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Gene

HSPG2

heparan sulfate proteoglycan 2

Summary

Cytogenetic location
1p36.12
Coordinates
Chromosome 1: 21,822,244–21,937,310 (GRCh38)
Exons
97 exons across 115.1 kb
Protein
4,391 amino acids
Also known as
perlecan, PRCAN
Previous symbols
SJS1
MANE Select transcript
ENST00000374695.8NM_005529.7
Locus type
gene with protein product

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

No Genome Test report reads HSPG2 yet. The test sequences your whole genome, so your data includes it all the same.

How HSPG2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 1, with a bracket where HSPG2 sits. HSPG2 and 11 genes near it on chromosome 1, from 21,379,777 to 22,379,776.Chromosome 11p36.12p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q4421.4 Mb21.6 Mb21.8 Mb22 Mb22.2 MbNBPF3: 21,439,853–21,485,005, forward strandNBPF3ALPL: 21,508,813–21,579,441, forward strandALPL: 21,547,404–21,554,002, forward strandRAP1GAP: 21,596,215–21,669,846, reverse strandRAP1GAPUSP48: 21,675,521–21,783,618, reverse strandUSP48LDLRAD2: 21,812,265–21,825,225, forward strandLDLRAD2HSPG2: 21,822,244–21,937,310, reverse strandHSPG2CELA3B: 21,977,022–21,998,642, forward strandCELA3BCELA3A: 22,001,657–22,012,542, forward strandCELA3A: 22,025,142–22,092,943, forward strandCDC42: 22,052,627–22,101,360, forward strandCDC42WNT4: 22,117,313–22,143,969, reverse strandWNT4Diagram of HSPG2: 97 exons on the reverse strand of chromosome 1Exon 97: 1 known disease-causing siteExon 86: 1 known disease-causing siteExon 79: 1 known disease-causing siteExon 74: 2 known disease-causing sitesExon 68: 1 known disease-causing siteExon 50: 1 known disease-causing siteExon 49: 1 known disease-causing siteExon 43: 1 known disease-causing siteExon 42: 1 known disease-causing siteExon 41: 1 known disease-causing siteExon 33: 1 known disease-causing siteExon 32: 1 known disease-causing siteExon 27: 1 known disease-causing siteExon 25: 1 known disease-causing siteExon 22: 1 known disease-causing siteExon 15: 1 known disease-causing siteExon 11: 2 known disease-causing sitesExon 10: 2 known disease-causing sitesExon 9: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 97: 21,822,244–21,823,488, 1,245 basesExon 96: 21,823,616–21,823,719, 104 basesExon 95: 21,824,121–21,824,204, 84 basesExon 94: 21,824,306–21,824,376, 71 basesExon 93: 21,824,537–21,824,615, 79 basesExon 92: 21,824,704–21,824,779, 76 basesExon 91: 21,827,863–21,827,919, 57 basesExon 90: 21,828,030–21,828,152, 123 basesExon 89: 21,828,255–21,828,426, 172 basesExon 88: 21,828,835–21,829,079, 245 basesExon 87: 21,829,383–21,829,604, 222 basesExon 86: 21,829,993–21,830,091, 99 basesExon 85: 21,830,982–21,831,090, 109 basesExon 84: 21,831,215–21,831,324, 110 basesExon 83: 21,831,463–21,831,562, 100 basesExon 82: 21,831,652–21,831,796, 145 basesExon 81: 21,832,495–21,832,606, 112 basesExon 80: 21,833,268–21,833,384, 117 basesExon 79: 21,833,467–21,833,614, 148 basesExon 78: 21,833,816–21,833,925, 110 basesExon 77: 21,834,679–21,834,945, 267 basesExon 76: 21,835,540–21,835,637, 98 basesExon 75: 21,836,802–21,837,006, 205 basesExon 74: 21,838,825–21,839,085, 261 basesExon 73: 21,839,371–21,839,550, 180 basesExon 72: 21,839,822–21,840,017, 196 basesExon 71: 21,841,101–21,841,285, 185 basesExon 70: 21,841,539–21,841,673, 135 basesExon 69: 21,842,002–21,842,142, 141 basesExon 68: 21,842,239–21,842,380, 142 basesExon 67: 21,842,770–21,842,921, 152 basesExon 66: 21,843,297–21,843,438, 142 basesExon 65: 21,844,148–21,844,299, 152 basesExon 64: 21,846,108–21,846,255, 148 basesExon 63: 21,846,448–21,846,599, 152 basesExon 62: 21,847,354–21,847,492, 139 basesExon 61: 21,847,689–21,847,840, 152 basesExon 60: 21,847,958–21,848,093, 136 basesExon 59: 21,848,643–21,848,794, 152 basesExon 58: 21,848,893–21,849,031, 139 basesExon 57: 21,850,041–21,850,192, 152 basesExon 56: 21,850,363–21,850,498, 136 basesExon 55: 21,851,546–21,851,697, 152 basesExon 54: 21,851,791–21,851,926, 136 basesExon 53: 21,852,088–21,852,233, 146 basesExon 52: 21,852,700–21,852,832, 133 basesExon 51: 21,852,919–21,853,070, 152 basesExon 50: 21,854,193–21,854,343, 151 basesExon 49: 21,854,611–21,854,765, 155 basesExon 48: 21,854,848–21,854,983, 136 basesExon 47: 21,855,304–21,855,446, 143 basesExon 46: 21,855,523–21,855,675, 153 basesExon 45: 21,855,787–21,855,912, 126 basesExon 44: 21,857,015–21,857,195, 181 basesExon 43: 21,857,285–21,857,385, 101 basesExon 42: 21,859,566–21,859,676, 111 basesExon 41: 21,859,835–21,860,002, 168 basesExon 40: 21,860,177–21,860,235, 59 basesExon 39: 21,861,757–21,861,843, 87 basesExon 38: 21,861,988–21,862,115, 128 basesExon 37: 21,864,100–21,864,213, 114 basesExon 36: 21,864,843–21,865,073, 231 basesExon 35: 21,865,285–21,865,365, 81 basesExon 34: 21,865,717–21,865,809, 93 basesExon 33: 21,872,186–21,872,377, 192 basesExon 32: 21,872,620–21,872,760, 141 basesExon 31: 21,872,997–21,873,091, 95 basesExon 30: 21,873,375–21,873,424, 50 basesExon 29: 21,873,925–21,874,011, 87 basesExon 28: 21,874,406–21,874,533, 128 basesExon 27: 21,874,616–21,874,729, 114 basesExon 26: 21,874,891–21,875,002, 112 basesExon 25: 21,875,629–21,875,747, 119 basesExon 24: 21,875,863–21,876,042, 180 basesExon 23: 21,876,229–21,876,405, 177 basesExon 22: 21,876,512–21,876,652, 141 basesExon 21: 21,878,186–21,878,253, 68 basesExon 20: 21,878,433–21,878,491, 59 basesExon 19: 21,878,577–21,878,663, 87 basesExon 18: 21,878,994–21,879,121, 128 basesExon 17: 21,880,107–21,880,254, 148 basesExon 16: 21,880,363–21,880,559, 197 basesExon 15: 21,880,656–21,880,835, 180 basesExon 14: 21,881,339–21,881,502, 164 basesExon 13: 21,884,528–21,884,674, 147 basesExon 12: 21,884,767–21,884,918, 152 basesExon 11: 21,885,013–21,885,157, 145 basesExon 10: 21,885,320–21,885,451, 132 basesExon 9: 21,887,215–21,887,334, 120 basesExon 8: 21,887,420–21,887,674, 255 basesExon 7: 21,887,938–21,888,066, 129 basesExon 6: 21,889,981–21,890,141, 161 basesExon 5: 21,890,427–21,890,485, 59 basesExon 4: 21,890,585–21,890,694, 110 basesExon 3: 21,895,922–21,895,966, 45 basesExon 2: 21,896,175–21,896,310, 136 basesExon 1: 21,937,155–21,937,310, 156 bases9790807060504030201015′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 14.3 kb of the gene's 115.1 kb; 13,176 of those bases code for the protein.

How a genome test reads HSPG2

40

positions in HSPG2 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 115.1 kb of HSPG2, introns included, not only the 14.3 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.
  • 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.). HSPG2 gene: heparan sulfate proteoglycan 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/hspg2

Vancouver

Dante Labs. HSPG2 gene: heparan sulfate proteoglycan 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/hspg2

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