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Gene

AFG3L2

AFG3 like matrix AAA peptidase subunit 2

Summary

Cytogenetic location
18p11.21
Coordinates
Chromosome 18: 12,328,944–12,377,227 (GRCh38)
Exons
17 exons across 48.3 kb
Protein
797 amino acids
Inheritance
Autosomal dominant
Also known as
SPAX5
Previous symbols
SCA28
MANE Select transcript
ENST00000269143.8NM_006796.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Curated reports relevant to this gene

  • Autosomal Dominant Cerebellar Ataxias (SCAs and DRPLA)

    • Autosomal Dominant Cerebellar AtaxiaAutosomal dominant

      A group of dominantly inherited ataxias, including SCA1, SCA2, SCA3 (Machado-Joseph disease), SCA6, SCA7, SCA17, SCA27B and DRPLA, caused by repeat expansions or point variants in genes such as ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, TBP, ATN1 and FGF14.

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

      Genetic counselling and presymptomatic testing for relatives, physiotherapy and symptom management; some forms, such as SCA27B, may respond to specific medication.

  • Hereditary Optic Neuropathy

    • Hereditary Optic Atrophy

      Inherited loss of optic nerve fibres, most often autosomal dominant optic atrophy caused by changes in OPA1, and including rarer types caused by OPA3, DNM1L, SSBP1 and other genes.

      • 2 GenCC submitters rate it definitive or strong

  • Primary Mitochondrial Disease

    • Mitochondrial DNA Depletion Syndrome

      Caused by variants in nuclear genes such as POLG, TWNK, TK2, DGUOK, MPV17, RRM2B and SUCLA2, which reduce the amount of mitochondrial DNA and can cause muscle, liver or brain disease.

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

      Knowing is directly actionable: valproate must be avoided in POLG disease because of the risk of fatal liver failure, and TK2 deficiency has a nucleoside therapy.

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 AFG3L2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 18, with a bracket where AFG3L2 sits. AFG3L2 and 12 genes near it on chromosome 18, from 11,853,086 to 12,853,085.Chromosome 1818p11.21p11.32p11.31p11.23p11.22p11.21p11.1q11.1q11.2q12.1q12.2q12.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q2312 Mb12.2 Mb12.4 Mb12.6 Mb12.8 MbGNAL: 11,689,243–11,885,685, forward strandGNALCHMP1B: 11,851,413–11,854,444, forward strandCHMP1BMPPE1: 11,882,622–11,909,180, reverse strandMPPE1IMPA2: 11,981,025–12,032,177, forward strandIMPA2ANKRD62: 12,093,729–12,129,764, forward strandANKRD62CIDEA: 12,254,165–12,277,595, forward strandCIDEATUBB6: 12,307,287–12,345,784, forward strandTUBB6AFG3L2: 12,328,944–12,377,227, reverse strandAFG3L2PRELID3A: 12,407,896–12,432,254, forward strandPRELID3ASPIRE1: 12,446,512–12,658,129, reverse strandSPIRE1PSMG2: 12,658,043–12,728,945, forward strandPSMG2CEP76: 12,660,738–12,702,777, reverse strandCEP76PTPN2: 12,785,478–12,929,643, reverse strandPTPN2Diagram of AFG3L2: 17 exons on the reverse strand of chromosome 18Exon 16: 8 known disease-causing sitesExon 15: 4 known disease-causing sitesExon 14: 3 known disease-causing sitesExon 13: 1 known disease-causing siteExon 11: 2 known disease-causing sitesExon 10: 2 known disease-causing sitesExon 9: 4 known disease-causing sitesExon 8: 2 known disease-causing sitesExon 7: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 3: 3 known disease-causing sitesExon 2: 1 known disease-causing siteExon 17: 12,328,944–12,329,783, 840 basesExon 16: 12,337,341–12,337,535, 195 basesExon 15: 12,340,201–12,340,401, 201 basesExon 14: 12,344,132–12,344,247, 116 basesExon 13: 12,348,273–12,348,383, 111 basesExon 12: 12,351,085–12,351,210, 126 basesExon 11: 12,351,306–12,351,413, 108 basesExon 10: 12,353,005–12,353,158, 154 basesExon 9: 12,356,694–12,356,831, 138 basesExon 8: 12,358,670–12,358,943, 274 basesExon 7: 12,359,927–12,360,051, 125 basesExon 6: 12,363,782–12,363,856, 75 basesExon 5: 12,366,965–12,367,117, 153 basesExon 4: 12,367,276–12,367,382, 107 basesExon 3: 12,370,849–12,370,926, 78 basesExon 2: 12,371,592–12,371,691, 100 basesExon 1: 12,376,969–12,377,227, 259 bases1716141210864215′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 3.2 kb of the gene's 48.3 kb; 2,394 of those bases code for the protein.

How a genome test reads AFG3L2

34

positions in AFG3L2 where ClinVar classes a change as pathogenic or likely pathogenic

3 of them (8.8%) fall in regions short reads find hard.

  • Segmental duplications (3 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 48.3 kb of AFG3L2, introns included, not only the 3.2 kb of exons.

Genes linked to the same conditions

Traits linked to AFG3L2

The Human Phenotype Ontology lists these as features of the rare conditions AFG3L2 can cause. Each trait's page lists the other genes linked to it.

External links

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.). AFG3L2 gene: AFG3 like matrix AAA peptidase subunit 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/afg3l2

Vancouver

Dante Labs. AFG3L2 gene: AFG3 like matrix AAA peptidase subunit 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/afg3l2

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