GCAT

glycine C-acetyltransferase

Basic information

Region (hg38): 22:37807904-37817176

Links

ENSG00000100116 ∙ NCBI:23464 ∙ OMIM:607422 ∙ HGNC:4188 ∙ Uniprot:O75600 ∙ 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 GCAT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCAT 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			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	38	0	0

Variants in GCAT

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

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

Position	Type	Phenotype	Significance	ClinVar
22-37807974-C-T		not specified	Uncertain significance (Dec 05, 2022)
22-37807975-C-T		not specified	Uncertain significance (Dec 19, 2022)
22-37808146-T-C		not specified	Uncertain significance (Oct 26, 2022)
22-37808161-G-A		not specified	Uncertain significance (Sep 29, 2023)
22-37809961-T-C		not specified	Uncertain significance (Jun 07, 2023)
22-37809983-G-T		not specified	Uncertain significance (Jun 12, 2023)
22-37810006-A-T		not specified	Uncertain significance (May 26, 2023)
22-37810017-T-C		not specified	Uncertain significance (May 29, 2024)
22-37810030-T-G		not specified	Uncertain significance (Sep 21, 2023)
22-37810100-G-C		not specified	Uncertain significance (Apr 08, 2024)
22-37810113-T-A		not specified	Uncertain significance (Sep 22, 2023)
22-37810114-T-C		not specified	Uncertain significance (Jun 29, 2023)
22-37812959-T-G		not specified	Uncertain significance (May 15, 2024)
22-37812960-G-T		not specified	Uncertain significance (Jan 04, 2022)
22-37813508-C-T		not specified	Uncertain significance (Dec 12, 2023)
22-37813532-C-T		not specified	Uncertain significance (Jun 22, 2023)
22-37813533-G-A		not specified	Uncertain significance (Feb 26, 2024)
22-37813547-C-T		not specified	Uncertain significance (Dec 07, 2021)
22-37813556-C-T		not specified	Uncertain significance (Mar 26, 2024)
22-37813557-G-T		not specified	Uncertain significance (Aug 14, 2023)
22-37813571-G-A		not specified	Uncertain significance (Dec 15, 2022)
22-37813576-G-A		not specified	Uncertain significance (May 09, 2022)
22-37813580-G-A		not specified	Uncertain significance (Mar 01, 2023)
22-37815182-C-G		not specified	Uncertain significance (Mar 20, 2023)
22-37815253-C-A		not specified	Uncertain significance (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCAT	protein_coding	protein_coding	ENST00000323205	9	9272

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.53e-8	0.388	125501	2	245	125748	0.000983

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.164	281	273	1.03	0.0000166	2814
Missense in Polyphen		95	108.19	0.87811		1158
Synonymous	1.68	92	115	0.800	0.00000693	958
Loss of Function	0.814	14	17.7	0.791	8.37e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00750	0.00746
Ashkenazi Jewish	0.000498	0.000496
East Asian	0.00373	0.00370
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000234	0.000229
Middle Eastern	0.00373	0.00370
South Asian	0.000196	0.000163
Other	0.00163	0.00163

dbNSFP

Source: dbNSFP

• Pathway: Glycine, serine and threonine metabolism - Homo sapiens (human);3-Phosphoglycerate dehydrogenase deficiency;Non Ketotic Hyperglycinemia;Glycine and Serine Metabolism;Dimethylglycine Dehydrogenase Deficiency;Hyperglycinemia, non-ketotic;Dimethylglycine Dehydrogenase Deficiency;Sarcosinemia;Dihydropyrimidine Dehydrogenase Deficiency (DHPD);Metabolism of amino acids and derivatives;Glycine Serine metabolism;Metabolism;Glycine, serine, alanine and threonine metabolism;Threonine catabolism (Consensus)

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.0849
• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.42

Haploinsufficiency Scores

• pHI: 0.0751
• hipred: N
• hipred_score: 0.219

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gcat
• Phenotype: normal phenotype

Gene ontology

• Biological process: cellular amino acid metabolic process;biosynthetic process;L-threonine catabolic process to glycine
• Cellular component: nucleoplasm;mitochondrion;mitochondrial inner membrane;nuclear speck
• Molecular function: glycine C-acetyltransferase activity;pyridoxal phosphate binding