SDHAF3
protein-codingsuccinate dehydrogenase complex assembly factor 3, the group of LYR motif containing|Mitochondrial respiratory chain complex assembly factors
Gene summary
Predicted to be involved in mitochondrial respiratory chain complex II assembly and regulation of gluconeogenesis. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]
- ACN9
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~64.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SDHAF3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020186.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 25 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 25 | 0 | 0 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_064571.1 | 2 | MANE Select | |
| Ensembl | ENSP00000414066.2 | 2 | MANE Select | |
| Ensembl | ENSP00000353548.4 | 2 | Standard | |
| Ensembl | ENSP00000353548.4 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- succinate metabolic process
- regulation of gluconeogenesis
- response to oxidative stress
- mitochondrial respiratory chain complex II assembly
Cellular Component
- mitochondrial intermembrane space
- mitochondrial matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000432641
- Coding exons
- 2
- Length
- 65174
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125748
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.752 | 87 | 69.4 | 1.25 | 0.00000335 | 811 |
| Missense (PolyPhen) | 36 | 25.042 | 1.4376 | 325 | ||
| Synonymous | -0.801 | 34 | 28.6 | 1.19 | 0.00000147 | 236 |
| Loss of Function | 0.332 | 4 | 4.78 | 0.836 | 2.06e-7 | 52 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays an essential role in the assembly of succinate dehydrogenase (SDH), an enzyme complex (also referred to as respiratory complex II) that is a component of both the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. Promotes maturation of the iron-sulfur protein subunit SDHB of the SDH catalytic dimer, protecting it from the deleterious effects of oxidants. May act together with SDHAF1. {ECO:0000250|UniProtKB:Q04401, ECO:0000250|UniProtKB:Q8SZ16}.;
Recessive Scores
- pRec
- 0.0879
Intolerance Scores
- RVIS EVS
- 0.3
- RVIS percentile EVS
- 72.01
Essentials
- Essential (gene trap)
- N