SDHAF4

succinate dehydrogenase complex assembly factor 4, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 6:70566916-70589569

Previous symbols: [ "C6orf57" ]

Links

ENSG00000154079 ∙ NCBI:135154 ∙ OMIM:619198 ∙ HGNC:20957 ∙ Uniprot:Q5VUM1 ∙ 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 SDHAF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDHAF4 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 SDHAF4

This is a list of pathogenic ClinVar variants found in the SDHAF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-70566945-C-T		not specified	Uncertain significance (Feb 27, 2024)
6-70566950-T-A		not specified	Uncertain significance (Dec 15, 2022)
6-70566951-C-T		not specified	Uncertain significance (Jun 28, 2022)
6-70566967-G-T		not specified	Uncertain significance (Jun 16, 2023)
6-70566992-T-C		not specified	Uncertain significance (Oct 13, 2023)
6-70566998-G-A		not specified	Uncertain significance (Feb 15, 2023)
6-70579476-C-T		not specified	Uncertain significance (May 13, 2024)
6-70579504-A-C		not specified	Uncertain significance (Apr 07, 2023)
6-70579519-G-A		not specified	Uncertain significance (Mar 04, 2024)
6-70579534-A-G		not specified	Uncertain significance (Mar 01, 2023)
6-70579536-G-T		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDHAF4	protein_coding	protein_coding	ENST00000370474	3	22653

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0989	0.782	124989	4	724	125717	0.00290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.249	52	57.3	0.908	0.00000301	671
Missense in Polyphen		17	24.118	0.70488		276
Synonymous	-0.932	25	19.7	1.27	9.32e-7	209
Loss of Function	1.20	2	4.84	0.413	2.88e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0170	0.0168
Ashkenazi Jewish	0.000596	0.000595
East Asian	0.00918	0.00918
Finnish	0.00	0.00
European (Non-Finnish)	0.000531	0.000528
Middle Eastern	0.00918	0.00918
South Asian	0.00543	0.00537
Other	0.00345	0.00343

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 (PubMed:24954416). Binds to the flavoprotein subunit SDHA in its FAD-bound form, blocking the generation of excess reactive oxigen species (ROS) and facilitating its assembly with the iron-sulfur protein subunit SDHB into the SDH catalytic dimer (By similarity). {ECO:0000250|UniProtKB:P38345, ECO:0000269|PubMed:24954416}.

Recessive Scores

• pRec: 0.0930

Intolerance Scores

• rvis_EVS: 0.57
• rvis_percentile_EVS: 81.89

Haploinsufficiency Scores

• pHI: 0.0442
• hipred: N
• hipred_score: 0.178
• ghis: 0.398

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Sdhaf4

Gene ontology

• Biological process: neural retina development;mitochondrial respiratory chain complex II assembly;innate immune response;cellular respiration
• Cellular component: cellular_component;mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone);mitochondrial matrix
• Molecular function: molecular_function;succinate dehydrogenase (ubiquinone) activity