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.

not_specified (45 variants)

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. These statistics are base on transcript: NM_000201648.3. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			43 clinvar	2 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	2	0

Loading clinvar variants...

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
Phenotype

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