SDHAF1

gene
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Also known as LYRM8

Summary

SDHAF1 (succinate dehydrogenase complex assembly factor 1, HGNC:33867) is a protein-coding gene on chromosome 19q13.12, encoding Succinate dehydrogenase assembly factor 1, mitochondrial (A6NFY7). 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…. It is a selective cancer dependency (DepMap: 14.2% of cell lines).

The succinate dehydrogenase (SDH) complex (or complex II) of the mitochondrial respiratory chain is composed of 4 individual subunits. The protein encoded by this gene resides in the mitochondria, and is essential for SDH assembly, but does not physically associate with the complex in vivo. Mutations in this gene are associated with SDH-defective infantile leukoencephalopathy (mitochondrial complex II deficiency).

Source: NCBI Gene 644096 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): mitochondrial disease (Definitive, ClinGen) — +4 more curated relationships
  • GWAS associations: 1
  • Clinical variants (ClinVar): 39 total
  • Phenotypes (HPO): 56
  • Cancer dependency (DepMap): dependent in 14.2% of screened cell lines
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_001042631

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:33867
Approved symbolSDHAF1
Namesuccinate dehydrogenase complex assembly factor 1
Location19q13.12
Locus typegene with protein product
StatusApproved
AliasesLYRM8
Ensembl geneENSG00000205138
Ensembl biotypeprotein_coding
OMIM612848
Entrez644096

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000378887

RefSeq mRNA: 1 — MANE Select: NM_001042631 NM_001042631

CCDS: CCDS32999

Canonical transcript exons

ENST00000378887 — 1 exons

ExonStartEnd
ENSE000014791543599518835996312

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 94.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.0912 / max 94.9461, expressed in 1790 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
17545013.09121790

Top tissues by expression

285 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
type B pancreatic cellCL:000016994.53silver quality
olfactory bulbUBERON:000226490.95silver quality
parotid glandUBERON:000183189.93gold quality
mucosa of transverse colonUBERON:000499189.31gold quality
lateral nuclear group of thalamusUBERON:000273689.25gold quality
pancreatic ductal cellCL:000207989.18silver quality
vena cavaUBERON:000408788.86silver quality
substantia nigra pars reticulataUBERON:000196688.14gold quality
middle temporal gyrusUBERON:000277188.13gold quality
lateral globus pallidusUBERON:000247687.91gold quality
substantia nigra pars compactaUBERON:000196587.86gold quality
prefrontal cortexUBERON:000045187.69gold quality
body of tongueUBERON:001187687.55gold quality
diaphragmUBERON:000110387.54silver quality
ponsUBERON:000098887.53gold quality
right lobe of liverUBERON:000111487.38gold quality
cerebellar vermisUBERON:000472087.37gold quality
right hemisphere of cerebellumUBERON:001489087.19gold quality
cerebellar cortexUBERON:000212987.17gold quality
cerebellar hemisphereUBERON:000224587.16gold quality
granulocyteCL:000009487.07gold quality
cerebellumUBERON:000203787.01gold quality
inferior vagus X ganglionUBERON:000536386.83gold quality
dorsal plus ventral thalamusUBERON:000189786.82gold quality
cardia of stomachUBERON:000116286.34gold quality
gingival epitheliumUBERON:000194986.30gold quality
lower esophagus muscularis layerUBERON:003583386.18gold quality
apex of heartUBERON:000209886.14gold quality
lower esophagusUBERON:001347386.14gold quality
muscle layer of sigmoid colonUBERON:003580586.06gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting SDHAF1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-468899.4864.68828
HSA-MIR-6743-5P99.4863.60721
HSA-MIR-127599.4767.902749
HSA-MIR-625-5P99.0268.642031
HSA-MIR-442498.9170.331145
HSA-MIR-393898.7266.07834
HSA-MIR-317998.2265.901445
HSA-MIR-4665-5P97.9167.691536
HSA-MIR-937-5P97.4368.39667
HSA-MIR-4749-3P96.4066.24798
HSA-MIR-4793-3P94.8765.85896

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 14.2% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

  • Leukoencephalopathy with accumulated succinate is a key symptom of defective complex II assembly due to SDHAF1 mutations (PMID:22995659)
  • Studies indicate that an array of tumor syndromes caused by complex II-associated mutations in genes SDHA, SDHB, SDHC, SDHD, SDHAF1 and SDHAF2 have been identified over a decade. (PMID:23174333)
  • that SDHAF1 contributes to iron-sulfur (Fe-S) cluster incorporation into the Fe-S subunit of CII, SDHB. (PMID:26749241)
  • Parallel functional assessment of m(6)A sites in human endodermal differentiation with base editor screens. (PMID:35078991)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusSdhaf1ENSMUSG00000074211
rattus_norvegicusSdhaf1ENSRNOG00000047045

Paralogs (1): LYRM4 (ENSG00000214113)

Protein

Protein identifiers

Succinate dehydrogenase assembly factor 1, mitochondrialA6NFY7 (reviewed: A6NFY7)

Alternative names: LYR motif-containing protein 8

All UniProt accessions (1): A6NFY7

UniProt curated annotations — full annotation on UniProt →

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 SDHAF3. Contributes to iron-sulfur cluster incorporation into SDHB by binding to SDHB and recruiting the iron-sulfur transfer complex formed by HSC20, HSPA9 and ISCU through direct binding to HSC20.

Subunit / interactions. Interacts with SDHB within an SDHA-SDHB subcomplex. Also interacts with the iron-sulfur transfer complex formed by HSC20, HSPA9 and ISCU through direct binding to HSC20. Binding of SDHAF1 to SDHB precedes and is necessary for recruitment of the iron-sulfur transfer complex by SDHAF1.

Subcellular location. Mitochondrion matrix.

Tissue specificity. Ubiquitously expressed.

Disease relevance. Mitochondrial complex II deficiency, nuclear type 2 (MC2DN2) [MIM:619166] A form of mitochondrial complex II deficiency, a disorder with heterogeneous clinical manifestations. Some patients have multisystem involvement of the brain, heart, muscle, liver, and kidneys resulting in death in infancy, whereas others have only isolated cardiac or muscle involvement with onset in adulthood and normal cognition. Clinical features include psychomotor regression in infants, poor growth with lack of speech development, severe spastic quadriplegia, dystonia, progressive leukoencephalopathy, muscle weakness, exercise intolerance, cardiomyopathy. Some patients manifest Leigh syndrome or Kearns-Sayre syndrome. MC2DN2 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. Riboflavin supplementation, which is used as a treatment in SDHAF1-deficient patients, enhances SDHA flavinylation and activity and reduces levels of HIF1A, HIF2A and succinate.

Similarity. Belongs to the complex I LYR family. SDHAF1 subfamily.

RefSeq proteins (1): NP_001036096* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008011Complex1_LYR_domDomain
IPR045295Complex1_LYR_SDHAF1_LYRM8Domain
IPR052687SDHAF1Family

Pfam: PF05347

UniProt features (14 total): sequence variant 6, region of interest 2, mutagenesis site 2, short sequence motif 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-A6NFY7-F177.460.46

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (2):

PositionPhenotype
14–16abolishes interaction with the iron-sulfur transfer complex composed of hsc20, hspa9 and iscu and reduces binding to sdh
53–55retains reduced ability to interact with hsc20 and sdhb.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-9854311Maturation of TCA enzymes and regulation of TCA cycle
R-HSA-1428517Aerobic respiration and respiratory electron transport
R-HSA-1430728Metabolism
R-HSA-71403Citric acid cycle (TCA cycle)

MSigDB gene sets: 223 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY, HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_4HR, HAN_SATB1_TARGETS_DN, GOCC_MITOCHONDRIAL_MATRIX, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS, FOSTER_KDM1A_TARGETS_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNAR_KO_DN, ARNT2_TARGET_GENES, CEBPZ_TARGET_GENES, CREB3L4_TARGET_GENES, HOXC6_TARGET_GENES, ZNF30_TARGET_GENES

GO Biological Process (1): mitochondrial respiratory chain complex II assembly (GO:0034553)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): nucleoplasm (GO:0005654), mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Citric acid cycle (TCA cycle)1
Metabolism1
Aerobic respiration and respiratory electron transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
mitochondrion2
mitochondrial respiratory chain complex assembly1
respiratory chain complex II assembly1
binding1
nuclear lumen1
cellular anatomical structure1
cytoplasm1
intracellular membrane-bounded organelle1
intracellular organelle lumen1

Protein interactions and networks

STRING

848 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SDHAF1SDHAP31040996
SDHAF1SDHBP21912959
SDHAF1F5H5T6F5H5T6941
SDHAF1SDHDO14521940
SDHAF1SDHAF2Q9NX18927
SDHAF1SDHCQ99643922
SDHAF1SDHAF3Q9NRP4899
SDHAF1SDHAF4Q5VUM1835
SDHAF1HSCBQ8IWL3755
SDHAF1LYRM7Q5U5X0728
SDHAF1LYRM4Q9HD34717
SDHAF1HSPA9P30036700
SDHAF1ISCUQ9H1K1693
SDHAF1LYRM9A8MSI8594
SDHAF1NFU1Q9UMS0574

IntAct

26 interactions, top by confidence:

ABTypeScore
SDHAF1SDHBpsi-mi:“MI:0914”(association)0.790
SDHAF1SDHBpsi-mi:“MI:0915”(physical association)0.790
SDHAF1SDHBpsi-mi:“MI:0407”(direct interaction)0.790
SDHBSDHAF1psi-mi:“MI:0914”(association)0.790
SDHBSDHAF1psi-mi:“MI:0915”(physical association)0.790
SDHAF1HSCBpsi-mi:“MI:0407”(direct interaction)0.750
HSCBSDHAF1psi-mi:“MI:0914”(association)0.750
SDHAF1psi-mi:“MI:0915”(physical association)0.560
SDHAF1KRT27psi-mi:“MI:0915”(physical association)0.560
SDHAF1CIDEBpsi-mi:“MI:0915”(physical association)0.560
HSCBRBP5psi-mi:“MI:0914”(association)0.350
SDHAF1NDUFAB1psi-mi:“MI:0914”(association)0.350
SDHAF1psi-mi:“MI:0915”(physical association)0.000
SDHAF1KRT27psi-mi:“MI:0915”(physical association)0.000
SDHAF1CIDEBpsi-mi:“MI:0915”(physical association)0.000

BioGRID (10): SDHAF1 (Two-hybrid), SDHAF1 (Two-hybrid), SDHAF1 (Two-hybrid), SDHAF1 (Affinity Capture-MS), SDHAF1 (Affinity Capture-MS), SDHAF1 (Affinity Capture-MS), SDHAF1 (Positive Genetic), NDUFAB1 (Affinity Capture-MS), SDHA (Affinity Capture-MS), SDHB (Affinity Capture-MS)

ESM2 similar proteins: A1A4I4, A2SXS5, A5PJV8, A6NFY7, A6QPI4, A8PU71, B0K036, O00192, O00255, O02718, O43189, O60232, O75208, O88559, P12755, P83369, Q0P5I0, Q16512, Q2KJ58, Q2NL34, Q32Q90, Q3MII6, Q3U276, Q504T8, Q5C9Z4, Q5QQ50, Q5RB75, Q5T6X4, Q68EN5, Q6DVA0, Q6WVG3, Q7T076, Q7Z6J2, Q86UD0, Q86UK7, Q8CEG5, Q8IVD9, Q8N6N2, Q8NC56, Q8QZV0

Diamond homologs: A6NFY7, A8PU71, B0K036, Q3U276, A6ZYX9, Q3E785, Q54HG5, Q55BM0, Q9US02

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

39 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance26
Likely benign5
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

164 predictions. Top by Δscore:

VariantEffectΔscore
19:35995990:T:TAacceptor_gain0.7500
19:35995990:TG:Tacceptor_gain0.7100
19:35995991:G:GCacceptor_gain0.7100
19:35995959:G:GTdonor_gain0.6400
19:35995665:G:GTdonor_gain0.5900
19:35996019:G:GTdonor_gain0.5300
19:35995923:A:Cacceptor_gain0.5200
19:35995989:CTG:Cacceptor_gain0.5200
19:35996048:G:GCacceptor_gain0.5200
19:35995831:GGAGA:Gacceptor_gain0.5000
19:35995961:A:Tdonor_gain0.4900
19:35995960:G:Tdonor_gain0.4800
19:35996049:AGAAG:Aacceptor_gain0.4800
19:35995988:CCTG:Cacceptor_gain0.4600
19:35996082:G:Tdonor_gain0.4600
19:35995830:TGGAG:Tacceptor_gain0.4500
19:35995921:CGAAG:Cdonor_loss0.4500
19:35995922:GAAG:Gdonor_loss0.4500
19:35995923:AAG:Adonor_loss0.4500
19:35995924:AG:Adonor_loss0.4500
19:35995925:GGT:Gdonor_loss0.4500
19:35995926:G:GCdonor_loss0.4500
19:35995927:T:Gdonor_loss0.4500
19:35996044:CTCTG:Cacceptor_gain0.4400
19:35995302:C:Tdonor_gain0.4300
19:35996039:T:Gacceptor_gain0.4300
19:35996050:G:GTdonor_gain0.4300
19:35995940:G:GTdonor_gain0.4200
19:35996043:A:Gacceptor_gain0.4200
19:35995928:A:Cdonor_loss0.4100

AlphaMissense

718 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:35995381:T:CF36S0.995
19:35995380:T:CF36L0.994
19:35995382:C:AF36L0.994
19:35995382:C:GF36L0.994
19:35995437:C:AR55S0.986
19:35995426:A:TE51V0.985
19:35995381:T:GF36C0.981
19:35995497:T:CF75L0.981
19:35995499:C:AF75L0.981
19:35995499:C:GF75L0.981
19:35995327:T:CL18P0.979
19:35995443:G:TG57W0.976
19:35995444:G:AG57E0.975
19:35995450:G:CR59P0.975
19:35995425:G:AE51K0.974
19:35995438:G:CR55P0.972
19:35995441:G:CR56P0.972
19:35995317:T:GY15D0.971
19:35995298:G:CQ8H0.969
19:35995298:G:TQ8H0.969
19:35995427:G:CE51D0.969
19:35995427:G:TE51D0.969
19:35995443:G:AG57R0.967
19:35995443:G:CG57R0.967
19:35995335:G:CA21P0.961
19:35995432:T:CL53P0.958
19:35995444:G:TG57V0.957
19:35995456:T:CL61P0.957
19:35995287:A:CS5R0.954
19:35995289:C:AS5R0.954

dbSNP variants (sampled 300 via entrez): RS1000071321 (19:35996285 A>C,G), RS1000123444 (19:35996537 C>T), RS1001072788 (19:35994919 T>C), RS1001123544 (19:35995169 G>A,C), RS1002072313 (19:35993776 G>A), RS1002124591 (19:35994012 G>A), RS1003625924 (19:35996103 G>A), RS1004082498 (19:35994254 C>A,T), RS1004084892 (19:35995798 G>T), RS1004434146 (19:35994068 G>T), RS1007594479 (19:35994567 C>A), RS1007748077 (19:35996544 C>T), RS1008093624 (19:35995058 G>A,T), RS1009551595 (19:35994894 C>A), RS1010242572 (19:35994592 C>T)

Disease associations

OMIM: gene MIM:612848 | disease phenotypes: MIM:252011, MIM:619166

GenCC curated gene-disease

DiseaseClassificationInheritance
mitochondrial complex 2 deficiency, nuclear type 2DefinitiveAutosomal recessive
mitochondrial complex II deficiency, nuclear type 1StrongAutosomal recessive
mitochondrial complex II deficiencyModerateAutosomal recessive

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Leigh syndromeLimitedAR
mitochondrial diseaseDefinitiveAR

Mondo (3): mitochondrial complex II deficiency, nuclear type 1 (MONDO:0100294), mitochondrial complex 2 deficiency, nuclear type 2 (MONDO:0030935), (MONDO:0009641)

Orphanet (1): Isolated succinate-CoQ reductase deficiency (Orphanet:3208)

HPO phenotypes

56 total (30 of 56 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000076Vesicoureteral reflux
HP:0000478Abnormality of the eye
HP:0000544External ophthalmoplegia
HP:0000580Pigmentary retinopathy
HP:0000618Blindness
HP:0000639Nystagmus
HP:0000726Dementia
HP:0000737Irritability
HP:0001250Seizure
HP:0001251Ataxia
HP:0001257Spasticity
HP:0001270Motor delay
HP:0001285Spastic tetraparesis
HP:0001290Generalized hypotonia
HP:0001510Growth delay
HP:0001511Intrauterine growth retardation
HP:0001626Abnormality of the cardiovascular system
HP:0001639Hypertrophic cardiomyopathy
HP:0001712Left ventricular hypertrophy
HP:0001824Weight loss
HP:0002123Generalized myoclonic seizure
HP:0002313Spastic paraparesis
HP:0002333Motor deterioration
HP:0002352Leukoencephalopathy
HP:0002359Frequent falls
HP:0002376Developmental regression
HP:0002421Poor head control
HP:0002474Expressive language delay
HP:0002505Loss of ambulation

GWAS associations

1 associations (top):

StudyTraitp-value
GCST011352_10Alanine aminotransferase levels6.000000e-09

MeSH disease descriptors (1)

DescriptorNameTree numbers
C565375Mitochondrial Complex II Deficiency (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Leflunomidedecreases expression2
Air Pollutantsdecreases expression, affects expression, increases abundance2
Methyl Methanesulfonatedecreases expression, increases expression2
bisphenol Faffects cotreatment, increases expression1
bisphenol Adecreases expression1
methylparabenincreases expression1
sodium arsenitedecreases expression1
benzo(e)pyrenedecreases methylation1
di-n-butylphosphoric acidaffects expression1
Adeninedecreases expression1
Benzo(a)pyrenedecreases methylation1
Cisplatindecreases expression1
Colchicinedecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Ethyl Methanesulfonatedecreases expression1
Etoposidedecreases expression1
Formaldehydedecreases expression1
Indomethacinaffects cotreatment, increases expression1
Methapyrilenedecreases methylation1
Ozoneaffects expression, increases abundance1
Smokedecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
Valproic Acidincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Aflatoxin B1decreases methylation1
Mitomycindecreases expression1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.