GLYATL3

glycine-N-acyltransferase like 3

Basic information

Region (hg38): 6:49499923-49528078

Previous symbols: [ "C6orf140" ]

Links

ENSG00000203972 ∙ NCBI:389396 ∙ OMIM:614763 ∙ HGNC:21349 ∙ Uniprot:Q5SZD4 ∙ 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 GLYATL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLYATL3 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	0

Variants in GLYATL3

This is a list of pathogenic ClinVar variants found in the GLYATL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-49512028-T-C		not specified	Uncertain significance (Feb 16, 2023)
6-49512038-G-A		not specified	Uncertain significance (Nov 21, 2022)
6-49512046-G-A		not specified	Uncertain significance (Dec 09, 2024)
6-49515674-A-C		not specified	Uncertain significance (Mar 26, 2024)
6-49515715-T-A		not specified	Uncertain significance (Feb 26, 2024)
6-49515747-G-A		not specified	Uncertain significance (Jun 02, 2023)
6-49515750-G-A		not specified	Uncertain significance (Dec 12, 2024)
6-49517457-A-T		not specified	Uncertain significance (May 30, 2024)
6-49517484-G-A		not specified	Uncertain significance (Dec 12, 2024)
6-49517546-T-A		not specified	Uncertain significance (Jan 02, 2025)
6-49521663-A-G		not specified	Uncertain significance (Dec 15, 2022)
6-49521678-C-T		not specified	Uncertain significance (Jan 26, 2023)
6-49521725-G-C		not specified	Uncertain significance (Feb 28, 2023)
6-49521741-C-T		not specified	Uncertain significance (Dec 05, 2024)
6-49521743-G-A		not specified	Uncertain significance (May 21, 2024)
6-49526540-C-T		not specified	Uncertain significance (May 13, 2024)
6-49526543-A-G		not specified	Uncertain significance (Dec 19, 2022)
6-49526559-G-A		not specified	Uncertain significance (Apr 07, 2022)
6-49526562-G-T		not specified	Uncertain significance (Nov 09, 2021)
6-49526591-G-A		not specified	Uncertain significance (Oct 13, 2023)
6-49526611-C-G		not specified	Uncertain significance (Nov 24, 2024)
6-49526646-C-A		not specified	Uncertain significance (Sep 23, 2023)
6-49526656-G-T		not specified	Uncertain significance (Dec 02, 2022)
6-49526729-C-T		not specified	Uncertain significance (Apr 18, 2023)
6-49526742-T-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GLYATL3	protein_coding	protein_coding	ENST00000371197	5	27090

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.07e-8	0.276	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.738	132	158	0.835	0.00000932	1856
Missense in Polyphen		59	62.328	0.9466		757
Synonymous	1.78	47	65.3	0.720	0.00000382	583
Loss of Function	0.468	12	13.9	0.865	9.15e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acyltransferase which transfers the acyl group to the N- terminus of glycine. {ECO:0000250}.
• Pathway: 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

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.28

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Glyatl3

Gene ontology

• Cellular component: mitochondrion
• Molecular function: glycine N-acyltransferase activity