GLYATL2

glycine-N-acyltransferase like 2

Basic information

Region (hg38): 11:58834065-58904215

Links

ENSG00000156689 ∙ NCBI:219970 ∙ OMIM:614762 ∙ HGNC:24178 ∙ Uniprot:Q8WU03 ∙ 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 GLYATL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLYATL2 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in GLYATL2

This is a list of pathogenic ClinVar variants found in the GLYATL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-58834465-C-A		not specified	Uncertain significance (Oct 17, 2023)
11-58834467-A-G		not specified	Uncertain significance (Mar 16, 2022)
11-58834486-A-T		not specified	Uncertain significance (Jan 30, 2024)
11-58834514-C-A		not specified	Uncertain significance (Feb 28, 2024)
11-58834600-C-T		not specified	Uncertain significance (Jan 23, 2024)
11-58834716-G-C		not specified	Uncertain significance (May 18, 2023)
11-58834781-T-C		not specified	Uncertain significance (Jul 20, 2021)
11-58834800-G-A		not specified	Uncertain significance (May 21, 2024)
11-58837049-T-G		not specified	Uncertain significance (Apr 05, 2023)
11-58837088-G-T		not specified	Uncertain significance (Jan 26, 2022)
11-58837108-A-G		not specified	Uncertain significance (Nov 07, 2023)
11-58837142-C-A		not specified	Uncertain significance (Oct 06, 2023)
11-58837162-A-C		not specified	Uncertain significance (Dec 16, 2022)
11-58837303-A-G		not specified	Uncertain significance (Oct 05, 2023)
11-58837307-T-A		not specified	Uncertain significance (Aug 02, 2023)
11-58837379-C-T		not specified	Uncertain significance (Jul 05, 2023)
11-58838322-A-C		not specified	Uncertain significance (Apr 23, 2024)
11-58838323-T-G		not specified	Likely benign (Sep 01, 2021)
11-58838342-T-G		not specified	Likely benign (Dec 20, 2021)
11-58838368-C-T		not specified	Uncertain significance (Sep 22, 2023)
11-58839575-A-G		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLYATL2	protein_coding	protein_coding	ENST00000287275	5	70147

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000158	0.245	124733	0	45	124778	0.000180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.467	165	149	1.11	0.00000694	1959
Missense in Polyphen		41	40.519	1.0119		557
Synonymous	1.26	42	53.7	0.782	0.00000256	495
Loss of Function	0.0849	9	9.28	0.970	3.91e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000880	0.000880
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000706
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000498	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial acyltransferase which transfers the acyl group to the N-terminus of glycine. Conjugates numerous substrates, such as arachidonoyl-CoA and saturated medium and long-chain acyl-CoAs ranging from chain-length C8:0-CoA to C18:0- CoA, to form a variety of N-acylglycines. Shows a preference for monounsaturated fatty acid oleoyl-CoA (C18:1-CoA) as an acyl donor. Does not exhibit any activity toward C22:6-CoA and chenodeoxycholoyl-CoA, nor toward serine or alanine. {ECO:0000269|PubMed:20305126}.
• 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: 0.903
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.01

Haploinsufficiency Scores

• pHI: 0.0856
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Gene ontology

• Biological process: long-chain fatty acid catabolic process;medium-chain fatty acid catabolic process;monounsaturated fatty acid catabolic process
• Cellular component: mitochondrion;endoplasmic reticulum
• Molecular function: glycine N-acyltransferase activity