SUGCT

succinyl-CoA:glutarate-CoA transferase

Basic information

Region (hg38): 7:40135005-40860763

Previous symbols: [ "C7orf10" ]

Links

ENSG00000175600NCBI:79783OMIM:609187HGNC:16001Uniprot:Q9HAC7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • glutaric acidemia type 3 (Supportive), mode of inheritance: AR
  • glutaric acidemia type 3 (Strong), mode of inheritance: AR
  • glutaric acidemia type 3 (Moderate), mode of inheritance: AR
  • glutaric acidemia type 3 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Glutaric aciduria IIIARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical1909402; 12555941; 18926513
The clinical significance of the condition is unclear

ClinVar

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

  • not_provided (80 variants)
  • not_specified (56 variants)
  • Glutaryl-CoA_oxidase_deficiency (9 variants)
  • SUGCT-related_disorder (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUGCT gene is commonly pathogenic or not. These statistics are base on transcript: NM_001193313.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
15
clinvar
3
clinvar
18
missense
73
clinvar
7
clinvar
80
nonsense
1
clinvar
1
clinvar
2
clinvar
4
start loss
0
frameshift
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
Total 1 2 78 22 3

Highest pathogenic variant AF is 0.000222729

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SUGCTprotein_codingprotein_codingENST00000309930 15725788
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.82e-90.73112446901771246460.000710
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5362252490.9040.00001263014
Missense in Polyphen10596.9781.08271134
Synonymous-0.02669594.71.000.00000532921
Loss of Function1.441724.70.6880.00000129318

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001460.00145
Ashkenazi Jewish0.0001040.0000994
East Asian0.002540.00251
Finnish0.0008460.000836
European (Non-Finnish)0.0004610.000451
Middle Eastern0.002540.00251
South Asian0.0009890.000883
Other0.0008620.000826

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalyzes the succinyl-CoA-dependent conversion of glutarate to glutaryl-CoA. Can use different dicarboxylic acids as CoA acceptors, the preferred ones are glutarate, succinate, adipate, and 3-hydroxymethylglutarate. {ECO:0000269|PubMed:23893049}.;

Recessive Scores

pRec
0.171

Intolerance Scores

loftool
rvis_EVS
0.02
rvis_percentile_EVS
55.45

Haploinsufficiency Scores

pHI
hipred
N
hipred_score
0.196
ghis
0.453

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sugct
Phenotype

Gene ontology

Biological process
Cellular component
mitochondrion
Molecular function
protein binding;succinate-hydroxymethylglutarate CoA-transferase activity