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Gene

PRDM12

PR/SET domain 12

Summary

Cytogenetic location
9q34.12
Coordinates
Chromosome 9: 130,664,594–130,682,983 (GRCh38)
Exons
5 exons across 18.4 kb
Protein
367 amino acids
Also known as
PFM9
MANE Select transcript
ENST00000253008.3NM_021619.3
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

  • Hereditary Sensory and Autonomic Neuropathies (incl. Familial Dysautonomia)

    • Hereditary Sensory and Autonomic Neuropathy

      A group of neuropathies, including familial dysautonomia (ELP1), HSAN1 (SPTLC1/SPTLC2), HSAN2 (WNK1, RETREG1) and congenital insensitivity to pain (NTRK1, SCN9A, PRDM12), most of which are recessive while HSAN1 is dominant.

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

      Protection against unnoticed injuries, burns and infections, management of autonomic symptoms, and carrier testing for relatives (familial dysautonomia is included in Ashkenazi Jewish carrier screening).

How PRDM12 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 PRDM12 sits. PRDM12 and 12 genes near it on chromosome 9, from 130,173,789 to 131,173,788.Chromosome 99q34.12p24.3p24.2p24.1p23p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q13q21.11q21.12q21.13q21.2q21.31q21.32q21.33q22.1q22.2q22.31q22.32q22.33q31.1q31.2q31.3q32q33.1q33.2q33.3q34.11q34.12q34.13q34.2q34.3130.2 Mb130.4 Mb130.6 Mb130.8 Mb131 MbNCS1: 130,172,315–130,237,737, forward strandNCS1HMCN2: 130,265,746–130,434,123, forward strandHMCN2ASS1: 130,443,282–130,502,361, forward strandASS1FUBP3: 130,578,965–130,638,354, forward strandFUBP3PRDM12: 130,664,594–130,682,983, forward strandPRDM12EXOSC2: 130,693,721–130,707,608, forward strandEXOSC2ABL1: 130,713,043–130,887,675, forward strandABL1: 130,713,626–130,713,724, forward strandQRFP: 130,892,707–130,896,812, reverse strandQRFPFIBCD1: 130,900,194–130,941,232, reverse strandFIBCD1LAMC3: 131,008,878–131,094,473, forward strandLAMC3AIF1L: 131,096,446–131,123,243, forward strandAIF1LNUP214: 131,124,868–131,234,667, forward strandNUP214Diagram of PRDM12: 5 exons on the forward strand of chromosome 9Exon 1: 1 known disease-causing siteExon 2: 1 known disease-causing siteExon 3: 3 known disease-causing sitesExon 4: 1 known disease-causing siteExon 5: 4 known disease-causing sitesExon 1: 130,664,594–130,664,876, 283 basesExon 2: 130,666,608–130,666,798, 191 basesExon 3: 130,668,158–130,668,313, 156 basesExon 4: 130,678,529–130,678,640, 112 basesExon 5: 130,681,248–130,682,983, 1,736 bases123455′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 2.5 kb of the gene's 18.4 kb; 1,104 of those bases code for the protein.

How a genome test reads PRDM12

13

positions in PRDM12 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 18.4 kb of PRDM12, introns included, not only the 2.5 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.). PRDM12 gene: PR/SET domain 12. Retrieved 16 October 2026, from https://dantelabs.com/genes/prdm12

Vancouver

Dante Labs. PRDM12 gene: PR/SET domain 12 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/prdm12

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