GLYATL1

glycine-N-acyltransferase like 1

Basic information

Region (hg38): 11:58905397-59043527

Links

ENSG00000166840 ∙ NCBI:92292 ∙ OMIM:614761 ∙ HGNC:30519 ∙ Uniprot:Q969I3 ∙ 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 GLYATL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLYATL1 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in GLYATL1

This is a list of pathogenic ClinVar variants found in the GLYATL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-58954798-C-T		not specified	Uncertain significance (Mar 25, 2024)
11-58954803-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-58954814-G-T		not specified	Likely benign (Aug 10, 2021)
11-58955208-G-C		not specified	Uncertain significance (Feb 05, 2024)
11-58955236-T-C		not specified	Uncertain significance (Apr 24, 2024)
11-58955261-G-T		not specified	Uncertain significance (May 17, 2023)
11-58955266-C-T		not specified	Uncertain significance (Nov 09, 2021)
11-58955286-A-T		not specified	Uncertain significance (May 17, 2023)
11-58955287-A-G		not specified	Uncertain significance (Mar 20, 2024)
11-58955292-T-A		not specified	Uncertain significance (May 17, 2023)
11-58955624-T-A		not specified	Uncertain significance (Jul 05, 2022)
11-58955651-A-G		not specified	Uncertain significance (Aug 30, 2021)
11-58955663-T-A		not specified	Uncertain significance (Feb 27, 2024)
11-58955724-A-G		not specified	Uncertain significance (Mar 14, 2023)
11-58955752-G-A		not specified	Uncertain significance (May 26, 2024)
11-58955768-C-T		not specified	Uncertain significance (Jul 05, 2022)
11-58955788-G-A		not specified	Uncertain significance (Jun 04, 2024)
11-58955812-G-A		not specified	Uncertain significance (Jun 17, 2024)
11-58955824-G-C		not specified	Uncertain significance (Nov 09, 2021)
11-58955876-A-G		not specified	Uncertain significance (May 26, 2023)
11-58955905-T-G		not specified	Uncertain significance (Jan 09, 2024)
11-58955939-G-A		not specified	Uncertain significance (Jun 27, 2022)
11-58955959-G-C		not specified	Uncertain significance (Mar 08, 2024)
11-58955971-G-A		not specified	Uncertain significance (Feb 28, 2024)
11-58955972-C-A		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLYATL1	protein_coding	protein_coding	ENST00000300079	7	138130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00337	0.955	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.619	209	185	1.13	0.00000993	2194
Missense in Polyphen		42	41.518	1.0116		560
Synonymous	-0.905	76	66.6	1.14	0.00000364	611
Loss of Function	1.78	6	12.9	0.465	6.31e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acyltransferase which transfers an acyl group to the N- terminus of glutamine. Can use phenylacetyl-CoA as an acyl donor. {ECO:0000269|PubMed:22475485}.
• Pathway: 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 (Consensus)

Intolerance Scores

• loftool: 0.701
• rvis_EVS: -1.16
• rvis_percentile_EVS: 6.17

Haploinsufficiency Scores

• pHI: 0.0566
• hipred: N
• hipred_score: 0.112
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0289

Gene Damage Prediction

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

Gene ontology

• Biological process: glutamine metabolic process
• Cellular component: mitochondrion
• Molecular function: glutamine N-acyltransferase activity;glycine N-acyltransferase activity