CHST2

Summary

CHST2 (carbohydrate sulfotransferase 2, HGNC:1970) is a protein-coding gene on chromosome 3q24, encoding Carbohydrate sulfotransferase 2 (Q9Y4C5). Sulfotransferase that utilizes 3’-phospho-5’-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues within keratan-like structures on N- and O-linked glycans and within O-linked mucin-typ….

This locus encodes a sulfotransferase protein. The encoded enzyme catalyzes the sulfation of a nonreducing N-acetylglucosamine residue, and may play a role in biosynthesis of 6-sulfosialyl Lewis X antigen.

Source: NCBI Gene 9435 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 73 total
• MANE Select transcript: NM_004267

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1970
Approved symbol	CHST2
Name	carbohydrate sulfotransferase 2
Location	3q24
Locus type	gene with protein product
Status	Approved
Aliases	C6ST
Ensembl gene	ENSG00000175040
Ensembl biotype	protein_coding
OMIM	603798
Entrez	9435

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000309575

RefSeq mRNA: 1 — MANE Select: NM_004267 NM_004267

CCDS: CCDS3129

Canonical transcript exons

ENST00000309575 — 2 exons

Exon	Start	End
ENSE00001205046	143119771	143120541
ENSE00001205050	143120644	143124014

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 98.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.0626 / max 219.3205, expressed in 1460 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
38975	6.5728	1390
38974	2.5513	841
38972	0.7487	93
38973	0.1898	99

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
decidua	UBERON:0002450	98.65	gold quality
lateral nuclear group of thalamus	UBERON:0002736	95.66	gold quality
hair follicle	UBERON:0002073	94.30	gold quality
trabecular bone tissue	UBERON:0002483	93.04	gold quality
cartilage tissue	UBERON:0002418	92.49	gold quality
spinal cord	UBERON:0002240	92.42	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.41	gold quality
olfactory bulb	UBERON:0002264	91.91	gold quality
dorsal plus ventral thalamus	UBERON:0001897	91.42	gold quality
granulocyte	CL:0000094	90.86	gold quality
subthalamic nucleus	UBERON:0001906	90.35	gold quality
medial globus pallidus	UBERON:0002477	89.14	gold quality
medulla oblongata	UBERON:0001896	89.05	gold quality
globus pallidus	UBERON:0001875	88.86	gold quality
cerebellar vermis	UBERON:0004720	88.52	gold quality
trigeminal ganglion	UBERON:0001675	88.02	gold quality
placenta	UBERON:0001987	87.83	gold quality
inferior olivary complex	UBERON:0002127	87.72	gold quality
postcentral gyrus	UBERON:0002581	87.67	gold quality
thymus	UBERON:0002370	87.66	gold quality
frontal pole	UBERON:0002795	87.66	gold quality
superior vestibular nucleus	UBERON:0007227	87.36	gold quality
lateral globus pallidus	UBERON:0002476	87.33	gold quality
parietal lobe	UBERON:0001872	87.32	gold quality
dorsal root ganglion	UBERON:0000044	87.05	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	86.96	gold quality
inferior vagus X ganglion	UBERON:0005363	86.83	gold quality
lower lobe of lung	UBERON:0008949	86.77	gold quality
nucleus accumbens	UBERON:0001882	86.61	gold quality
ventral tegmental area	UBERON:0002691	86.43	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-8221	yes	620.14
E-ANND-3	yes	10.45

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GATA2, GATA3, HAND2, NFKB

miRNA regulators (miRDB)

134 targeting CHST2, 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-6867-5P	100.00	82.21	3464
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-8063	99.91	69.76	3146

Literature-anchored findings (GeneRIF, showing 7)

• is distributed throughout the Golgi apparatus and orchestrates the biosynthesis of L-selectin ligands (PMID:12855678)
• A novel tumor antigen that is specifically expressed in ovarian mucinous, clear cell and papillary serous adenocarcinomas. (PMID:16897186)
• report the sites at which N-Acetylglucosamine-6-sulfotransferase-1 is modified with N-linked glycans and the effects that each glycan has on enzyme activity, specificity, and localization.[N-Acetylglucosamine-6-sulfotransferase-1] (PMID:19571171)
• A method for O-GlcNAc detection using in vitro sulfation with two N-acetylglucosamine (GlcNAc)-specific sulfotransferases, carbohydrate sulfotransferase 2 and carbohydrate sulfotransferase 4. (PMID:24799377)
• GlcNAc6ST1 is up-regulated in the brains of Alzheimer’s disease patients. (PMID:28320965)
• mRNA transcript analyses on the genes involved in synthesizing GlcNAc-6-O-sulfated glycans in human colon cancer tissues indicated that GlcNAc6ST-2 (CHST4) is preferentially expressed in cancer cells … GlcNAc6ST-3 (CHST5) was only expressed in nonmalignant epithelial cells, whereas GlcNAc6ST-1 (CHST2) was expressed equally in both cancerous and nonmalignant epithelial cells. (PMID:30093410)
• Site-selective sulfation of N-glycans by human GlcNAc-6-O-sulfotransferase 1 (CHST2) and chemoenzymatic synthesis of sulfated antibody glycoforms. (PMID:35939855)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	chst2b	ENSDARG00000058585
danio_rerio	chst2a	ENSDARG00000075007
mus_musculus	Chst2	ENSMUSG00000033350
rattus_norvegicus	Chst2	ENSRNOG00000047734
drosophila_melanogaster	CG9550	FBGN0031826
drosophila_melanogaster	CG31637	FBGN0051637

Paralogs (6): CHST3 (ENSG00000122863), CHST5 (ENSG00000135702), CHST4 (ENSG00000140835), CHST7 (ENSG00000147119), CHST1 (ENSG00000175264), CHST6 (ENSG00000183196)

Protein

Protein identifiers

Carbohydrate sulfotransferase 2 — Q9Y4C5 (reviewed: Q9Y4C5)

Alternative names: Galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 2, N-acetylglucosamine 6-O-sulfotransferase 1

All UniProt accessions (2): Q9Y4C5, V9HVX9

UniProt curated annotations — full annotation on UniProt →

Function. Sulfotransferase that utilizes 3’-phospho-5’-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues within keratan-like structures on N- and O-linked glycans and within O-linked mucin-type glycans. Selectively transfers the sulfate group onto the terminal GlcNAc of alpha1,3-Man or alpha1,6-Man antenna of complex-type N-glycans depending on glycan composition. Only sulfates terminal GlcNAc of alpha1,3-Man antenna of G0 complex-type N-glycans. Can sulfate keratan-type N-acetyllactosamine (LacNAc) repeats generating epitopes for self versus non-self immune recognition by C-type lectins. Transfers the sulfate group primarily on core 2 GlcNAcbeta1-6(Galbeta1-3)GalNAcalpha-Ser/Thr and with lower efficiency on extended core 1 GlcNAcbeta1-3Galbeta1-3GalNAcalpha-Ser/Thr based O-linked glycans on peripheral node addressins (PNAds) expressed on the lumenal side of high endothelial venules (HEVs). Shares substrate specificity with CHST4 and both contribute to generate sialyl 6-sulfo Lewis X determinant (also known as MECA-79 epitope) for SELL recognition, a prerequisite for continuous lymphocyte homing into peripheral lymph nodes and antigen immune surveillance. Has no activity toward alpha-linked GlcNAc moiety exposed at the non-reducing ends or to internally located GlcNAc residues.

Subunit / interactions. Homodimer; disulfide-linked. Homodimerization is not essential for enzyme activity.

Subcellular location. Golgi apparatus. trans-Golgi network membrane.

Tissue specificity. Widely expressed. Highly expressed in bone marrow, peripheral blood leukocytes, spleen, brain, spinal cord, ovary and placenta. Expressed by high endothelial cells (HEVs) and leukocytes.

Post-translational modifications. Glycosylation at Asn-475 is required for catalytic activity.

Induction. Up-regulated upon cytokine activation.

Pathway. Protein modification; carbohydrate sulfation.

Miscellaneous. Higher levels of expression compared to isoform 1 when expressed in HeLa cells. Exhibits similar intracellular GlcNAc-6-O-sulfation activity.

Similarity. Belongs to the sulfotransferase 1 family. Gal/GlcNAc/GalNAc subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y4C5-1	1	yes
Q9Y4C5-2	2

RefSeq proteins (1): NP_004258* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000863	Sulfotransferase_dom	Domain
IPR016469	Carbohydrate_sulfotransferase	Family
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR051135	Gal/GlcNAc/GalNAc_ST	Family

Pfam: PF00685

Catalyzed reactions (Rhea), 7 shown:

• 3-O-{N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + 3’-phosphoadenylyl sulfate = 3-O-{6-O-sulfo-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + adenosine 3’,5’-bisphosphate + H(+) (RHEA:67856)
• 3-O-{N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + 3’-phosphoadenylyl sulfate = 3-O-{6-O-sulfo-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + adenosine 3’,5’-bisphosphate + H(+) (RHEA:67860)
• a 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + 3’-phosphoadenylyl sulfate = 3-O-{beta-D-galactosyl-(1->3)-[6-O-sulfo-N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + adenosine 3’,5’-bisphosphate + H(+) (RHEA:67864)
• 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + 3’-phosphoadenylyl sulfate = 3-O-{beta-D-galactosyl-(1->3)-[6-O-sulfo-N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + adenosine 3’,5’-bisphosphate + H(+) (RHEA:67868)
• an N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + 3’-phosphoadenylyl sulfate = a 6-O-sulfo-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + adenosine 3’,5’-bisphosphate + H(+) (RHEA:82911)
• an N(4)-{alpha-Neu5Ac-(2->6)-beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + 3’-phosphoadenylyl sulfate = an N(4)-{alpha-Neu5Ac-(2->6)-beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[6-O-sulfo-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + adenosine 3’,5’-bisphosphate + H(+) (RHEA:82975)
• N(4)-{beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L-asparaginyl-[protein] + 3’-phosphoadenylyl sulfate = an N(4)-{6-O-sulfo-beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-[beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc}-L–asparaginyl-[protein] + adenosine 3’,5’-bisphosphate + H(+) (RHEA:84275)

UniProt features (36 total): mutagenesis site 23, glycosylation site 3, topological domain 2, binding site 2, chain 1, splice variant 1, transmembrane region 1, sequence conflict 1, region of interest 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y4C5-F1	78.61	0.59

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 152 (not glycosylated)

Ligand- & substrate-binding residues (2): 173–179; 332–340

Glycosylation sites (3): 475, 243, 457

Mutagenesis-validated functional residues (23):

Position	Phenotype
59	does not affect homodimerization. abolishes homodimerization but not enzyme activity; when associated with s-39.
86	induces migration in both homodimeric and monomeric forms. abolishes homodimerization but not enzyme activity; when asso
174	induces a strong decrease in enzyme activity.
296	induces a strong decrease in enzyme activity.
304	loss of function.
332	loss of function.
341	induces a strong decrease in enzyme activity.
457	reduced localization in the golgi.
475	unable to sulfate the sialyl lewis x tetrasaccharide.
518	has weak or no effect.
519	has weak or no effect.
520	has weak or no effect.
521	no effect.
522	no effect.
523	has weak or no effect.
524	induces a strong decrease in enzyme activity.
525	induces a strong decrease in enzyme activity.
525	has weak or no effect.
526	has weak or no effect.
527	no effect.
528	has weak or no effect.
529	no effect.
530	induces a strong decrease in enzyme activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-2022854	Keratan sulfate biosynthesis

MSigDB gene sets: 242 (showing top): AGGAAGC_MIR5163P, chr3q24, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_INFLAMMATORY_RESPONSE, PEREZ_TP63_TARGETS, TATTATA_MIR374, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GOBP_REGULATION_OF_LEUKOCYTE_MIGRATION, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GOBP_CELL_CELL_ADHESION, GOBP_CELLULAR_EXTRAVASATION, GOBP_LEUKOCYTE_MIGRATION, GOCC_TRANS_GOLGI_NETWORK, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS

GO Biological Process (6): carbohydrate metabolic process (GO:0005975), N-acetylglucosamine metabolic process (GO:0006044), sulfur compound metabolic process (GO:0006790), inflammatory response (GO:0006954), keratan sulfate proteoglycan biosynthetic process (GO:0018146), positive regulation of leukocyte tethering or rolling (GO:1903238)

GO Molecular Function (3): N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517), sulfotransferase activity (GO:0008146), transferase activity (GO:0016740)

GO Cellular Component (6): Golgi membrane (GO:0000139), nucleoplasm (GO:0005654), Golgi apparatus (GO:0005794), trans-Golgi network (GO:0005802), cytosol (GO:0005829), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Keratan sulfate/keratin metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cytoplasm	2
primary metabolic process	1
amino sugar metabolic process	1
metabolic process	1
defense response	1
proteoglycan biosynthetic process	1
keratan sulfate proteoglycan metabolic process	1
leukocyte tethering or rolling	1
regulation of leukocyte tethering or rolling	1
positive regulation of leukocyte adhesion to vascular endothelial cell	1
sulfotransferase activity	1
transferase activity, transferring sulphur-containing groups	1
catalytic activity	1
Golgi apparatus	1
bounding membrane of organelle	1
nuclear lumen	1
endomembrane system	1
intracellular membrane-bounded organelle	1
Golgi apparatus subcompartment	1

Protein interactions and networks

STRING

782 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CHST2	NTAN1	Q96AB6	913
CHST2	GALNT6	Q8NCL4	496
CHST2	CHST15	Q7LFX5	495
CHST2	B4GALT4	O60513	467
CHST2	GCNT1	Q02742	467
CHST2	B3GNT3	Q9Y2A9	459
CHST2	ST3GAL6	Q9Y274	451
CHST2	FUT7	Q11130	442
CHST2	ST3GAL5	Q9UNP4	438
CHST2	LUM	P51884	421
CHST2	CHST14	Q8NCH0	420
CHST2	ALG12	Q9BV10	418
CHST2	ARHGAP44	Q17R89	416
CHST2	CHST12	Q9NRB3	411
CHST2	B3GALT2	O43825	406
CHST2	SELL	P14151	406

IntAct

1 interactions, top by confidence:

A	B	Type	Score
CHST2	HSPA5	psi-mi:“MI:0914”(association)	0.350

BioGRID (4): CHST2 (Affinity Capture-MS), CHST2 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), CANX (Affinity Capture-MS)

ESM2 similar proteins: A2A699, A2BD09, A5D7T4, A8MVW0, B0BN44, O77681, O88829, P0CG36, P0CG37, P15907, P51693, P59383, P61132, P70277, P97325, Q03157, Q07105, Q11203, Q3UPI1, Q3UY90, Q5K027, Q5QQ37, Q64685, Q66NC0, Q68BL7, Q6P7B4, Q6UWH4, Q701R2, Q701R3, Q701R4, Q70D51, Q766D5, Q76K27, Q76KP1, Q80WV3, Q866Y3, Q86VZ4, Q8BHP7, Q8CB67, Q8VCS0

Diamond homologs: O43916, O88199, O93403, Q0VBN2, Q5RJQ0, Q6DBY9, Q6XQG8, Q7LGC8, Q80WV3, Q8IZU8, Q8NCG5, Q92179, Q9EP78, Q9EQC0, Q9GZS9, Q9GZX3, Q9NS84, Q9QUP4, Q9QZL2, Q9R1I1, Q9Y4C5, P0C2H4, Q8BLI4, Q9UL01

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

147 predictions. Top by Δscore:

Variant	Effect	Δscore
3:143120539:CAG:C	donor_loss	0.9600
3:143120541:GGTGA:G	donor_loss	0.9600
3:143120542:GT:G	donor_loss	0.9600
3:143120543:T:A	donor_loss	0.9600
3:143119813:G:T	donor_gain	0.8500
3:143120395:GGA:G	donor_gain	0.8300
3:143120542:G:GG	donor_gain	0.8300
3:143120638:TCGCA:T	acceptor_loss	0.8200
3:143120639:CGCA:C	acceptor_loss	0.8200
3:143120640:GCA:G	acceptor_loss	0.8200
3:143120641:CA:C	acceptor_loss	0.8200
3:143120642:AGGTC:A	acceptor_loss	0.8200
3:143120643:G:T	acceptor_loss	0.8200
3:143120506:A:AG	donor_gain	0.7800
3:143119823:AGC:A	donor_gain	0.7400
3:143120625:ACTCC:A	acceptor_loss	0.7200
3:143119822:T:TA	donor_gain	0.7100
3:143119813:G:GT	donor_gain	0.7000
3:143120358:CGAG:C	acceptor_gain	0.7000
3:143120252:G:GT	donor_gain	0.6900
3:143120642:A:AG	acceptor_gain	0.6800
3:143120643:G:GG	acceptor_gain	0.6800
3:143120624:CACT:C	acceptor_loss	0.6500
3:143120621:GCTCA:G	acceptor_loss	0.6400
3:143120622:CTCAC:C	acceptor_loss	0.6400
3:143120623:TCACT:T	acceptor_loss	0.6400
3:143120630:GCTTC:G	acceptor_loss	0.6300
3:143120631:CTTCC:C	acceptor_loss	0.6300
3:143120629:CGCTT:C	acceptor_loss	0.6200
3:143120636:CCTCG:C	acceptor_loss	0.6100

AlphaMissense

3373 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:143121328:C:T	T171I	1.000
3:143121333:T:A	W173R	1.000
3:143121333:T:C	W173R	1.000
3:143121335:G:C	W173C	1.000
3:143121335:G:T	W173C	1.000
3:143121336:C:A	R174S	1.000
3:143121336:C:T	R174C	1.000
3:143121337:G:C	R174P	1.000
3:143121342:G:T	G176C	1.000
3:143121343:G:A	G176D	1.000
3:143121343:G:T	G176V	1.000
3:143121357:G:C	G181R	1.000
3:143121358:G:A	G181D	1.000
3:143121371:C:A	N185K	1.000
3:143121371:C:G	N185K	1.000
3:143121399:G:A	E195K	1.000
3:143121400:A:C	E195A	1.000
3:143121400:A:T	E195V	1.000
3:143121401:G:C	E195D	1.000
3:143121401:G:T	E195D	1.000
3:143121403:C:A	P196Q	1.000
3:143121403:C:G	P196R	1.000
3:143121410:G:C	W198C	1.000
3:143121410:G:T	W198C	1.000
3:143121417:T:A	W201R	1.000
3:143121417:T:C	W201R	1.000
3:143121419:G:C	W201C	1.000
3:143121419:G:T	W201C	1.000
3:143121451:T:C	L212P	1.000
3:143121469:A:T	D218V	1.000

dbSNP variants (sampled 300 via entrez): RS1000384931 (3:143119066 A>G), RS1000816726 (3:143120172 C>T), RS1000886468 (3:143121531 A>G), RS1001191807 (3:143122902 C>T), RS1001254892 (3:143121107 G>A,T), RS1001266654 (3:143119573 C>A,T), RS1001654016 (3:143119699 C>A,T), RS1002942118 (3:143120533 C>A,T), RS1003725102 (3:143121890 C>T), RS1004545819 (3:143122629 G>A), RS1005340388 (3:143118657 G>A,C), RS1005395320 (3:143119662 T>TGGGGGC), RS1005490718 (3:143118602 G>A,T), RS1005842274 (3:143119801 C>T), RS1006600926 (3:143124050 C>G,T)

Disease associations

OMIM: gene MIM:603798 | 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
GCST003542_32	Night sleep phenotypes	7.000000e-07
GCST012248_1	IgG N-glycosylation phenotypes (multivariate analysis)	9.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005193	serum IgG glycosylation measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	8
Tobacco Smoke Pollution	increases expression	3
bisphenol A	decreases expression, affects cotreatment, increases methylation	2
Silicon Dioxide	increases expression	2
Smoke	decreases expression, increases expression	2
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
mono-(2-ethylhexyl)phthalate	increases expression	1
sulforaphane	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	increases expression	1
potassium chromate(VI)	increases expression	1
cupric chloride	increases expression	1
hydroquinone	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
pentanal	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
MRK 003	decreases expression	1
MT19c compound	decreases expression	1
Bortezomib	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1

Clinical trials (associated diseases)

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