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Gene

SMPD4

sphingomyelin phosphodiesterase 4

Summary

Cytogenetic location
2q21.1
Coordinates
Chromosome 2: 130,151,408–130,181,602 (GRCh38)
Exons
20 exons across 30.2 kb
Protein
827 amino acids
Also known as
FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13
MANE Select transcript
ENST00000680298.1NM_017951.5
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 reports relevant to this gene

No Genome Test report reads SMPD4 yet. The test sequences your whole genome, so your data includes it all the same.

How SMPD4 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where SMPD4 sits. SMPD4 and 12 genes near it on chromosome 2, from 129,666,505 to 130,666,504.Chromosome 22q21.1p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3129.8 Mb130 Mb130.2 Mb130.4 Mb130.6 MbRAB6C: 129,979,666–129,982,738, forward strandRAB6CPOTEF: 130,073,535–130,129,371, reverse strandPOTEFCCDC74B: 130,139,287–130,145,134, reverse strandCCDC74BSMPD4: 130,151,408–130,181,602, reverse strandSMPD4MZT2B: 130,181,737–130,190,729, forward strandMZT2BTUBA3E: 130,191,743–130,198,461, reverse strandTUBA3EVMA22: 130,337,922–130,342,699, reverse strandVMA22IMP4: 130,342,403–130,348,550, forward strandIMP4PTPN18: 130,356,026–130,375,409, forward strandPTPN18POTEI: 130,459,455–130,509,707, reverse strandPOTEICFC1B: 130,521,197–130,528,604, forward strandCFC1BCFC1: 130,592,165–130,599,575, reverse strandCFC1POTEJ: 130,611,440–130,658,037, forward strandPOTEJDiagram of SMPD4: 20 exons on the reverse strand of chromosome 2Exon 20: 1 known disease-causing siteExon 19: 1 known disease-causing siteExon 18: 3 known disease-causing sitesExon 17: 1 known disease-causing siteExon 16: 1 known disease-causing siteExon 15: 1 known disease-causing siteExon 14: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 8: 3 known disease-causing sitesExon 5: 1 known disease-causing siteExon 4: 2 known disease-causing sitesExon 3: 1 known disease-causing siteExon 2: 1 known disease-causing siteExon 20: 130,151,408–130,152,884, 1,477 basesExon 19: 130,153,043–130,153,171, 129 basesExon 18: 130,153,319–130,153,450, 132 basesExon 17: 130,153,702–130,153,935, 234 basesExon 16: 130,154,277–130,154,482, 206 basesExon 15: 130,155,096–130,155,259, 164 basesExon 14: 130,156,035–130,156,135, 101 basesExon 13: 130,156,585–130,156,675, 91 basesExon 12: 130,157,251–130,157,396, 146 basesExon 11: 130,161,186–130,161,272, 87 basesExon 10: 130,164,374–130,164,445, 72 basesExon 9: 130,167,458–130,167,590, 133 basesExon 8: 130,172,349–130,172,500, 152 basesExon 7: 130,172,625–130,172,677, 53 basesExon 6: 130,172,787–130,172,895, 109 basesExon 5: 130,173,279–130,173,354, 76 basesExon 4: 130,173,514–130,173,656, 143 basesExon 3: 130,174,914–130,175,000, 87 basesExon 2: 130,176,554–130,176,637, 84 basesExon 1: 130,181,530–130,181,602, 73 bases201510515′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 3.7 kb of the gene's 30.2 kb; 2,484 of those bases code for the protein.

How a genome test reads SMPD4

25

positions in SMPD4 where ClinVar classes a change as pathogenic or likely pathogenic

25 of them (100%) fall in regions short reads find hard.

  • Low mappability (9 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (25 sites)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 30.2 kb of SMPD4, introns included, not only the 3.7 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.). SMPD4 gene: sphingomyelin phosphodiesterase 4. Retrieved 17 October 2026, from https://dantelabs.com/genes/smpd4

Vancouver

Dante Labs. SMPD4 gene: sphingomyelin phosphodiesterase 4 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/smpd4

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