Skip to content
Use your HSA or FSA funds

Gene

SMPD1

sphingomyelin phosphodiesterase 1

Summary

Cytogenetic location
11p15.4
Coordinates
Chromosome 11: 6,390,474–6,394,996 (GRCh38)
Exons
6 exons across 4.5 kb
Protein
631 amino acids
Inheritance
Autosomal recessive
Also known as
ASM
MANE Select transcript
ENST00000342245.9NM_000543.5
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

  • Acid Sphingomyelinase Deficiency (Niemann-Pick Disease Types A and B)

    • Niemann-Pick disease type A (infantile neurovisceral ASMD)Autosomal recessive

      Enlarged liver and spleen in infancy with feeding problems and rapid neurological decline, caused by near-complete loss of acid sphingomyelinase.

      • 3 GenCC submitters rate it definitive or strong
    • Niemann-Pick disease type B (chronic visceral ASMD)Autosomal recessive

      Enlarged liver and spleen, low platelets, abnormal blood lipids and interstitial lung disease beginning in childhood or adulthood, usually without brain involvement.

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

      Enzyme replacement therapy (olipudase alfa) treats the non-neurological features of ASMD.

    • Acid sphingomyelinase deficiency, other formsAutosomal recessive

      Includes the intermediate chronic neurovisceral form, with features between types A and B.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong

Broader groupings

  • Lysosomal Storage Disease

    • Lysosomal storage disease (other and unspecified types)

      One of 59 genes linked to it

      Covers lysosomal storage diseases without a dedicated report, such as Farber disease and other ASAH1-related disorders, prosaposin (PSAP) deficiencies, multiple sulfatase deficiency, mucopolysaccharidosis types IX and X, and Dorfman-Chanarin disease; inheritance varies by subtype, most often autosomal recessive.

      • ClinGen rates the link definitive
      • 7 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 SMPD1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 11, with a bracket where SMPD1 sits. SMPD1 and 35 genes near it on chromosome 11, from 5,892,735 to 6,892,734.Chromosome 1111p15.4p15.5p15.4p15.3p15.2p15.1p14.3p14.2p14.1p13p12p11.2p11.12p11.11q11q12.1q12.2q12.3q13.1q13.2q13.3q13.4q13.5q14.1q14.2q14.3q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q256 Mb6.2 Mb6.4 Mb6.6 Mb6.8 MbTRIM5: 5,663,195–5,938,619, reverse strandTRIM5OR52E5: 5,893,208–5,902,730, forward strandOR52E5OR56A3: 5,938,751–5,951,347, forward strandOR56A3OR56A5: 5,967,553–5,968,494, reverse strandOR56A5OR52L1: 5,985,892–5,986,985, reverse strandOR52L1OR56A4: 5,999,445–6,006,946, reverse strandOR56A4OR56A1: 6,019,336–6,034,338, reverse strandOR56A1OR56B4: 6,107,684–6,108,835, forward strandOR56B4OR52B2: 6,169,355–6,170,326, reverse strandOR52B2OR52W1: 6,199,224–6,200,186, forward strandOR52W1C11orf42: 6,205,557–6,211,135, forward strandC11orf42FHIP1B: 6,211,334–6,234,711, reverse strandFHIP1BCNGA4: 6,234,765–6,245,922, forward strandCNGA4CCKBR: 6,259,698–6,272,127, forward strandCCKBRCAVIN3: 6,318,946–6,320,622, reverse strandCAVIN3SMPD1: 6,390,474–6,394,996, forward strandSMPD1APBB1: 6,395,111–6,419,515, reverse strandAPBB1HPX: 6,426,176–6,442,617, reverse strandHPXTRIM3: 6,448,613–6,474,459, reverse strandTRIM3ARFIP2: 6,474,683–6,481,479, reverse strandARFIP2TIMM10B: 6,481,446–6,493,041, forward strandTIMM10B: 6,481,485–6,508,978, forward strandRRP8: 6,496,506–6,603,638, reverse strandDNHD1: 6,497,260–6,593,758, forward strandDNHD1ILK: 6,603,708–6,610,874, forward strandILKTAF10: 6,606,294–6,612,539, reverse strandTAF10TPP1: 6,612,768–6,619,448, reverse strandDCHS1: 6,621,330–6,655,834, reverse strandDCHS1MRPL17: 6,680,364–6,683,411, reverse strandMRPL17OR2AG2: 6,765,626–6,771,976, reverse strandOR2AG2OR2AG1: 6,783,020–6,791,558, forward strandOR2AG1OR6A2: 6,791,736–6,799,689, reverse strandOR6A2OR10A5: 6,845,683–6,846,636, forward strandOR10A5OR10A2: 6,863,057–6,874,717, forward strandOR10A2OR10A4: 6,876,625–6,877,619, forward strandOR10A4OR2D2: 6,891,574–6,892,500, reverse strandOR2D2Diagram of SMPD1: 6 exons on the forward strand of chromosome 11Exon 1: 41 known disease-causing sitesExon 2: 147 known disease-causing sitesExon 3: 32 known disease-causing sitesExon 4: 19 known disease-causing sitesExon 5: 29 known disease-causing sitesExon 6: 62 known disease-causing sitesExon 1: 6,390,474–6,390,916, 443 basesExon 2: 6,391,384–6,392,156, 773 basesExon 3: 6,393,216–6,393,387, 172 basesExon 4: 6,393,617–6,393,693, 77 basesExon 5: 6,393,896–6,394,041, 146 basesExon 6: 6,394,198–6,394,996, 799 bases1234565′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 2.4 kb of the gene's 4.5 kb; 1,896 of those bases code for the protein.

How a genome test reads SMPD1

349

positions in SMPD1 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 4.5 kb of SMPD1, introns included, not only the 2.4 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.). SMPD1 gene: sphingomyelin phosphodiesterase 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/smpd1

Vancouver

Dante Labs. SMPD1 gene: sphingomyelin phosphodiesterase 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/smpd1

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test