SUGCT

succinyl-CoA:glutarate-CoA transferase

Basic information

Region (hg38): 7:40135005-40860763

Previous symbols: [ "C7orf10" ]

Links

ENSG00000175600 ∙ NCBI:79783 ∙ OMIM:609187 ∙ HGNC:16001 ∙ Uniprot:Q9HAC7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Glutaric aciduria III	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical	1909402; 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.

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.

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				15	6	21
missense			54	3		57
nonsense			3			3
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)		1	1			2
splice region				4	2	6
non coding			2	3	40	45
Total	0	1	61	21	46

Variants in SUGCT

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

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

Position	Type	Phenotype	Significance	ClinVar
7-40135012-A-C			Uncertain significance (Aug 31, 2024)
7-40135015-C-T		not specified	Uncertain significance (Feb 21, 2024)
7-40135017-C-CGCGATGCTG			Likely benign (Feb 16, 2024)
7-40135027-G-C		not specified	Uncertain significance (Jan 27, 2022)
7-40135045-G-A			Uncertain significance (May 22, 2024)
7-40135051-C-G		not specified	Uncertain significance (Sep 30, 2024)
7-40135058-G-T		not specified	Uncertain significance (Jan 22, 2025)
7-40135074-C-A			Benign (Jan 23, 2025)
7-40135077-C-T			Likely benign (May 15, 2024)
7-40135079-G-A			Uncertain significance (May 25, 2022)
7-40135087-G-T			Uncertain significance (Jul 21, 2022)
7-40135112-C-T		not specified	Conflicting classifications of pathogenicity (Jan 15, 2025)
7-40180813-T-C			Benign (Jul 09, 2018)
7-40180876-A-G			Benign (Jul 10, 2018)
7-40180908-C-G			Benign (Jul 09, 2018)
7-40180949-A-G		not specified	Uncertain significance (Feb 16, 2023)
7-40180972-A-C			Conflicting classifications of pathogenicity (Dec 23, 2024)
7-40181006-T-C			Likely benign (Oct 22, 2024)
7-40181126-G-A			Benign (Jul 09, 2018)
7-40181746-C-CA			Benign (Oct 05, 2019)
7-40181974-G-A			Uncertain significance (Feb 28, 2022)
7-40181994-T-A		not specified	Uncertain significance (Oct 05, 2023)
7-40182002-C-A		not specified	Uncertain significance (Feb 28, 2023)
7-40182024-A-T		not specified	Uncertain significance (Sep 26, 2024)
7-40182025-C-G		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUGCT	protein_coding	protein_coding	ENST00000309930	15	725788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.82e-9	0.731	124469	0	177	124646	0.000710

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.536	225	249	0.904	0.0000126	3014
Missense in Polyphen		105	96.978	1.0827		1134
Synonymous	-0.0266	95	94.7	1.00	0.00000532	921
Loss of Function	1.44	17	24.7	0.688	0.00000129	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00146	0.00145
Ashkenazi Jewish	0.000104	0.0000994
East Asian	0.00254	0.00251
Finnish	0.000846	0.000836
European (Non-Finnish)	0.000461	0.000451
Middle Eastern	0.00254	0.00251
South Asian	0.000989	0.000883
Other	0.000862	0.000826

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

• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.196
• ghis: 0.453

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sugct

Gene ontology

• Cellular component: mitochondrion
• Molecular function: protein binding;succinate-hydroxymethylglutarate CoA-transferase activity