GLYATL3

protein-coding

glycine-N-acyltransferase like 3

Gene summary

Predicted to enable glycine N-acyltransferase activity. Predicted to be involved in lipid metabolic process. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf140

MANE transcript

NM_001010904.2

Inheritance

—

ClinVar variants

U:43B:1

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr6:49,499,923-49,528,078

External References & Databases

Ensembl (ENSG00000203972)

Transcript & Mutation Effects

hg38 • Region Span ~28.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GLYATL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001010904.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			43 clinvar	1 clinvar		44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	1	0	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001010904.2	RefSeq	NP_001010904.1	5	MANE Select
ENST00000371197.9	Ensembl	ENSP00000360240.4	5	MANE Select
ENST00000545705.1	Ensembl	ENSP00000440029.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Conjugation of benzoate with glycine
Conjugation of salicylate with glycine
Conjugation of carboxylic acids
Amino Acid conjugation
Phase II - Conjugation of compounds

Molecular Function

glycine N-acyltransferase activity

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371197
Coding exons: 5
Length: 27090
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.738	132	158	0.835	0.00000932	1856
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

RVIS EVS: 0.46
RVIS percentile EVS: 78.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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