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Gene

ABCA1

ATP binding cassette subfamily A member 1

Summary

Cytogenetic location
9q31.1
Coordinates
Chromosome 9: 104,781,006–104,928,155 (GRCh38)
Exons
50 exons across 147.2 kb
Protein
2,261 amino acids
Also known as
TGD
Previous symbols
ABC1, HDLDT1
MANE Select transcript
ENST00000374736.8NM_005502.4
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

  • Hereditary Hypolipoproteinemias

    • Hypoalphalipoproteinemia

      Includes Tangier disease (ABCA1), LCAT deficiency including fish-eye disease, and apolipoprotein A-I deficiency (APOA1), which cause very low HDL cholesterol and can lead to corneal clouding, kidney disease, nerve problems or early heart disease.

      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing explains very low HDL results and supports kidney, eye and cardiovascular monitoring.

How ABCA1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 9, with a bracket where ABCA1 sits. ABCA1 and 11 genes near it on chromosome 9, from 104,354,581 to 105,354,580.Chromosome 99q31.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q13q21.11q21.12q21.13q21.2q21.31q21.32q21.33q22.1q22.2q22.31q22.32q22.33q31.1q31.2q31.3q32q33.1q33.2q33.3q34.11q34.12q34.13q34.2q34.3104.4 Mb104.6 Mb104.8 Mb105 Mb105.2 MbOR13F1: 104,504,263–104,505,222, forward strandOR13F1OR13C4: 104,526,253–104,527,209, reverse strandOR13C4OR13C3: 104,535,749–104,536,856, reverse strandOR13C3OR13C8: 104,569,168–104,570,130, forward strandOR13C8OR13C5: 104,598,457–104,599,413, reverse strandOR13C5OR13C2: 104,604,671–104,605,627, reverse strandOR13C2OR13C9: 104,617,248–104,618,204, reverse strandOR13C9OR13D1: 104,694,518–104,695,462, forward strandOR13D1NIPSNAP3A: 104,747,664–104,760,369, forward strandNIPSNAP3ANIPSNAP3B: 104,763,727–104,777,764, forward strandNIPSNAP3BABCA1: 104,781,006–104,928,155, reverse strandABCA1SLC44A1: 105,244,519–105,439,873, forward strandSLC44A1Diagram of ABCA1: 50 exons on the reverse strand of chromosome 9Exon 47: 1 known disease-causing siteExon 40: 2 known disease-causing sitesExon 38: 1 known disease-causing siteExon 32: 1 known disease-causing siteExon 22: 1 known disease-causing siteExon 19: 1 known disease-causing siteExon 16: 1 known disease-causing siteExon 15: 1 known disease-causing siteExon 14: 1 known disease-causing siteExon 12: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 50: 104,781,006–104,784,455, 3,450 basesExon 49: 104,785,396–104,785,639, 244 basesExon 48: 104,786,298–104,786,390, 93 basesExon 47: 104,786,873–104,786,976, 104 basesExon 46: 104,787,920–104,788,054, 135 basesExon 45: 104,788,426–104,788,567, 142 basesExon 44: 104,790,922–104,791,028, 107 basesExon 43: 104,791,936–104,791,998, 63 basesExon 42: 104,792,786–104,792,906, 121 basesExon 41: 104,793,171–104,793,300, 130 basesExon 40: 104,794,387–104,794,510, 124 basesExon 39: 104,796,053–104,796,197, 145 basesExon 38: 104,796,309–104,796,424, 116 basesExon 37: 104,798,421–104,798,598, 178 basesExon 36: 104,799,819–104,799,988, 170 basesExon 35: 104,800,510–104,800,584, 75 basesExon 34: 104,802,054–104,802,159, 106 basesExon 33: 104,803,284–104,803,316, 33 basesExon 32: 104,804,626–104,804,720, 95 basesExon 31: 104,806,241–104,806,430, 190 basesExon 30: 104,809,466–104,809,564, 99 basesExon 29: 104,810,800–104,810,924, 125 basesExon 28: 104,812,574–104,812,722, 149 basesExon 27: 104,814,118–104,814,231, 114 basesExon 26: 104,814,427–104,814,475, 49 basesExon 25: 104,816,143–104,816,345, 203 basesExon 24: 104,817,332–104,817,404, 73 basesExon 23: 104,818,663–104,818,883, 221 basesExon 22: 104,819,586–104,819,723, 138 basesExon 21: 104,819,927–104,820,069, 143 basesExon 20: 104,821,375–104,821,506, 132 basesExon 19: 104,822,496–104,822,667, 172 basesExon 18: 104,824,465–104,824,578, 114 basesExon 17: 104,825,683–104,825,887, 205 basesExon 16: 104,826,948–104,827,169, 222 basesExon 15: 104,828,916–104,829,138, 223 basesExon 14: 104,830,925–104,831,101, 177 basesExon 13: 104,831,622–104,831,827, 206 basesExon 12: 104,832,574–104,832,771, 198 basesExon 11: 104,836,980–104,837,096, 117 basesExon 10: 104,837,428–104,837,567, 140 basesExon 9: 104,840,279–104,840,519, 241 basesExon 8: 104,845,477–104,845,569, 93 basesExon 7: 104,858,522–104,858,698, 177 basesExon 6: 104,861,679–104,861,800, 122 basesExon 5: 104,883,039–104,883,157, 119 basesExon 4: 104,884,427–104,884,568, 142 basesExon 3: 104,889,102–104,889,195, 94 basesExon 2: 104,903,614–104,903,771, 158 basesExon 1: 104,927,935–104,928,155, 221 bases504540353025201510515′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 10.4 kb of the gene's 147.2 kb; 6,786 of those bases code for the protein.

How a genome test reads ABCA1

15

positions in ABCA1 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 147.2 kb of ABCA1, introns included, not only the 10.4 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.). ABCA1 gene: ATP binding cassette subfamily A member 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/abca1

Vancouver

Dante Labs. ABCA1 gene: ATP binding cassette subfamily A member 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/abca1

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