Skip to content
Use your HSA or FSA funds

Gene

PIK3CD

phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta

Summary

Cytogenetic location
1p36.22
Coordinates
Chromosome 1: 9,651,731–9,729,114 (GRCh38)
Exons
24 exons across 77.4 kb
Protein
1,044 amino acids
Inheritance
Autosomal dominant
Also known as
p110D
MANE Select transcript
ENST00000377346.9NM_005026.5
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

  • Activated PI3K-Delta Syndrome (APDS)

    • Activated PI3K-delta syndromeAutosomal dominant

      Immunodeficiency with lymphoproliferation caused by a single activating change in PIK3CD or PIK3R1.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      A genetic diagnosis allows targeted treatment with leniolisib, a PI3K-delta inhibitor, alongside immunoglobulin replacement and lymphoma monitoring.

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.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
    • Immunodeficiency Disease

      One of 170 genes linked to it

      Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      HSCT for SCID and severe PIDs; immunoglobulin replacement (IVIG/SCIG) for antibody deficiencies; leniolisib (Joenja, FDA 2023) for APDS; gene therapy for ADA-SCID; abatacept for CTLA4/LRBA deficiency; prophylactic antibiotics; G-CSF for CGD

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.

How PIK3CD is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome 1, with a bracket where PIK3CD sits. PIK3CD and 10 genes near it on chromosome 1, from 9,190,423 to 10,190,422.Chromosome 11p36.22p36.33p36.32p36.31p36.23p36.22p36.21p36.13p36.12p36.11p35.3p35.2p35.1p34.3p34.2p34.1p33p32.3p32.2p32.1p31.3p31.2p31.1p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q21.1q21.2q21.3q22q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q31.1q31.2q31.3q32.1q32.2q32.3q41q42.11q42.12q42.13q42.2q42.3q43q449.2 Mb9.4 Mb9.6 Mb9.8 Mb10 MbH6PD: 9,234,739–9,278,217, forward strandH6PDSPSB1: 9,292,101–9,369,532, forward strandSPSB1SLC25A33: 9,539,437–9,585,173, forward strandSLC25A33TMEM201: 9,588,718–9,614,879, forward strandTMEM201PIK3CD: 9,651,731–9,729,114, forward strandPIK3CDCLSTN1: 9,728,911–9,823,993, reverse strandCLSTN1CTNNBIP1: 9,848,269–9,910,378, reverse strandCTNNBIP1LZIC: 9,922,113–9,943,407, reverse strandLZICNMNAT1: 9,943,428–9,996,898, forward strandNMNAT1RBP7: 9,997,050–10,016,022, forward strandRBP7UBE4B: 10,032,832–10,181,244, forward strandUBE4BDiagram of PIK3CD: 24 exons on the forward strand of chromosome 1Exon 3: 1 known disease-causing siteExon 4: 7 known disease-causing sitesExon 5: 2 known disease-causing sitesExon 6: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 10: 3 known disease-causing sitesExon 13: 5 known disease-causing sitesExon 14: 1 known disease-causing siteExon 17: 1 known disease-causing siteExon 21: 1 known disease-causing siteExon 24: 2 known disease-causing sitesExon 1: 9,651,731–9,651,802, 72 basesExon 2: 9,691,467–9,691,571, 105 basesExon 3: 9,710,424–9,710,596, 173 basesExon 4: 9,715,541–9,715,769, 229 bases. 1 variant with a page in exon 4. List themExon 5: 9,715,849–9,716,078, 230 bases. 1 variant with a page in exon 5. List themExon 6: 9,716,440–9,716,619, 180 basesExon 7: 9,716,959–9,717,108, 150 basesExon 8: 9,717,537–9,717,626, 90 bases. 2 variants with a page in exon 8. List themExon 9: 9,718,694–9,718,915, 222 basesExon 10: 9,719,921–9,720,017, 97 bases. 1 variant with a page in exon 10. List themExon 11: 9,720,112–9,720,242, 131 basesExon 12: 9,720,611–9,720,661, 51 basesExon 13: 9,720,742–9,720,909, 168 bases. 5 variants with a page in exon 13. List themExon 14: 9,721,127–9,721,248, 122 basesExon 15: 9,721,444–9,721,587, 144 basesExon 16: 9,721,761–9,721,860, 100 basesExon 17: 9,721,975–9,722,153, 179 basesExon 18: 9,722,244–9,722,356, 113 basesExon 19: 9,722,528–9,722,606, 79 basesExon 20: 9,723,125–9,723,292, 168 basesExon 21: 9,723,969–9,724,092, 124 basesExon 22: 9,724,276–9,724,421, 146 basesExon 23: 9,724,804–9,724,936, 133 basesExon 24: 9,726,909–9,729,114, 2,206 bases. 2 variants with a page in exon 24. List them11020245′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 5.4 kb of the gene's 77.4 kb; 3,135 of those bases code for the protein.

How a genome test reads PIK3CD

26

positions in PIK3CD where ClinVar classes a change as pathogenic or likely pathogenic

2 of them (7.7%) fall in regions short reads find hard.

  • Segmental duplications (2 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 77.4 kb of PIK3CD, introns included, not only the 5.4 kb of exons.

Variants with a page (12)

The PIK3CD variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
c.1002C>GExon 89,717,608Likely pathogenic3 stars out of 4 reviewed by expert panel
C416Rc.1246T>CExon 109,719,924Likely pathogenic3 stars out of 4 reviewed by expert panel
E81Kc.241G>AExon 49,715,640Likely pathogenic3 stars out of 4 reviewed by expert panel
E525Ac.1574A>CExon 139,720,794Likely pathogenic3 stars out of 4 reviewed by expert panel
E525Gc.1574A>GExon 139,720,794Likely pathogenic3 stars out of 4 reviewed by expert panel
E525Kc.1573G>AExon 139,720,793Pathogenic3 stars out of 4 reviewed by expert panel
E1021Kc.3061G>AExon 249,726,972Pathogenic3 stars out of 4 reviewed by expert panel
E1025Gc.3074A>GExon 249,726,985Pathogenic3 stars out of 4 reviewed by expert panel
G124Dc.371G>AExon 59,715,849Likely pathogenic3 stars out of 4 reviewed by expert panel
N334Kc.1002C>AExon 89,717,608Likely pathogenic3 stars out of 4 reviewed by expert panel

See all 12 PIK3CD variants →

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.). PIK3CD gene: phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta. Retrieved 16 October 2026, from https://dantelabs.com/genes/pik3cd

Vancouver

Dante Labs. PIK3CD gene: phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pik3cd

One test. A lifetime of answers.

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

Get my Genome Test