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Gene

NCF1

neutrophil cytosolic factor 1

Summary

Cytogenetic location
7q11.23
Coordinates
Chromosome 7: 74,774,011–74,789,315 (GRCh38)
Exons
11 exons across 15.3 kb
Protein
390 amino acids
Inheritance
Autosomal recessive
Also known as
p47phox, NOXO2, NCF1A, SH3PXD1A
MANE Select transcript
ENST00000289473.11NM_000265.7
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

  • Chronic Granulomatous Disease

    • Granulomatous Disease, Chronic, Autosomal Recessive, Cytochrome B-Positive, Type 1Autosomal recessive

      Any chronic granulomatous disease in which the cause of the disease is a mutation in the NCF1 gene.

      • 2 GenCC submitters rate it definitive or strong

    • Chronic granulomatous disease (CGD) is a rare primary immunodeficiency, mainly affecting phagocytes, which is characterized by an increased susceptibility to severe and recurrent bacterial and fungal infections, along with the development of granulomas.

      • 2 GenCC submitters rate it definitive or strong
    • Phagocyte Bactericidal Dysfunction

      Disorders in which phagocytic cells cannot kill ingested bacteria; characterized by frequent recurring infection with formulation of granulomas.

      • 2 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.

      • 2 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 NCF1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 7, with a bracket where NCF1 sits. NCF1 and 10 genes near it on chromosome 7, from 74,281,663 to 75,281,662.Chromosome 77q11.23p22.3p22.2p22.1p21.3p21.2p21.1p15.3p15.2p15.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.21q11.22q11.23q21.11q21.12q21.13q21.2q21.3q22.1q22.2q22.3q31.1q31.2q31.31q31.32q31.33q32.1q32.2q32.3q33q34q35q36.1q36.2q36.374.4 Mb74.6 Mb74.8 Mb75 Mb75.2 MbCLIP2: 74,289,407–74,405,943, forward strandCLIP2GTF2IRD1: 74,452,463–74,602,619, forward strandGTF2IRD1GTF2I: 74,650,226–74,760,706, forward strandGTF2INCF1: 74,774,011–74,789,315, forward strandNCF1GTF2IRD2: 74,796,144–74,852,471, reverse strandGTF2IRD2: 74,796,150–74,890,585, reverse strandSPDYE12: 74,904,289–74,915,078, reverse strandSPDYE12CASTOR2: 74,964,664–75,031,530, forward strandCASTOR2RCC1L: 75,026,190–75,074,228, reverse strandRCC1LGTF2IRD2B: 75,091,567–75,149,818, forward strandGTF2IRD2BSPDYE13: 75,280,790–75,289,501, forward strandSPDYE13Diagram of NCF1: 11 exons on the forward strand of chromosome 7Exon 2: 2 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 1: 74,774,011–74,774,103, 93 basesExon 2: 74,777,267–74,777,347, 81 basesExon 3: 74,779,082–74,779,157, 76 basesExon 4: 74,779,257–74,779,422, 166 basesExon 5: 74,780,780–74,780,835, 56 basesExon 6: 74,782,939–74,783,061, 123 basesExon 7: 74,783,525–74,783,632, 108 basesExon 8: 74,785,182–74,785,299, 118 basesExon 9: 74,787,984–74,788,088, 105 basesExon 10: 74,788,559–74,788,704, 146 basesExon 11: 74,789,039–74,789,315, 277 bases1246810115′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 1.3 kb of the gene's 15.3 kb; 1,173 of those bases code for the protein.

How a genome test reads NCF1

7

positions in NCF1 where ClinVar classes a change as pathogenic or likely pathogenic

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

  • Low mappability (7 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (7 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 15.3 kb of NCF1, introns included, not only the 1.3 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.). NCF1 gene: neutrophil cytosolic factor 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/ncf1

Vancouver

Dante Labs. NCF1 gene: neutrophil cytosolic factor 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/ncf1

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