GGACT

gamma-glutamylamine cyclotransferase

Basic information

Region (hg38): 13:100530164-100589528

Previous symbols: [ "A2LD1" ]

Links

ENSG00000134864 ∙ NCBI:87769 ∙ OMIM:613378 ∙ HGNC:25100 ∙ Uniprot:Q9BVM4 ∙ 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 GGACT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGACT 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6	4	1	11
Total	0	0	19	4	1

Variants in GGACT

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

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

Position	Type	Phenotype	Significance	ClinVar
13-100530200-A-C		Propionic acidemia	Uncertain significance (Mar 02, 2018)
13-100530222-TTCAC-T		Propionic acidemia	Likely benign (Jun 19, 2018)
13-100530257-A-G		Propionic acidemia	Uncertain significance (Jan 13, 2018)
13-100530281-C-T		Propionic acidemia	Likely benign (Jan 13, 2018)
13-100530282-G-A		Propionic acidemia	Uncertain significance (Jan 12, 2018)
13-100530318-C-CA		Propionic acidemia	Benign/Likely benign (Aug 15, 2020)
13-100530325-T-G		Propionic acidemia	Likely benign (Jan 13, 2018)
13-100530356-C-G		Propionic acidemia	Uncertain significance (Jan 12, 2018)
13-100530356-C-T		Propionic acidemia	Uncertain significance (Jan 13, 2018)
13-100530389-T-G		Propionic acidemia	Uncertain significance (Jan 13, 2018)
13-100530454-TTGAA-T			Benign (Jul 03, 2019)
13-100532156-G-A		not specified	Uncertain significance (Aug 26, 2024)
13-100532189-C-T		not specified	Uncertain significance (Mar 03, 2025)
13-100532201-G-C		not specified	Uncertain significance (Sep 20, 2024)
13-100532213-C-T		not specified	Uncertain significance (Aug 08, 2022)
13-100532218-G-A		not specified	Uncertain significance (Sep 14, 2022)
13-100532258-T-C		not specified	Uncertain significance (Jan 23, 2024)
13-100532288-C-T		not specified	Uncertain significance (Oct 08, 2024)
13-100532341-C-T		not specified	Uncertain significance (Feb 22, 2025)
13-100532344-C-A		not specified	Uncertain significance (Dec 05, 2024)
13-100532402-C-G		not specified	Uncertain significance (Jan 27, 2025)
13-100532413-C-T		not specified	Uncertain significance (Nov 11, 2024)
13-100532420-C-A		not specified	Uncertain significance (Feb 01, 2025)
13-100532455-C-T		not specified	Uncertain significance (Jan 18, 2023)
13-100532458-G-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGACT	protein_coding	protein_coding	ENST00000376250	1	57973

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000754	0.332	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	73	106	0.692	0.00000869	956
Missense in Polyphen		29	41.672	0.69591		399
Synonymous	2.03	36	55.2	0.652	0.00000484	341
Loss of Function	-0.594	4	2.91	1.38	1.25e-7	30

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contributes to degradation of proteins cross-linked by transglutaminases by degrading the cross-link between a lysine and a glutamic acid residue. Catalyzes the formation of 5-oxo-L- proline from L-gamma-glutamyl-L-epsilon-lysine. Inactive with L- gamma-glutamyl-alpha-amino acid substrates such as L-gamma- glutamyl-L-alpha-cysteine and L-gamma-glutamyl-L-alpha-alanine. {ECO:0000269|PubMed:20110353}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.32

Haploinsufficiency Scores

• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Ggact

Gene ontology

• Biological process: cellular modified amino acid catabolic process
• Cellular component: extracellular exosome
• Molecular function: protein binding;gamma-glutamylaminecyclotransferase activity