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Gene

SMC3

structural maintenance of chromosomes 3

Summary

Cytogenetic location
10q25.2
Coordinates
Chromosome 10: 110,567,695–110,606,048 (GRCh38)
Exons
29 exons across 38.4 kb
Protein
1,217 amino acids
Also known as
HCAP, BAM, SMC3L1, bamacan
Previous symbols
CSPG6
MANE Select transcript
ENST00000361804.5NM_005445.4
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

  • Cornelia de Lange Syndrome

    • A developmental disorder caused by variants in NIPBL, SMC1A, SMC3, RAD21, HDAC8 or BRD4, with a wide range of severity.

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

      Diagnosis guides monitoring for associated problems such as reflux, heart defects, hearing and vision issues.

How SMC3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 10, with a bracket where SMC3 sits. SMC3 and 9 genes near it on chromosome 10, from 110,086,872 to 111,086,871.Chromosome 1010q25.2p15.3p15.2p15.1p14p13p12.33p12.32p12.31p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.31q23.32q23.33q24.1q24.2q24.31q24.32q24.33q25.1q25.2q25.3q26.11q26.12q26.13q26.2q26.3110.2 Mb110.4 Mb110.6 Mb110.8 Mb111 MbADD3: 109,996,347–110,135,565, forward strandADD3MXI1: 110,207,546–110,287,916, forward strandMXI1SMNDC1: 110,289,425–110,305,001, reverse strandSMNDC1DUSP5: 110,497,907–110,511,544, forward strandDUSP5SMC3: 110,567,695–110,606,048, forward strandSMC3RBM20: 110,643,874–110,839,471, forward strandRBM20PDCD4: 110,871,790–110,900,013, forward strandPDCD4BBIP1: 110,898,730–110,919,371, reverse strandBBIP1SHOC2: 110,917,932–111,017,314, forward strandSHOC2ADRA2A: 111,077,029–111,080,907, forward strandADRA2ADiagram of SMC3: 29 exons on the forward strand of chromosome 10Exon 6: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 9: 3 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 12: 1 known disease-causing siteExon 13: 2 known disease-causing sitesExon 14: 1 known disease-causing siteExon 15: 5 known disease-causing sitesExon 17: 1 known disease-causing siteExon 18: 5 known disease-causing sitesExon 19: 4 known disease-causing sitesExon 20: 1 known disease-causing siteExon 21: 3 known disease-causing sitesExon 22: 3 known disease-causing sitesExon 23: 1 known disease-causing siteExon 25: 4 known disease-causing sitesExon 27: 3 known disease-causing sitesExon 28: 1 known disease-causing siteExon 29: 1 known disease-causing siteExon 1: 110,567,695–110,567,831, 137 basesExon 2: 110,568,938–110,569,013, 76 basesExon 3: 110,573,707–110,573,745, 39 basesExon 4: 110,575,336–110,575,403, 68 basesExon 5: 110,577,421–110,577,492, 72 basesExon 6: 110,577,835–110,577,914, 80 basesExon 7: 110,578,628–110,578,706, 79 basesExon 8: 110,580,904–110,581,021, 118 basesExon 9: 110,581,923–110,582,098, 176 basesExon 10: 110,582,562–110,582,642, 81 basesExon 11: 110,583,384–110,583,548, 165 basesExon 12: 110,583,841–110,583,962, 122 basesExon 13: 110,584,183–110,584,396, 214 basesExon 14: 110,589,605–110,589,708, 104 basesExon 15: 110,589,892–110,589,991, 100 basesExon 16: 110,590,412–110,590,572, 161 basesExon 17: 110,590,991–110,591,132, 142 basesExon 18: 110,593,073–110,593,223, 151 basesExon 19: 110,596,398–110,596,550, 153 basesExon 20: 110,598,139–110,598,290, 152 basesExon 21: 110,599,654–110,599,812, 159 basesExon 22: 110,600,439–110,600,546, 108 basesExon 23: 110,601,022–110,601,130, 109 basesExon 24: 110,601,637–110,601,884, 248 basesExon 25: 110,601,966–110,602,178, 213 basesExon 26: 110,602,474–110,602,665, 192 basesExon 27: 110,602,825–110,603,002, 178 basesExon 28: 110,603,184–110,603,290, 107 basesExon 29: 110,604,231–110,606,048, 1,818 bases1510152025295′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 5.5 kb of the gene's 38.4 kb; 3,654 of those bases code for the protein.

How a genome test reads SMC3

45

positions in SMC3 where ClinVar classes a change as pathogenic or likely pathogenic

1 of them (2.2%) falls in a region short reads find hard.

  • Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 38.4 kb of SMC3, introns included, not only the 5.5 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.). SMC3 gene: structural maintenance of chromosomes 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/smc3

Vancouver

Dante Labs. SMC3 gene: structural maintenance of chromosomes 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/smc3

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