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Gene

PNPLA6

patatin like domain 6, lysophospholipase

Summary

Cytogenetic location
19p13.2
Coordinates
Chromosome 19: 7,535,717–7,561,764 (GRCh38)
Exons
32 exons across 26 kb
Protein
1,365 amino acids
Inheritance
Autosomal recessive
Also known as
NTE, sws, iPLA2delta, SPG39
MANE Select transcript
ENST00000600737.6NM_001166114.2
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 Spastic Paraplegia

    • Hereditary Spastic Paraplegia 39Autosomal recessive

      This syndrome is characterized by progressive spastic paraplegia and distal muscle wasting.

      • ClinGen rates the link definitive
      • 3 GenCC submitters rate it definitive or strong
    • Hereditary Spastic Paraplegia (All Types)

      One of 66 genes linked to it

      Umbrella term covering all hereditary spastic paraplegias, including SPG4 (SPAST), the most common dominant form, and SPG5A, SPG6, SPG10, SPG18, SPG30 and SPG31.

      • ClinGen rates the link definitive
      • 3 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 PNPLA6 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 19, with a bracket where PNPLA6 sits. PNPLA6 and 35 genes near it on chromosome 19, from 7,048,741 to 8,048,740.Chromosome 1919p13.2p13.3p13.2p13.13p13.12p13.11p12p11q11q12q13.11q13.12q13.13q13.2q13.31q13.32q13.33q13.41q13.42q13.437.2 Mb7.4 Mb7.6 Mb7.8 Mb8 MbMBD3L2: 7,049,321–7,051,735, forward strandMBD3L2MBD3L3: 7,056,207–7,069,665, reverse strandMBD3L3ZNF557: 7,069,416–7,096,206, forward strandZNF557INSR: 7,112,255–7,294,443, reverse strandINSRARHGEF18: 7,348,931–7,472,485, forward strandARHGEF18PEX11G: 7,476,869–7,497,449, reverse strandSAXO5: 7,492,976–7,509,030, forward strand: 7,507,052–7,519,622, forward strandZNF358: 7,515,292–7,521,027, forward strandZNF358MCOLN1: 7,522,611–7,534,009, forward strandMCOLN1: 7,533,595–7,540,059, forward strandPNPLA6: 7,535,717–7,561,764, forward strandPNPLA6CAMSAP3: 7,595,826–7,618,352, forward strandCAMSAP3XAB2: 7,619,523–7,629,573, reverse strandXAB2PET100: 7,629,711–7,631,956, forward strandPET100: 7,629,796–7,647,477, forward strandPCP2: 7,631,611–7,635,831, reverse strandPCP2STXBP2: 7,636,772–7,647,875, forward strandRETN: 7,669,044–7,670,456, forward strandMCEMP1: 7,677,056–7,679,834, forward strand: 7,678,501–7,682,854, forward strandTRAPPC5: 7,680,823–7,687,703, forward strandFCER2: 7,688,758–7,702,146, reverse strandFCER2CLEC4G: 7,728,943–7,733,906, reverse strandCLEC4G: 7,728,958–7,745,662, reverse strandCD209: 7,739,993–7,747,623, reverse strandCD209CLEC4M: 7,763,031–7,769,606, forward strandCLEC4MEVI5L: 7,830,182–7,864,980, forward strandEVI5LPRR36: 7,868,719–7,874,674, reverse strandPRR36LRRC8E: 7,888,500–7,902,021, forward strandLRRC8EMAP2K7: 7,903,823–7,914,480, forward strandMAP2K7TGFBR3L: 7,914,760–7,919,097, forward strandTGFBR3LSNAPC2: 7,920,314–7,923,250, forward strandCTXN1: 7,924,491–7,926,174, reverse strandTIMM44: 7,926,715–7,943,773, reverse strandELAVL1: 7,958,573–8,006,062, reverse strandELAVL1Diagram of PNPLA6: 32 exons on the forward strand of chromosome 19Exon 1: 2 known disease-causing sitesExon 2: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 7: 4 known disease-causing sitesExon 8: 1 known disease-causing siteExon 10: 2 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 12: 2 known disease-causing sitesExon 13: 1 known disease-causing siteExon 14: 5 known disease-causing sitesExon 15: 4 known disease-causing sitesExon 16: 4 known disease-causing sitesExon 18: 1 known disease-causing siteExon 19: 1 known disease-causing siteExon 20: 1 known disease-causing siteExon 21: 4 known disease-causing sitesExon 22: 4 known disease-causing sitesExon 23: 2 known disease-causing sitesExon 24: 4 known disease-causing sitesExon 25: 3 known disease-causing sitesExon 26: 2 known disease-causing sitesExon 27: 10 known disease-causing sitesExon 28: 9 known disease-causing sitesExon 29: 1 known disease-causing siteExon 30: 2 known disease-causing sitesExon 31: 5 known disease-causing sitesExon 32: 3 known disease-causing sitesExon 1: 7,535,717–7,536,020, 304 basesExon 2: 7,536,191–7,536,273, 83 basesExon 3: 7,536,449–7,536,546, 98 basesExon 4: 7,539,918–7,540,058, 141 basesExon 5: 7,540,149–7,540,308, 160 basesExon 6: 7,540,630–7,540,710, 81 basesExon 7: 7,540,923–7,541,051, 129 basesExon 8: 7,541,354–7,541,434, 81 basesExon 9: 7,541,522–7,541,684, 163 basesExon 10: 7,541,984–7,542,067, 84 basesExon 11: 7,542,561–7,542,670, 110 basesExon 12: 7,542,761–7,542,928, 168 basesExon 13: 7,543,007–7,543,084, 78 basesExon 14: 7,549,907–7,550,112, 206 basesExon 15: 7,550,298–7,550,429, 132 basesExon 16: 7,550,517–7,550,640, 124 basesExon 17: 7,550,994–7,551,107, 114 basesExon 18: 7,551,362–7,551,437, 76 basesExon 19: 7,553,875–7,554,015, 141 basesExon 20: 7,554,209–7,554,272, 64 basesExon 21: 7,554,555–7,554,723, 169 basesExon 22: 7,554,893–7,555,075, 183 basesExon 23: 7,555,249–7,555,367, 119 basesExon 24: 7,555,607–7,555,763, 157 basesExon 25: 7,556,453–7,556,569, 117 basesExon 26: 7,556,655–7,556,724, 70 basesExon 27: 7,557,168–7,557,284, 117 basesExon 28: 7,558,850–7,559,151, 302 basesExon 29: 7,560,648–7,560,764, 117 basesExon 30: 7,561,014–7,561,110, 97 basesExon 31: 7,561,208–7,561,317, 110 basesExon 32: 7,561,488–7,561,764, 277 bases120325′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 4.4 kb of the gene's 26 kb; 4,098 of those bases code for the protein.

How a genome test reads PNPLA6

103

positions in PNPLA6 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 26 kb of PNPLA6, introns included, not only the 4.4 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.). PNPLA6 gene: patatin like domain 6, lysophospholipase. Retrieved 16 October 2026, from https://dantelabs.com/genes/pnpla6

Vancouver

Dante Labs. PNPLA6 gene: patatin like domain 6, lysophospholipase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pnpla6

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