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Gene

NDUFA9

NADH:ubiquinone oxidoreductase subunit A9

Summary

Cytogenetic location
12p13.3
Coordinates
Chromosome 12: 4,649,114–4,694,317 (GRCh38)
Exons
11 exons across 45.2 kb
Protein
377 amino acids
Also known as
SDR22E1, CI-39k, COQ11
Previous symbols
NDUFS2L
MANE Select transcript
ENST00000266544.10NM_005002.5
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

    • Leigh Syndrome

      • One of 69 genes linked to it

        A progressive neurological disease defined by specific neuropathological features associating brainstem and basal ganglia lesions.

        • ClinGen rates the link moderate

    • Primary Mitochondrial Disease

      • Mitochondrial Respiratory Chain Complex Deficiency

        One of 61 genes linked to it

        Isolated deficiencies of complex I, II, III, IV or V, caused by variants in nuclear or mitochondrial genes, which can affect the brain, muscles, heart, liver and other energy-demanding organs.

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

        Knowing can end a diagnostic search and guide surveillance of affected organs and avoidance of drugs toxic to mitochondria.

    How NDUFA9 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 12, with a bracket where NDUFA9 sits. NDUFA9 and 15 genes near it on chromosome 12, from 4,171,716 to 5,171,715.Chromosome 1212p13.3p13.33p13.32p13.31p13.2p13.1p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11q12q13.11q13.12q13.13q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.11q24.12q24.13q24.21q24.22q24.23q24.31q24.32q24.334.2 Mb4.4 Mb4.6 Mb4.8 Mb5 MbCCND2: 4,269,755–4,306,933, forward strandCCND2: 4,273,762–4,405,490, forward strandTIGAR: 4,307,763–4,360,028, forward strandTIGARFGF23: 4,368,227–4,379,713, reverse strandFGF23FGF6: 4,428,155–4,445,816, reverse strandFGF6FERRY3: 4,487,735–4,538,519, reverse strandFERRY3RAD51AP1: 4,538,775–4,560,254, forward strandRAD51AP1DYRK4: 4,562,187–4,616,764, forward strandDYRK4: 4,604,944–4,662,643, forward strandAKAP3: 4,613,383–4,649,072, reverse strandAKAP3: 4,649,101–4,774,184, forward strandNDUFA9: 4,649,114–4,694,317, forward strandNDUFA9GALNT8: 4,719,870–4,851,927, forward strandGALNT8KCNA6: 4,809,334–4,813,318, forward strandKCNA6KCNA1: 4,909,905–4,918,256, forward strandKCNA1KCNA5: 5,043,879–5,052,613, forward strandKCNA5Diagram of NDUFA9: 11 exons on the forward strand of chromosome 12Exon 3: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 10: 1 known disease-causing siteExon 11: 1 known disease-causing siteExon 1: 4,649,114–4,649,175, 62 basesExon 2: 4,654,292–4,654,462, 171 basesExon 3: 4,654,825–4,654,922, 98 basesExon 4: 4,657,748–4,657,839, 92 basesExon 5: 4,659,036–4,659,177, 142 basesExon 6: 4,662,533–4,662,635, 103 basesExon 7: 4,668,457–4,668,524, 68 basesExon 8: 4,669,741–4,669,817, 77 basesExon 9: 4,682,205–4,682,300, 96 basesExon 10: 4,685,259–4,685,325, 67 basesExon 11: 4,686,938–4,694,317, 7,380 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 8.4 kb of the gene's 45.2 kb; 1,134 of those bases code for the protein.

    How a genome test reads NDUFA9

    6

    positions in NDUFA9 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 45.2 kb of NDUFA9, introns included, not only the 8.4 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.). NDUFA9 gene: NADH:ubiquinone oxidoreductase subunit A9. Retrieved 16 October 2026, from https://dantelabs.com/genes/ndufa9

    Vancouver

    Dante Labs. NDUFA9 gene: NADH:ubiquinone oxidoreductase subunit A9 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ndufa9

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