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Gene

SAMHD1

SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1

Summary

Cytogenetic location
20q11.23
Coordinates
Chromosome 20: 36,890,229–36,951,708 (GRCh38)
Exons
16 exons across 61.5 kb
Protein
626 amino acids
Inheritance
Autosomal dominant Autosomal recessive
Also known as
SBBI88, Mg11, HDDC1, MOP-5, AGS5
MANE Select transcript
ENST00000646673.2NM_015474.4
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

  • Aicardi-Goutieres Syndrome

    • SAMHD1-related type 1 interferonopathyAutosomal recessive

      SAMHD1 variants causing Aicardi-Goutieres syndrome, sometimes with cerebral vasculopathy.

      • ClinGen rates the link definitive
      • 7 GenCC submitters rate it definitive or strong
    • Autosomal recessive

      Aicardi-Goutieres syndrome (AGS) is an inherited, subacute encephalopathy characterized by the association of basal ganglia calcification, leukodystrophy and cerebrospinal fluid (CSF) lymphocytosis.

      • 6 GenCC submitters rate it definitive or strong

  • Moyamoya Disease

    • Progressive narrowing of the arteries at the base of the brain, linked to changes in RNF213 (a susceptibility gene with reduced penetrance, especially common in East Asian populations), ACTA2 or GUCY1A1, which can cause strokes or mini-strokes.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Knowing about it supports early assessment of symptoms such as transient weakness, and access to specialist stroke prevention and surgical treatment.

  • Rare Monogenic Autoinflammatory Diseases

    • PTPN2-related autoinflammation and autoimmunityAutosomal dominant

      Early-onset inflammatory and autoimmune disease, including colitis and arthritis, caused by variants in PTPN2.

      • 6 GenCC submitters rate it definitive or strong

Broader groupings

  • Other Inborn Errors of Immunity

    • Inborn error of immunity

      One of 114 genes linked to it

      Inherited disorders of the immune system caused by changes in single genes, affecting how the body fights infection or regulates inflammation.

      • 6 GenCC submitters rate it definitive or strong

  • Other Inherited Leukodystrophies

    • Leukodystrophy (other and unspecified types)

      One of 80 genes linked to it

      Inherited conditions that damage or prevent the normal formation of myelin, the white matter of the brain and spinal cord. Different types follow autosomal recessive, autosomal dominant or X-linked inheritance depending on the gene involved.

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

      Knowing the specific genetic cause can end a diagnostic search, guide supportive care and surveillance, show whether a specific treatment exists, and allow testing of relatives.

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.
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 SAMHD1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 20, with a bracket where SAMHD1 sits. SAMHD1 and 16 genes near it on chromosome 20, from 36,420,969 to 37,420,968.Chromosome 2020q11.23p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.3336.6 Mb36.8 Mb37 Mb37.2 Mb37.4 MbDLGAP4: 36,306,302–36,528,637, forward strandDLGAP4MYL9: 36,541,482–36,551,950, forward strandMYL9TGIF2: 36,571,894–36,593,950, forward strandTGIF2TGIF2-RAB5IF: 36,574,553–36,612,384, forward strandTGIF2-RAB5IFRAB5IF: 36,605,718–36,612,557, forward strandRAB5IFSLA2: 36,612,318–36,646,219, reverse strandSLA2NDRG3: 36,651,766–36,746,157, reverse strandNDRG3DSN1: 36,751,791–36,774,298, reverse strandDSN1MTCL2: 36,777,447–36,863,795, reverse strandMTCL2TLDC2: 36,873,061–36,898,931, forward strandTLDC2SAMHD1: 36,890,229–36,951,708, reverse strandSAMHD1RBL1: 36,996,088–37,096,034, reverse strandRBL1MROH8: 37,101,226–37,179,588, reverse strandMROH8RPN2: 37,178,396–37,241,630, forward strandRPN2GHRH: 37,251,082–37,261,819, reverse strandGHRHMANBAL: 37,289,559–37,317,260, forward strandMANBALSRC: 37,344,673–37,406,050, forward strandSRCDiagram of SAMHD1: 16 exons on the reverse strand of chromosome 20Exon 15: 7 known disease-causing sitesExon 14: 5 known disease-causing sitesExon 13: 5 known disease-causing sitesExon 12: 9 known disease-causing sitesExon 11: 7 known disease-causing sitesExon 10: 3 known disease-causing sitesExon 9: 5 known disease-causing sitesExon 8: 10 known disease-causing sitesExon 7: 8 known disease-causing sitesExon 6: 5 known disease-causing sitesExon 5: 7 known disease-causing sitesExon 4: 14 known disease-causing sitesExon 3: 3 known disease-causing sitesExon 2: 1 known disease-causing siteExon 1: 10 known disease-causing sitesExon 16: 36,890,229–36,893,066, 2,838 basesExon 15: 36,897,822–36,897,959, 138 basesExon 14: 36,898,440–36,898,544, 105 basesExon 13: 36,904,157–36,904,249, 93 basesExon 12: 36,905,364–36,905,503, 140 basesExon 11: 36,911,218–36,911,333, 116 basesExon 10: 36,912,461–36,912,552, 92 basesExon 9: 36,916,722–36,916,830, 109 basesExon 8: 36,916,949–36,917,049, 101 basesExon 7: 36,919,364–36,919,519, 156 basesExon 6: 36,927,182–36,927,252, 71 basesExon 5: 36,930,760–36,930,875, 116 basesExon 4: 36,935,029–36,935,189, 161 basesExon 3: 36,941,039–36,941,111, 73 basesExon 2: 36,946,738–36,946,804, 67 basesExon 1: 36,951,436–36,951,708, 273 bases16141210864215′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 4.6 kb of the gene's 61.5 kb; 1,881 of those bases code for the protein.

How a genome test reads SAMHD1

122

positions in SAMHD1 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 61.5 kb of SAMHD1, introns included, not only the 4.6 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.). SAMHD1 gene: SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/samhd1

Vancouver

Dante Labs. SAMHD1 gene: SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/samhd1

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