GGTA1

Summary

GGTA1 (glycoprotein alpha-galactosyltransferase 1 (inactive), HGNC:4253) is a protein-coding gene on chromosome 9q33.2, encoding Inactive N-acetyllactosaminide alpha-1,3-galactosyltransferase (Q4G0N0).

Alpha-1,3-galactosyltransferase (GGTA1) is an enzyme present in most mammals except man, apes, and Old World monkeys. This gene is thought to encode a truncated, non-enzymatic form of the GGTA1 protein that lacks the C-terminal catalytic domain. Aberrant expression of the GGTA1 protein in man can lead to autoimmune diseases and sometimes germ cell tumors.

Source: NCBI Gene 2681 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001382585

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4253
Approved symbol	GGTA1
Name	glycoprotein alpha-galactosyltransferase 1 (inactive)
Location	9q33.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000204136
Ensembl biotype	protein_coding
OMIM	104175
Entrez	2681

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 15 protein_coding, 3 nonsense_mediated_decay

ENST00000373793, ENST00000481534, ENST00000481799, ENST00000488429, ENST00000495328, ENST00000863973, ENST00000863974, ENST00000863975, ENST00000863976, ENST00000863977, ENST00000863978, ENST00000863979, ENST00000955018, ENST00000955019, ENST00000955020, ENST00000955021, ENST00000955022, ENST00000955023

RefSeq mRNA: 4 — MANE Select: NM_001382585 NM_001382584, NM_001382585, NM_001382586, NM_001382587

CCDS: CCDS94476

Canonical transcript exons

ENST00000481799 — 6 exons

Exon	Start	End
ENSE00001840856	121455040	121455841
ENSE00002075049	121499650	121499844
ENSE00002315241	121467843	121467931
ENSE00003606666	121463293	121463328
ENSE00003620773	121460104	121460219
ENSE00003662793	121461252	121461317

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 97.53.

FANTOM5 (CAGE): breadth broad, TPM avg 8.4353 / max 324.9559, expressed in 522 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
102358	3.6713	415
102359	2.4097	399
102361	0.8407	240
102360	0.7893	288
102357	0.3398	151
102356	0.1392	83
102362	0.1004	31
102363	0.0506	14
102364	0.0485	17
102355	0.0459	16

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	97.53	gold quality
cardiac muscle of right atrium	UBERON:0003379	96.94	gold quality
descending thoracic aorta	UBERON:0002345	96.82	gold quality
right coronary artery	UBERON:0001625	96.43	gold quality
layer of synovial tissue	UBERON:0007616	95.58	gold quality
popliteal artery	UBERON:0002250	95.52	gold quality
tibial artery	UBERON:0007610	95.52	gold quality
upper arm skin	UBERON:0004263	95.47	gold quality
aorta	UBERON:0000947	95.40	gold quality
thoracic aorta	UBERON:0001515	95.25	gold quality
ascending aorta	UBERON:0001496	95.08	gold quality
synovial joint	UBERON:0002217	95.08	gold quality
vena cava	UBERON:0004087	95.04	gold quality
trabecular bone tissue	UBERON:0002483	94.32	gold quality
monocyte	CL:0000576	94.16	gold quality
coronary artery	UBERON:0001621	93.79	gold quality
left coronary artery	UBERON:0001626	93.47	gold quality
leukocyte	CL:0000738	93.40	gold quality
myocardium	UBERON:0002349	93.30	gold quality
left ventricle myocardium	UBERON:0006566	92.50	gold quality
putamen	UBERON:0001874	92.13	gold quality
heart right ventricle	UBERON:0002080	91.95	gold quality
saliva-secreting gland	UBERON:0001044	91.88	gold quality
skin of hip	UBERON:0001554	91.71	gold quality
subthalamic nucleus	UBERON:0001906	91.39	gold quality
calcaneal tendon	UBERON:0003701	91.38	gold quality
bone marrow	UBERON:0002371	91.17	gold quality
mammalian vulva	UBERON:0000997	90.87	gold quality
penis	UBERON:0000989	90.79	gold quality
mouth mucosa	UBERON:0003729	90.46	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-MTAB-7381	yes	312.59
E-MTAB-6701	yes	52.46
E-CURD-46	yes	30.20
E-MTAB-10553	yes	22.41
E-HCAD-13	yes	21.88
E-ANND-3	yes	15.72
E-CURD-112	yes	14.33
E-MTAB-8410	yes	8.71

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT3

Literature-anchored findings (GeneRIF, showing 3)

• Molecular basis of evolutionary loss of the alpha 1,3-galactosyltransferase gene (PMID:11773054)
• A transcription of the complete gene sequence for this enzyme (PMID:12499400)
• GGTA1/CMAH knockout pig samples had increased relative amounts of high-mannose, incomplete, and xylosylated N-linked glycans (PMID:24033743)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Inactive N-acetyllactosaminide alpha-1,3-galactosyltransferase — Q4G0N0 (reviewed: Q4G0N0)

Alternative names: Glycoprotein alpha-galactosyltransferase 1 pseudogene

All UniProt accessions (2): A0A7I2V4B2, Q4G0N0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Golgi apparatus. Golgi stack membrane.

Similarity. Belongs to the glycosyltransferase 6 family.

RefSeq proteins (4): NP_001369513, NP_001369514, NP_001369515, NP_001369516 (=MANE)

Domains & families (InterPro)

Enzyme classification (BRENDA):

• EC 2.4.1.87 — N-acetyllactosaminide 3-alpha-galactosyltransferase (BRENDA: 30 organisms, 74 substrates, 6 inhibitors, 69 Km, 27 kcat entries)

Substrate kinetics (BRENDA)

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

Substrate	Km (mM)	Measurements
UDP-GALACTOSE	0.0007–270	26
LACTOSE	4.5–330	12
UDP-N-ACETYLGALACTOSAMINE	0.068–45.8	8
N-ACETYLLACTOSAMINE	0.6–15	5
ASIALO-ALPHA1-ACID GLYCOPROTEIN	1.25–3.7	2
BETA-D-GAL(1-4)-D-GLCNAC	1.15–1.39	2
BETA-D-GAL(1-3)BETA-D-GLCNAC(1-3)BETA-D-GAL(1-4)	16	1
BETA-D-GAL(1-4)-D-GLC	9	1
BETA-D-GAL(1-4)-D-GLCNAC(1-2)-[BETA-D-GAL(1-4)BE	0.1	1
BETA-D-GAL(1-4)BETA-D-GLCNAC(1-2)-D-MAN	0.25	1
BETA-D-GAL(1-4)BETA-D-GLCNAC(1-6)-D-MAN	0.31	1
D-GALACTOSE	392	1
GAL-BETA-1,4-GLCNAC-(CH2)8CO2CH3	0.31	1
GALACTOSYL-1,3-N-ACETYLGLUCOSAMINYL-1,3-GALACTOS	1.67	1
GALBETA(1-4)GLCNACBETA(1-2)MAN(1-3)MANBETA(1-4)G	0.57	1

UniProt features (5 total): topological domain 2, chain 1, transmembrane region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q4G0N0-F1	63.15	0.11

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 108 (showing top): GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_LEUKOTRIENE_BIOSYNTHETIC_PROCESS, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, GOBP_SULFUR_COMPOUND_BIOSYNTHETIC_PROCESS, GOBP_AMIDE_METABOLIC_PROCESS, GOBP_AMIDE_BIOSYNTHETIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN, YAMAZAKI_TCEB3_TARGETS_UP, GOBP_FATTY_ACID_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_FATTY_ACID_DERIVATIVE_METABOLIC_PROCESS

GO Biological Process (1): leukotriene D4 biosynthetic process (GO:1901750)

GO Molecular Function (0):

GO Cellular Component (4): Golgi cisterna (GO:0031985), Golgi cisterna membrane (GO:0032580), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
leukotriene biosynthetic process	1
sulfur compound biosynthetic process	1
fatty acid derivative biosynthetic process	1
Golgi stack	1
Golgi apparatus subcompartment	1
organelle membrane	1
Golgi cisterna	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

2 interactions, top by confidence:

A	B	Type	Score
GGTA1	KHDRBS1	psi-mi:“MI:0915”(physical association)	0.400

ESM2 similar proteins: A0A0U1RRN3, A0T0A3, A0T0U2, A2BP97, A2CCQ0, A3PB19, A4IHD1, A5GIB0, A5GQF4, A8G2V8, A9BDU4, O10337, O29734, P12363, P36704, P49473, P53348, P62324, P62325, P86929, P86994, P92528, Q00LT9, Q06450, Q06FN9, Q06J11, Q0IDJ7, Q20EW2, Q2JLQ8, Q31CN5, Q3AN56, Q3KPU7, Q3V0X1, Q3ZJ22, Q498U0, Q4G0N0, Q61979, Q63073, Q6B0Z2, Q6B8K4

Diamond homologs: A0A4Z3, A1YGR5, A1YGR6, A2AUQ7, D3ZNQ3, G3V9Q9, P14769, P16442, P23336, P38649, P50127, Q2NKH9, Q2YDM8, Q3L7M0, Q3V1N9, Q4G0N0, Q4R5T7, Q5JBG6, Q5ZLK4, Q7Z4J2, Q8CFC4, Q8HY56, Q8HYB2, Q8N5D6, Q8SPR2, Q8SQ20, Q8VI38, Q95158, Q9ET32, U3KPV4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000074690 (9:121448580 G>A,T), RS1000195370 (9:121485029 T>C), RS1000202094 (9:121450169 G>T), RS1000226007 (9:121494097 A>C,G), RS1000292195 (9:121500059 C>T), RS1000298554 (9:121477748 T>A), RS1000320308 (9:121454091 A>G), RS1000339136 (9:121472172 T>C), RS1000442822 (9:121478357 C>A,T), RS1000455185 (9:121471855 C>T), RS1000461571 (9:121499867 C>A,G,T), RS1000532709 (9:121486674 C>A,T), RS1000560036 (9:121479794 C>G), RS1000626466 (9:121477920 T>A), RS1000632223 (9:121479416 C>G)

Disease associations

OMIM: gene MIM:104175 | 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

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, increases methylation	4
Progesterone	affects expression, decreases reaction, affects cotreatment, increases expression	2
2,4,5,2’,4’,5’-hexachlorobiphenyl	decreases expression	1
3,4,5,3’,4’-pentachlorobiphenyl	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	increases expression	1
Benzo(a)pyrene	decreases expression	1
Estradiol	increases expression, affects cotreatment	1
Polychlorinated Biphenyls	affects expression	1
Mifepristone	affects expression, decreases reaction	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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