GLYATL3

Summary

GLYATL3 (glycine-N-acyltransferase like 3, HGNC:21349) is a protein-coding gene on chromosome 6p12.3, encoding Glycine N-acyltransferase-like protein 3 (Q5SZD4). Catalyzes the conjugation of long-chain fatty acyl-CoA thioester and glycine to produce long-chain N-(fatty acyl)glycine, an intermediate in the primary fatty acid amide biosynthetic pathway.

Predicted to enable glycine N-acyltransferase activity. Predicted to be involved in lipid metabolic process. Predicted to be located in mitochondrion.

Source: NCBI Gene 389396 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 45 total
• MANE Select transcript: NM_001010904

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21349
Approved symbol	GLYATL3
Name	glycine-N-acyltransferase like 3
Location	6p12.3
Locus type	gene with protein product
Status	Approved
Aliases	bA28H17.2
Ensembl gene	ENSG00000203972
Ensembl biotype	protein_coding
OMIM	614763
Entrez	389396

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000371197, ENST00000545705

RefSeq mRNA: 1 — MANE Select: NM_001010904 NM_001010904

CCDS: CCDS47440

Canonical transcript exons

ENST00000371197 — 6 exons

Exon	Start	End
ENSE00001454581	49526488	49528078
ENSE00001454583	49515653	49515760
ENSE00001454585	49511963	49512068
ENSE00001556331	49499923	49500042
ENSE00001655451	49517430	49517556
ENSE00001699123	49521645	49521771

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 84.94.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1619 / max 293.0327, expressed in 1 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
68183	0.0515	1
68184	0.0411	1
68182	0.0400	1
68185	0.0171	1
68181	0.0124	1

Top tissues by expression

129 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.94	gold quality
rectum	UBERON:0001052	53.01	gold quality
endometrium	UBERON:0001295	48.84	gold quality
liver	UBERON:0002107	47.67	gold quality
right lobe of liver	UBERON:0001114	45.46	silver quality
colonic epithelium	UBERON:0000397	41.42	gold quality
islet of Langerhans	UBERON:0000006	38.95	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
hindlimb stylopod muscle	UBERON:0004252	35.53	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
sural nerve	UBERON:0015488	35.29	gold quality
granulocyte	CL:0000094	34.95	gold quality
skeletal muscle tissue	UBERON:0001134	34.79	gold quality
leukocyte	CL:0000738	32.70	silver quality
monocyte	CL:0000576	32.65	silver quality
duodenum	UBERON:0002114	32.59	gold quality
muscle tissue	UBERON:0002385	32.09	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.35	gold quality
vermiform appendix	UBERON:0001154	29.28	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	28.85	gold quality
tonsil	UBERON:0002372	28.72	gold quality
pancreas	UBERON:0001264	28.50	gold quality
transverse colon	UBERON:0001157	28.40	gold quality
urinary bladder	UBERON:0001255	27.68	gold quality
lymph node	UBERON:0000029	27.57	gold quality
primary visual cortex	UBERON:0002436	27.42	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

64 targeting GLYATL3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-3681-5P	99.82	66.88	387
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-377-5P	99.70	65.28	712
HSA-MIR-6086	99.70	65.38	699
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-7156-5P	99.64	68.81	1369

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-76k16.5	ENSDARG00000075561
danio_rerio	si:dkey-76k16.6	ENSDARG00000077481
danio_rerio	si:ch73-106k19.2	ENSDARG00000102568
mus_musculus	Glyatl3	ENSMUSG00000091043
rattus_norvegicus	Glyatl3	ENSRNOG00000050990
caenorhabditis_elegans		WBGENE00011681
caenorhabditis_elegans		WBGENE00018400
caenorhabditis_elegans		WBGENE00022683

Paralogs (4): GLYAT (ENSG00000149124), GLYATL2 (ENSG00000156689), GLYATL1 (ENSG00000166840), GLYATL1B (ENSG00000255151)

Protein

Protein identifiers

Glycine N-acyltransferase-like protein 3 — Q5SZD4 (reviewed: Q5SZD4)

Alternative names: Acyl-CoA:glycine-N-acyltransferase-like protein 3

All UniProt accessions (2): Q5SZD4, F5GXQ5

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the conjugation of long-chain fatty acyl-CoA thioester and glycine to produce long-chain N-(fatty acyl)glycine, an intermediate in the primary fatty acid amide biosynthetic pathway.

Pathway. Lipid metabolism.

Similarity. Belongs to the glycine N-acyltransferase family.

RefSeq proteins (1): NP_001010904* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010313	Glycine_N-acyltransferase	Family
IPR013652	Glycine_N-acyltransferase_C	Domain
IPR015938	Glycine_N-acyltransferase_N	Domain
IPR016181	Acyl_CoA_acyltransferase	Homologous_superfamily

Pfam: PF06021, PF08444

Catalyzed reactions (Rhea), 3 shown:

• an acyl-CoA + glycine = an N-acylglycine + CoA + H(+) (RHEA:19869)
• (9Z)-octadecenoyl-CoA + glycine = N-(9Z-octadecenoyl)glycine + CoA + H(+) (RHEA:51272)
• hexadecanoyl-CoA + glycine = N-hexadecanoylglycine + CoA + H(+) (RHEA:58536)

UniProt features (2 total): chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5SZD4-F1	94.93	0.89

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-159424	Conjugation of carboxylic acids
R-HSA-177128	Conjugation of salicylate with glycine
R-HSA-177135	Conjugation of benzoate with glycine
R-HSA-9749641	Aspirin ADME

MSigDB gene sets: 26 (showing top): REACTOME_BIOLOGICAL_OXIDATIONS, chr6p12, GOBP_LIPID_METABOLIC_PROCESS, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_N_ACYLTRANSFERASE_ACTIVITY, REACTOME_PHASE_II_CONJUGATION_OF_COMPOUNDS, GOMF_GLYCINE_N_ACYLTRANSFERASE_ACTIVITY, REACTOME_AMINO_ACID_CONJUGATION, REACTOME_CONJUGATION_OF_BENZOATE_WITH_GLYCINE, MIR335_3P, MIR340_5P, MIR186_5P, MIR6739_5P, MIR6733_5P, MIR4528

GO Biological Process (1): lipid metabolic process (GO:0006629)

GO Molecular Function (4): glycine N-acyltransferase activity (GO:0047961), obsolete N-acyltransferase activity (GO:0016410), transferase activity (GO:0016740), acyltransferase activity (GO:0016746)

GO Cellular Component (1): mitochondrion (GO:0005739)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Conjugation of carboxylic acids	2
Amino Acid conjugation	1
Drug ADME	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary metabolic process	1
amino acid acyltransferase activity	1
catalytic activity	1
transferase activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLYATL3	SPINT3	P49223	577
GLYATL3	FAM174A	Q8TBP5	472
GLYATL3	HEATR5B	Q9P2D3	453
GLYATL3	SMIM3	Q9BZL3	420
GLYATL3	TBC1D21	Q8IYX1	414
GLYATL3	VSIG10	Q8N0Z9	411
GLYATL3	TTC17	Q96AE7	402
GLYATL3	FAM72B	Q86X60	397
GLYATL3	PAM	P19021	394
GLYATL3	THAP4	Q8WY91	394
GLYATL3	TP53TG3	Q9ULZ0	393
GLYATL3	SNTN	A6NMZ2	390
GLYATL3	OR51C1	A0A3B3IT45	374
GLYATL3	ELMOD3	Q96FG2	370
GLYATL3	AASDH	Q4L235	350

IntAct

2 interactions, top by confidence:

A	B	Type	Score
PPP4C	TCP1	psi-mi:“MI:0914”(association)	0.730

BioGRID (1): GLYATL3 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L1SUL6, F1LQY6, O35465, O43379, O75293, O88910, O88954, P0C0T1, P21964, P22339, P41214, P50747, Q13368, Q13572, Q14318, Q16342, Q1HAQ0, Q28955, Q2T9Z1, Q3B7U9, Q3TFD2, Q3TMX7, Q496Y0, Q4AC99, Q5BIM1, Q5E9A5, Q5R812, Q5RA63, Q5SZD4, Q64311, Q6DC64, Q6P5G6, Q6PFY8, Q80YV4, Q8BNV1, Q8BYN3, Q8NFZ0, Q8R1C6, Q8R1T1, Q8TCU6

Diamond homologs: A0A0U1RQE8, E9Q5L8, O77512, Q2KIR7, Q5FW57, Q5PQT3, Q5RFP0, Q5SZD4, Q6IB77, Q8WU03, Q91XE0, Q969I3, Q9DCY0, Q9Z2Y0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

45 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	42
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

857 predictions. Top by Δscore:

Variant	Effect	Δscore
6:49517552:ACAAG:A	donor_loss	1.0000
6:49517553:CAAG:C	donor_loss	1.0000
6:49517554:AAGG:A	donor_loss	1.0000
6:49517555:AGGT:A	donor_loss	1.0000
6:49517556:GGT:G	donor_loss	1.0000
6:49517557:G:GA	donor_loss	1.0000
6:49517558:T:A	donor_loss	1.0000
6:49517563:TC:T	donor_gain	1.0000
6:49526480:T:A	acceptor_gain	1.0000
6:49500039:GCAG:G	donor_gain	0.9900
6:49500041:AGGT:A	donor_loss	0.9900
6:49515636:T:TA	acceptor_gain	0.9900
6:49515637:G:A	acceptor_gain	0.9900
6:49515645:T:TA	acceptor_gain	0.9900
6:49517422:T:TA	acceptor_gain	0.9900
6:49517425:CCTA:C	acceptor_loss	0.9900
6:49517426:CTAG:C	acceptor_loss	0.9900
6:49517428:A:AC	acceptor_loss	0.9900
6:49517428:A:AG	acceptor_gain	0.9900
6:49517429:G:GG	acceptor_gain	0.9900
6:49517429:G:GT	acceptor_loss	0.9900
6:49517429:GGCT:G	acceptor_gain	0.9900
6:49521902:G:GT	donor_gain	0.9900
6:49526476:ATTCT:A	acceptor_gain	0.9900
6:49526481:G:A	acceptor_gain	0.9900
6:49526486:A:AG	acceptor_gain	0.9900
6:49526487:G:GA	acceptor_gain	0.9900
6:49526487:GC:G	acceptor_gain	0.9900
6:49526487:GCA:G	acceptor_gain	0.9900
6:49526487:GCAA:G	acceptor_gain	0.9900

AlphaMissense

1875 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:49526654:T:A	W203R	0.991
6:49526654:T:C	W203R	0.991
6:49526615:A:C	S190R	0.981
6:49526617:T:A	S190R	0.981
6:49526617:T:G	S190R	0.981
6:49515719:T:A	W49R	0.974
6:49515719:T:C	W49R	0.974
6:49526651:T:C	S202P	0.972
6:49526672:T:C	F209L	0.968
6:49526674:T:A	F209L	0.968
6:49526674:T:G	F209L	0.968
6:49515738:T:A	V55D	0.967
6:49526552:T:A	W169R	0.967
6:49526552:T:C	W169R	0.967
6:49526598:T:C	L184P	0.967
6:49517475:T:C	F78L	0.965
6:49517477:C:A	F78L	0.965
6:49517477:C:G	F78L	0.965
6:49526656:G:C	W203C	0.964
6:49526656:G:T	W203C	0.964
6:49517556:G:A	G105R	0.961
6:49517556:G:C	G105R	0.961
6:49526657:T:C	S204P	0.961
6:49526667:A:T	D207V	0.961
6:49526861:T:C	F272L	0.961
6:49526863:C:A	F272L	0.961
6:49526863:C:G	F272L	0.961
6:49512040:T:C	L17S	0.960
6:49526666:G:C	D207H	0.955
6:49526712:G:C	R222P	0.949

dbSNP variants (sampled 300 via entrez): RS1000080877 (6:49503394 C>T), RS1000111572 (6:49526755 G>A,T), RS1000188039 (6:49498332 G>A), RS1000213533 (6:49508327 A>G), RS1000323984 (6:49514504 G>A), RS1000397524 (6:49514797 A>G), RS1000442637 (6:49519965 T>C), RS1000451597 (6:49528240 A>G), RS1000529393 (6:49507692 T>C), RS1000584858 (6:49527837 T>C), RS1000731874 (6:49513414 T>C), RS1000743884 (6:49521160 C>T), RS1000814490 (6:49521846 T>C,G), RS1000881827 (6:49520295 C>G), RS1001136680 (6:49525440 T>A)

Disease associations

OMIM: gene MIM:614763 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST000597_13	Brain structure	8.000000e-07
GCST009733_77	Urinary metabolite levels in chronic kidney disease	1.000000e-179

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005116	urinary metabolite measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
mancozeb	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
bisphenol S	decreases methylation	1
Aldehydes	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Catechin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.