GLYATL1

Summary

GLYATL1 (glycine-N-acyltransferase like 1, HGNC:30519) is a protein-coding gene on chromosome 11q12.1, encoding Glycine N-acyltransferase-like protein 1 (Q969I3). Acyltransferase which transfers an acyl group to the N-terminus of glutamine.

Enables glutamine N-acyltransferase activity. Involved in glutamine metabolic process. Predicted to be located in mitochondrion.

Source: NCBI Gene 92292 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_001389712

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30519
Approved symbol	GLYATL1
Name	glycine-N-acyltransferase like 1
Location	11q12.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC15397, FLJ34646
Ensembl gene	ENSG00000166840
Ensembl biotype	protein_coding
OMIM	614761
Entrez	92292

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 8 protein_coding, 5 protein_coding_CDS_not_defined, 5 nonsense_mediated_decay, 3 retained_intron

ENST00000300079, ENST00000317391, ENST00000524403, ENST00000524629, ENST00000524881, ENST00000525608, ENST00000526351, ENST00000527708, ENST00000530240, ENST00000530774, ENST00000531245, ENST00000532726, ENST00000533864, ENST00000534063, ENST00000534119, ENST00000534241, ENST00000534612, ENST00000534674, ENST00000612196, ENST00000685442, ENST00000689150

RefSeq mRNA: 12 — MANE Select: NM_001389712 NM_001220494, NM_001220496, NM_001354699, NM_001389711, NM_001389712, NM_001389713, NM_001389714, NM_001389715, NM_001389716, NM_001389717, NM_001389718, NM_080661

CCDS: CCDS31556, CCDS55768, CCDS91475

Canonical transcript exons

ENST00000532726 — 7 exons

Exon	Start	End
ENSE00003470753	58943543	58943666
ENSE00003532973	58947046	58947165
ENSE00003554774	58955176	58955353
ENSE00003588226	58947858	58947965
ENSE00003648121	58954770	58954896
ENSE00003929779	58939488	58939650
ENSE00003937293	58955610	58956406

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 99.34.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2340 / max 314.7568, expressed in 188 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114367	0.5056	7
114363	0.3272	164
206292	0.0956	46
114364	0.0786	37
114369	0.0647	5
114368	0.0595	6
114365	0.0529	21
114370	0.0356	3
114366	0.0143	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	99.34	gold quality
right lobe of liver	UBERON:0001114	98.65	gold quality
secondary oocyte	CL:0000655	97.77	gold quality
liver	UBERON:0002107	97.76	gold quality
oocyte	CL:0000023	97.34	gold quality
adult mammalian kidney	UBERON:0000082	96.50	gold quality
kidney	UBERON:0002113	93.41	gold quality
renal medulla	UBERON:0000362	91.58	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.00	gold quality
adult organism	UBERON:0007023	87.88	gold quality
cortex of kidney	UBERON:0001225	83.59	gold quality
metanephros cortex	UBERON:0010533	76.51	gold quality
metanephros	UBERON:0000081	74.23	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.32	gold quality
buccal mucosa cell	CL:0002336	70.89	silver quality
prostate gland	UBERON:0002367	69.85	gold quality
ileal mucosa	UBERON:0000331	69.62	gold quality
ventricular zone	UBERON:0003053	69.59	gold quality
cortical plate	UBERON:0005343	69.07	gold quality
pancreatic ductal cell	CL:0002079	68.51	silver quality
gall bladder	UBERON:0002110	67.12	gold quality
ganglionic eminence	UBERON:0004023	66.35	gold quality
embryo	UBERON:0000922	66.34	gold quality
minor salivary gland	UBERON:0001830	65.89	gold quality
saliva-secreting gland	UBERON:0001044	62.83	gold quality
mouth mucosa	UBERON:0003729	62.58	gold quality
body of stomach	UBERON:0001161	60.14	gold quality
body of pancreas	UBERON:0001150	59.71	gold quality
upper leg skin	UBERON:0004262	59.43	gold quality
stomach	UBERON:0000945	59.34	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-114530	yes	668.42
E-HCAD-10	yes	37.22
E-CURD-11	no	43.24
E-MTAB-7249	no	16.74
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

49 targeting GLYATL1, 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-4668-3P	100.00	68.74	2635
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-26A-1-3P	99.64	66.81	788
HSA-MIR-26A-2-3P	99.64	66.82	786
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-141-5P	99.57	67.86	897
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-4999-5P	99.35	69.15	926
HSA-MIR-488-5P	99.28	68.12	821
HSA-MIR-3191-5P	99.24	66.52	1722

Literature-anchored findings (GeneRIF, showing 1)

• study characterizes the expression of glycine-N-acyltransferase like 1(GLYATL1) in prostate cancer and explores its regulation in prostate cancer (PMID:31376196)

Cross-species orthologs

6 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
caenorhabditis_elegans		WBGENE00011681
caenorhabditis_elegans		WBGENE00018400
caenorhabditis_elegans		WBGENE00022683

Paralogs (4): GLYAT (ENSG00000149124), GLYATL2 (ENSG00000156689), GLYATL3 (ENSG00000203972), GLYATL1B (ENSG00000255151)

Protein

Protein identifiers

Glycine N-acyltransferase-like protein 1 — Q969I3 (reviewed: Q969I3)

Alternative names: Acyl-CoA:glycine N-acyltransferase-like protein 1, Glutamine N-acyltransferase

All UniProt accessions (10): Q969I3, A0A8I5KR82, A0A8I5KVG3, A9ZM15, E9PJV1, E9PK55, E9PNJ8, E9PP95, E9PP99, E9PR27

UniProt curated annotations — full annotation on UniProt →

Function. Acyltransferase which transfers an acyl group to the N-terminus of glutamine. Can use phenylacetyl-CoA as an acyl donor.

Tissue specificity. Expressed in liver and kidney and, at lower levels, in pancreas, testis, ovary and stomach.

Similarity. Belongs to the glycine N-acyltransferase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q969I3-1	1	yes
Q969I3-2	2

RefSeq proteins (12): NP_001207423, NP_001207425, NP_001341628, NP_001376640, NP_001376641, NP_001376642, NP_001376643, NP_001376644, NP_001376645, NP_001376646, NP_001376647, NP_542392 (=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

Enzyme classification (BRENDA):

• EC 2.3.1.13 — glycine N-acyltransferase (BRENDA: 7 organisms, 40 substrates, 29 inhibitors, 71 Km, 14 kcat entries)
• EC 2.3.1.68 — glutamine N-acyltransferase (BRENDA: 2 organisms, 6 substrates, 2 inhibitors, 1 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

17 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
BENZOYL-COA	0.0094–998	28
GLYCINE	0.0016–79	19
BUTYRYL-COA	0.052–0.7	3
SALICYL-COA	0.03–83.7	3
ACETYL-COA	0.209	2
ALANINE	997–1573	2
HEXANOYL-COA	0.045–450	2
ISOVALERYL-COA	73.3–124	2
OCTANOYL-COA	108.6–198	2
ASPARAGINE	129	1
GLUTAMIC ACID	1150	1
GLUTAMINE	353	1
GLYCINE ETHYL ESTER	9.7	1
GLYCINE METHYL ESTER	29	1
OLEOYL-COA	0.0044	1

Catalyzed reactions (Rhea), 1 shown:

• an acyl-CoA + L-glutamine = an N(2)-acyl-L-glutamine + CoA + H(+) (RHEA:18469)

UniProt features (2 total): chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q969I3-F1	91.16	0.82

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: 55 (showing top): REACTOME_BIOLOGICAL_OXIDATIONS, GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, GOBP_GLUTAMINE_FAMILY_AMINO_ACID_METABOLIC_PROCESS, GOBP_GLUTAMINE_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN, 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, HES2_TARGET_GENES, NFKBIA_TARGET_GENES, PAX3_TARGET_GENES

GO Biological Process (1): L-glutamine metabolic process (GO:0006541)

GO Molecular Function (5): L-glutamine N-acyltransferase activity (GO:0047946), 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
L-amino acid metabolic process	1
proteinogenic amino acid metabolic process	1
L-amino-acid N-acetyltransferase activity	1
amino acid acyltransferase activity	1
catalytic activity	1
transferase activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

898 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GLYATL1	KAT2A	Q92830	916
GLYATL1	KAT2B	Q92831	900
GLYATL1	NAA80	Q93015	873
GLYATL1	ESCO1	Q5FWF5	872
GLYATL1	ESCO2	Q56NI9	869
GLYATL1	OPN4	Q9UHM6	851
GLYATL1	CNGA3	Q16281	812
GLYATL1	SAT1	P21673	806
GLYATL1	SAT2	Q96F10	800
GLYATL1	RGS9BP	Q6ZS82	783
GLYATL1	AANAT	Q16613	776
GLYATL1	ASXL2	Q76L83	765
GLYATL1	PAOX	Q6QHF9	762
GLYATL1	GNB5	O14775	755
GLYATL1	GNAT2	P19087	739

IntAct

2 interactions, top by confidence:

A	B	Type	Score
GLYATL1	HSPD1	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): ACTB (Affinity Capture-MS), DARS2 (Affinity Capture-MS), ELAC2 (Affinity Capture-MS), HSPD1 (Affinity Capture-MS), GLYATL1 (Reconstituted Complex), GLYATL1 (Proximity Label-MS), GLYATL1 (Affinity Capture-MS), GLYATL1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQE8, F1S5L4, O43010, O77512, P06592, P13233, P14714, P42498, P49895, P55004, P97564, Q07071, Q09305, Q0P464, Q0P4Y1, Q1LYL8, Q2KHV5, Q2KIR7, Q3UW68, Q5BK10, Q5FW57, Q5GJ77, Q5PQT3, Q5RFP0, Q60462, Q61586, Q62240, Q64112, Q6IB77, Q6MZZ7, Q6P5U7, Q6QN13, Q6QR59, Q6V915, Q7L7V1, Q804E1, Q8CBA2, Q8T773, Q8WU03, Q91754

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	48
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1554 predictions. Top by Δscore:

Variant	Effect	Δscore
11:58905627:G:GT	donor_gain	1.0000
11:58943540:CAGAT:C	acceptor_loss	1.0000
11:58943541:A:G	acceptor_loss	1.0000
11:58943541:AGAT:A	acceptor_gain	1.0000
11:58943542:GAT:G	acceptor_gain	1.0000
11:58943542:GATG:G	acceptor_gain	1.0000
11:58943659:GATAA:G	donor_gain	1.0000
11:58943663:ATAGG:A	donor_loss	1.0000
11:58943664:TAGGT:T	donor_loss	1.0000
11:58943666:GGT:G	donor_loss	1.0000
11:58943667:G:GA	donor_loss	1.0000
11:58943667:G:GG	donor_gain	1.0000
11:58943668:T:G	donor_loss	1.0000
11:58947045:GA:G	acceptor_gain	1.0000
11:58947045:GAGT:G	acceptor_gain	1.0000
11:58947045:GAGTT:G	acceptor_gain	1.0000
11:58947163:AAG:A	donor_loss	1.0000
11:58947164:AG:A	donor_loss	1.0000
11:58947165:GGT:G	donor_loss	1.0000
11:58947166:G:A	donor_loss	1.0000
11:58947167:T:A	donor_loss	1.0000
11:58955608:A:AG	acceptor_gain	1.0000
11:58955609:G:GG	acceptor_gain	1.0000
11:58905628:A:T	donor_gain	0.9900
11:58905636:GGGCA:G	donor_gain	0.9900
11:58905637:GGCAG:G	donor_gain	0.9900
11:58905638:G:GT	donor_gain	0.9900
11:58905638:G:T	donor_gain	0.9900
11:58905660:TGGTA:T	donor_loss	0.9900
11:58905661:GGTA:G	donor_loss	0.9900

AlphaMissense

517 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:58954815:T:C	F78L	0.969
11:58954817:C:A	F78L	0.969
11:58954817:C:G	F78L	0.969
11:58947924:T:A	W49R	0.937
11:58947924:T:C	W49R	0.937
11:58947897:T:C	F40L	0.935
11:58947899:C:A	F40L	0.935
11:58947899:C:G	F40L	0.935
11:58947926:G:C	W49C	0.882
11:58947926:G:T	W49C	0.882
11:58947165:G:C	K26N	0.869
11:58947165:G:T	K26N	0.869
11:58947157:T:C	S24P	0.864
11:58947952:G:C	R58P	0.864
11:58947943:T:A	V55D	0.847
11:58947865:G:A	G29D	0.816
11:58947920:T:A	D47E	0.806
11:58947920:T:G	D47E	0.806
11:58947910:T:A	V44E	0.797
11:58954816:T:C	F78S	0.791
11:58947871:T:A	V31E	0.789
11:58947861:T:G	Y28D	0.788
11:58947137:T:C	L17S	0.778
11:58947161:T:C	L25P	0.778
11:58947893:C:A	N38K	0.778
11:58947893:C:G	N38K	0.778
11:58947934:A:C	Y52S	0.771
11:58954816:T:G	F78C	0.766
11:58947921:T:C	S48P	0.763
11:58947916:T:A	V46E	0.761

dbSNP variants (sampled 300 via entrez): RS1000105126 (11:58949825 G>A), RS1000113372 (11:58944248 C>T), RS1000137872 (11:58949502 A>T), RS1000138727 (11:58909709 C>T), RS1000168154 (11:58907261 C>T), RS1000196323 (11:58919579 G>A), RS1000273901 (11:58911753 C>T), RS1000366248 (11:58942778 A>G), RS1000373132 (11:58930733 C>A), RS1000375010 (11:58924551 A>G), RS1000473620 (11:58912863 C>A,T), RS1000480277 (11:58918177 A>G), RS1000553094 (11:58916925 C>T), RS1000559076 (11:58905728 T>A), RS1000622972 (11:58918446 C>A,T)

Disease associations

OMIM: gene MIM:614761 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, decreases methylation, increases expression	4
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation	3
Aflatoxin B1	affects expression, decreases expression, decreases methylation	3
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression, affects expression	2
Cyclosporine	decreases expression	2
lasiocarpine	decreases expression	1
methyleugenol	decreases expression	1
trichostatin A	increases expression	1
sodium arsenite	affects expression	1
zinc chromate	increases expression, increases abundance	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
nickel sulfate	decreases expression	1
chromium hexavalent ion	increases abundance, increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Vorinostat	increases expression	1
Acetaminophen	decreases expression	1
Carbamazepine	affects expression	1
Endosulfan	affects cotreatment, decreases expression	1
Hydrogen Peroxide	affects expression	1
Methapyrilene	increases methylation	1
Methotrexate	increases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Nickel	decreases expression	1
Niclosamide	decreases expression	1

Clinical trials (associated diseases)

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