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Gene

PLEKHM1

pleckstrin homology and RUN domain containing M1

Summary

Cytogenetic location
17q21.31
Coordinates
Chromosome 17: 45,435,900–45,490,721 (GRCh38)
Exons
12 exons across 54.8 kb
Protein
1,056 amino acids
Also known as
KIAA0356
MANE Select transcript
ENST00000430334.8NM_014798.3
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

  • Osteopetrosis

    • Osteopetrosis, also known as marble bone disease, is a descriptive term that refers to a group of rare, heritable disorders of the skeleton characterized by increased bone density on radiographs.

      • ClinGen rates the link moderate
      • 1 GenCC submitter rates it definitive or strong

How PLEKHM1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 17, with a bracket where PLEKHM1 sits. PLEKHM1 and 15 genes near it on chromosome 17, from 44,963,311 to 45,963,310.Chromosome 1717q21.31p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.345 Mb45.2 Mb45.4 Mb45.6 Mb45.8 MbNMT1: 44,957,992–45,109,016, forward strandNMT1C1QL1: 44,958,933–44,968,369, reverse strandC1QL1DCAKD: 45,023,338–45,061,137, reverse strandDCAKDPLCD3: 45,108,959–45,133,354, reverse strandPLCD3ACBD4: 45,132,597–45,144,181, forward strandACBD4HEXIM1: 45,148,475–45,152,099, forward strandHEXIM1HEXIM2: 45,160,695–45,170,701, forward strandHEXIM2FMNL1: 45,220,736–45,247,319, forward strandFMNL1SPATA32: 45,254,388–45,262,116, reverse strandSPATA32MAP3K14: 45,263,119–45,317,112, reverse strandMAP3K14ARHGAP27: 45,393,898–45,434,421, reverse strandARHGAP27PLEKHM1: 45,435,900–45,490,721, reverse strandPLEKHM1LINC02210-CRHR1: 45,620,344–45,835,826, forward strandLINC02210-CRHR1CRHR1: 45,784,277–45,835,828, forward strandCRHR1SPPL2C: 45,844,881–45,847,067, forward strandSPPL2CMAPT: 45,894,278–46,028,334, forward strandMAPTDiagram of PLEKHM1: 12 exons on the reverse strand of chromosome 17Exon 3: 1 known disease-causing siteExon 12: 45,435,900–45,437,969, 2,070 basesExon 11: 45,439,477–45,439,634, 158 basesExon 10: 45,440,163–45,440,226, 64 basesExon 9: 45,445,470–45,445,663, 194 basesExon 8: 45,450,618–45,450,763, 146 basesExon 7: 45,453,355–45,454,272, 918 basesExon 6: 45,458,169–45,458,439, 271 basesExon 5: 45,468,209–45,468,593, 385 basesExon 4: 45,475,100–45,475,726, 627 basesExon 3: 45,477,900–45,478,147, 248 basesExon 2: 45,482,437–45,482,525, 89 basesExon 1: 45,490,652–45,490,721, 70 bases1210864215′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 5.2 kb of the gene's 54.8 kb; 3,171 of those bases code for the protein.

How a genome test reads PLEKHM1

1

position in PLEKHM1 where ClinVar classes a change as pathogenic or likely pathogenic

1 of them (100%) falls in a region short reads find hard.

  • Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (1 site)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 54.8 kb of PLEKHM1, introns included, not only the 5.2 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.). PLEKHM1 gene: pleckstrin homology and RUN domain containing M1. Retrieved 17 October 2026, from https://dantelabs.com/genes/plekhm1

Vancouver

Dante Labs. PLEKHM1 gene: pleckstrin homology and RUN domain containing M1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/plekhm1

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