SDHAF4
Basic information
Region (hg38): 6:70566917-70589569
Previous symbols: [ "C6orf57" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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) | ||
6-70566956-C-T | not specified | Uncertain significance (Aug 12, 2024) | ||
6-70566967-G-T | not specified | Uncertain significance (Jun 16, 2023) | ||
6-70566971-A-T | not specified | Uncertain significance (Sep 12, 2024) | ||
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) | ||
6-70579501-C-T | not specified | Uncertain significance (Jul 30, 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) | ||
6-70579560-C-A | not specified | Uncertain significance (Dec 03, 2024) | ||
6-70588652-A-C | not specified | Uncertain significance (Sep 30, 2024) |
GnomAD
Source:
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:
- 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
- loftool
- 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_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Sdhaf4
- Phenotype
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