SDHAF3

succinate dehydrogenase complex assembly factor 3, the group of LYR motif containing|Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 7:97117698-97181763

Previous symbols: [ "ACN9" ]

Links

ENSG00000196636 ∙ NCBI:57001 ∙ OMIM:615773 ∙ HGNC:21752 ∙ Uniprot:Q9NRP4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDHAF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDHAF3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in SDHAF3

This is a list of pathogenic ClinVar variants found in the SDHAF3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-97117728-C-T		not specified	Uncertain significance (Apr 15, 2024)
7-97117733-C-T		not specified	Uncertain significance (Mar 11, 2022)
7-97117738-C-A		not specified	Uncertain significance (Jun 22, 2023)
7-97117749-T-C		not specified	Uncertain significance (Nov 13, 2024)
7-97117751-C-T		not specified	Uncertain significance (Jan 17, 2023)
7-97117784-C-G		not specified	Uncertain significance (Aug 15, 2023)
7-97117796-C-T		not specified	Uncertain significance (Feb 10, 2022)
7-97181063-A-G		not specified	Uncertain significance (Jun 18, 2024)
7-97181173-T-G		not specified	Uncertain significance (Nov 03, 2023)
7-97181198-A-G		not specified	Uncertain significance (Aug 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDHAF3	protein_coding	protein_coding	ENST00000432641	2	65174

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00264	0.576	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.752	87	69.4	1.25	0.00000335	811
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000622	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.240
• ghis: 0.396

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Sdhaf3

Gene ontology

• 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