitoring of the kidneys, blood counts and cancer risk.

Broader groupings

  • Other Inborn Errors of Immunity

    • Inborn error of immunity

      One of 114 genes linked to it

      Inherited disorders of the immune system caused by changes in single genes, affecting how the body fights infection or regulates inflammation.

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

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 SMARCAL1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where SMARCAL1 sits. SMARCAL1 and 9 genes near it on chromosome 2, from 215,947,769 to 216,947,768.Chromosome 22q35p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3216 Mb216.2 Mb216.4 Mb216.6 Mb216.8 MbMREG: 215,942,584–216,034,096, reverse strandMREGPECR: 215,954,720–216,082,955, reverse strandPECRTMEM169: 216,081,866–216,102,783, forward strandTMEM169XRCC5: 216,107,464–216,207,528, forward strandXRCC5MARCHF4: 216,257,865–216,372,483, reverse strandMARCHF4SMARCAL1: 216,412,484–216,483,053, forward strandSMARCAL1RPL37A: 216,498,797–216,580,097, forward strandRPL37AIGFBP2: 216,632,828–216,664,454, forward strandIGFBP2IGFBP5: 216,672,105–216,695,549, reverse strandIGFBP5TNP1: 216,859,458–216,865,732, reverse strandTNP1Diagram of SMARCAL1: 18 exons on the forward strand of chromosome 2Exon 3: 38 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 5: 9 known disease-causing sitesExon 6: 4 known disease-causing sitesExon 7: 10 known disease-causing sitesExon 8: 5 known disease-causing sitesExon 9: 10 known disease-causing sitesExon 10: 4 known disease-causing sitesExon 11: 7 known disease-causing sitesExon 12: 15 known disease-causing sitesExon 13: 3 known disease-causing sitesExon 14: 3 known disease-causing sitesExon 15: 8 known disease-causing sitesExon 16: 5 known disease-causing sitesExon 17: 3 known disease-causing sitesExon 1: 216,412,484–216,412,648, 165 basesExon 2: 216,413,856–216,413,892, 37 basesExon 3: 216,414,647–216,415,515, 869 basesExon 4: 216,416,257–216,416,307, 51 basesExon 5: 216,420,299–216,420,532, 234 basesExon 6: 216,423,633–216,423,683, 51 basesExon 7: 216,428,596–216,428,782, 187 basesExon 8: 216,432,718–216,432,868, 151 basesExon 9: 216,435,338–216,435,496, 159 basesExon 10: 216,438,420–216,438,485, 66 basesExon 11: 216,447,018–216,447,158, 141 basesExon 12: 216,450,846–216,451,064, 219 basesExon 13: 216,464,597–216,464,667, 71 basesExon 14: 216,467,944–216,468,046, 103 basesExon 15: 216,475,269–216,475,451, 183 basesExon 16: 216,477,109–216,477,209, 101 basesExon 17: 216,478,203–216,478,299, 97 basesExon 18: 216,482,738–216,483,053, 316 bases1246810121416185′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 3.2 kb of the gene's 70.6 kb; 2,865 of those bases code for the protein.

How a genome test reads SMARCAL1

145

positions in SMARCAL1 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 70.6 kb of SMARCAL1, introns included, not only the 3.2 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.). SMARCAL1 gene: SNF2 related chromatin remodeling annealing helicase 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/smarcal1

Vancouver

Dante Labs. SMARCAL1 gene: SNF2 related chromatin remodeling annealing helicase 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/smarcal1

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