GLYAT

glycine-N-acyltransferase

Basic information

Region (hg38): 11:58640426-58731974

Links

ENSG00000149124 ∙ NCBI:10249 ∙ OMIM:607424 ∙ HGNC:13734 ∙ Uniprot:Q6IB77 ∙ 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 GLYAT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLYAT 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in GLYAT

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

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

Position	Type	Phenotype	Significance	ClinVar
11-58709776-A-G		not specified	Uncertain significance (Jan 19, 2022)
11-58709899-T-A		not specified	Uncertain significance (Oct 13, 2023)
11-58709944-C-T		not specified	Uncertain significance (Aug 02, 2022)
11-58709960-T-G		not specified	Uncertain significance (Jun 06, 2023)
11-58709968-A-C		not specified	Uncertain significance (Aug 17, 2022)
11-58709984-T-C		not specified	Uncertain significance (Nov 20, 2023)
11-58710008-C-G		not specified	Uncertain significance (Oct 21, 2021)
11-58710011-G-T		not specified	Uncertain significance (Sep 28, 2022)
11-58710016-C-A		not specified	Uncertain significance (May 16, 2023)
11-58710035-A-G		not specified	Uncertain significance (Aug 16, 2021)
11-58710038-A-G		not specified	Uncertain significance (Feb 22, 2023)
11-58710071-A-G		not specified	Uncertain significance (Dec 12, 2023)
11-58710104-A-G		not specified	Uncertain significance (Jul 14, 2021)
11-58710137-C-G		not specified	Uncertain significance (Sep 29, 2023)
11-58710609-C-G		not specified	Uncertain significance (Apr 27, 2023)
11-58710663-T-C		not specified	Uncertain significance (Oct 12, 2021)
11-58710665-T-G		not specified	Uncertain significance (Jun 22, 2023)
11-58710680-A-C		not specified	Uncertain significance (May 24, 2023)
11-58710687-G-T		not specified	Uncertain significance (May 17, 2023)
11-58712793-G-A		not specified	Uncertain significance (Aug 17, 2022)
11-58715318-G-T		not specified	Uncertain significance (Jul 08, 2022)
11-58715338-A-G		not specified	Uncertain significance (Nov 08, 2022)
11-58715400-T-C		not specified	Likely benign (Nov 22, 2021)
11-58724481-G-T		not specified	Uncertain significance (Jan 16, 2024)
11-58724491-C-T		not specified	Uncertain significance (Feb 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLYAT	protein_coding	protein_coding	ENST00000344743	5	91549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.64e-8	0.106	125657	0	47	125704	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.907	187	155	1.20	0.00000720	1959
Missense in Polyphen		62	45.578	1.3603		647
Synonymous	0.475	51	55.5	0.919	0.00000258	532
Loss of Function	-0.213	11	10.3	1.07	4.34e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000762	0.000761
Finnish	0.00	0.00
European (Non-Finnish)	0.000248	0.000238
Middle Eastern	0.000762	0.000761
South Asian	0.0000654	0.0000653
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial acyltransferase which transfers an acyl group to the N-terminus of glycine and glutamine, although much less efficiently. Can conjugate numerous substrates to form a variety of N-acylglycines, with a preference for benzoyl-CoA over phenylacetyl-CoA as acyl donors. Thereby detoxify xenobiotics, such as benzoic acid or salicylic acid, and endogenous organic acids, such as isovaleric acid. {ECO:0000269|PubMed:22475485, ECO:0000269|PubMed:7802672}.
• Pathway: Phenylalanine metabolism - Homo sapiens (human);Phenylacetate Metabolism;Amino acid conjugation of benzoic acid;Metapathway biotransformation Phase I and II;Conjugation of benzoate with glycine;Conjugation of salicylate with glycine;Conjugation of carboxylic acids;Amino Acid conjugation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.274

Intolerance Scores

• loftool: 0.852
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0911
• hipred: N
• hipred_score: 0.112
• ghis: 0.382

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.584

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Glyat

Gene ontology

• Biological process: glycine metabolic process;acyl-CoA metabolic process;xenobiotic metabolic process;response to toxic substance;monocarboxylic acid metabolic process;benzoyl-CoA metabolic process
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: protein binding;transferase activity, transferring acyl groups;glycine N-acyltransferase activity;glycine N-benzoyltransferase activity