B4GALNT2

Summary

B4GALNT2 (beta-1,4-N-acetyl-galactosaminyltransferase 2 (SID blood group), HGNC:24136) is a protein-coding gene on chromosome 17q21.32, encoding Beta-1,4 N-acetylgalactosaminyltransferase 2 (Q8NHY0). Beta-1,4 N-acetylgalactosaminyltransferase involved in the biosynthesis of Sd(a) histo-blood group antigen.

B4GALNT2 catalyzes the last step in the biosynthesis of the human Sd(a) antigen through the addition of an N-acetylgalactosamine residue via a beta-1,4 linkage to a subterminal galactose residue substituted with an alpha-2,3-linked sialic acid. B4GALNT2 also catalyzes the last step in the biosynthesis of the Cad antigen (Montiel et al., 2003 [PubMed 12678917]).

Source: NCBI Gene 124872 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 110 total
• MANE Select transcript: NM_001159387

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24136
Approved symbol	B4GALNT2
Name	beta-1,4-N-acetyl-galactosaminyltransferase 2 (SID blood group)
Location	17q21.32
Locus type	gene with protein product
Status	Approved
Aliases	Sda, Cad
Ensembl gene	ENSG00000167080
Ensembl biotype	protein_coding
OMIM	111730
Entrez	124872

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000300404, ENST00000393354, ENST00000504681, ENST00000888693, ENST00000954078

RefSeq mRNA: 3 — MANE Select: NM_001159387 NM_001159387, NM_001159388, NM_153446

CCDS: CCDS11544, CCDS54139, CCDS54140

Canonical transcript exons

ENST00000393354 — 11 exons

Exon	Start	End
ENSE00001109442	49156566	49156603
ENSE00001109453	49168681	49168900
ENSE00001192902	49166114	49166254
ENSE00001192909	49164088	49164275
ENSE00001192912	49160555	49160641
ENSE00001192915	49159037	49159217
ENSE00001192921	49152800	49152906
ENSE00001192922	49142035	49142172
ENSE00001640527	49132769	49132806
ENSE00002659612	49169523	49176840
ENSE00003550282	49141247	49141447

Expression profiles

Bgee: expression breadth broad, 74 present calls, max score 83.88.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2964 / max 92.0898, expressed in 73 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
161516	0.2178	55
161515	0.0786	30

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	83.88	gold quality
transverse colon	UBERON:0001157	76.30	gold quality
rectum	UBERON:0001052	74.99	gold quality
vermiform appendix	UBERON:0001154	70.95	gold quality
caecum	UBERON:0001153	69.17	gold quality
metanephros cortex	UBERON:0010533	69.04	gold quality
body of stomach	UBERON:0001161	64.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	63.85	gold quality
colonic epithelium	UBERON:0000397	63.84	gold quality
adult mammalian kidney	UBERON:0000082	63.45	gold quality
colonic mucosa	UBERON:0000317	62.18	gold quality
left lobe of thyroid gland	UBERON:0001120	62.10	gold quality
large intestine	UBERON:0000059	61.96	gold quality
colon	UBERON:0001155	61.82	gold quality
stomach	UBERON:0000945	61.76	gold quality
thyroid gland	UBERON:0002046	61.11	gold quality
right lobe of thyroid gland	UBERON:0001119	61.06	gold quality
intestine	UBERON:0000160	60.87	gold quality
cortex of kidney	UBERON:0001225	60.85	gold quality
metanephros	UBERON:0000081	60.57	gold quality
gall bladder	UBERON:0002110	59.38	gold quality
vena cava	UBERON:0004087	58.63	gold quality
mucosa of sigmoid colon	UBERON:0004993	58.62	silver quality
kidney	UBERON:0002113	58.48	gold quality
small intestine Peyer’s patch	UBERON:0003454	58.32	gold quality
small intestine	UBERON:0002108	58.03	gold quality
fundus of stomach	UBERON:0001160	56.74	gold quality
nipple	UBERON:0002030	55.56	gold quality
endothelial cell	CL:0000115	54.90	gold quality
epithelium of nasopharynx	UBERON:0001951	54.71	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-119	yes	16.82
E-ANND-3	yes	5.04

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ESR1

miRNA regulators (miRDB)

18 targeting B4GALNT2, 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-LET-7C-3P	99.95	73.42	2862
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-150-3P	99.43	70.51	920
HSA-MIR-4317	98.49	67.09	987
HSA-MIR-1199-5P	98.44	66.51	829
HSA-MIR-6751-3P	98.44	66.35	835
HSA-MIR-509-3P	98.12	67.25	612
HSA-MIR-3977	98.00	68.17	1500
HSA-MIR-4433A-3P	97.75	62.82	1435
HSA-MIR-1289	97.46	65.37	655
HSA-MIR-3194-5P	96.80	64.90	1027
HSA-MIR-874-3P	95.02	65.66	806

Literature-anchored findings (GeneRIF, showing 15)

• molecular cloning; cDNA predicts a 566 aa protein showing 66.6% and 39% identity with mouse CT beta4GalNAc-T and human GM2/GD2 synthase (PMID:14688233)
• A putative CpG island encompassing the promoter and exon 1 regions in the human Sd(a) beta4GalNAcT-II gene was identified. (PMID:17965433)
• Epigenetic changes in a group of glycosyltransferases including B4GALNT2 and ST3GAL6 represent a malignant phenotype of gastric cancer caused by silencing of the activity of these enzymes (PMID:18485915)
• These experiments demonstrate successful transduction of rhesus macaque muscle with rAAVrh74.MCK.GALGT2 after vascular delivery and induction of molecular changes thought to be therapeutic in several forms of muscular dystrophy. (PMID:24145553)
• In normal colon samples a significant relationship between sLe(x) expression and the ratio between FUT6/B4GALNT2 activities exists, demonstrating for the first time a role for B4GALNT2 in sLe(x) inhibition in vivo. (PMID:24953560)
• B4GALNT2 overexpression prevented the infection of every avian influenza virus strain tested, including the H5, H9, and H7 subtypes, which have previously caused disease in humans. (PMID:28813663)
• Results found that demonstrate that EGFR ligands can activate the human GALGT2 promoter. Deletion analysis of the GALGT2 promoter identified a 45-bp region containing a TFAP4-binding site that was required for soluble HB-EGF activation. (PMID:31036568)
• High Expression of the Sd(a) Synthase B4GALNT2 Associates with Good Prognosis and Attenuates Stemness in Colon Cancer. (PMID:32290493)
• The role of the blood group-related glycosyltransferases FUT2 and B4GALNT2 in susceptibility to infectious disease. (PMID:33662872)
• Short-term treatment of golden retriever muscular dystrophy (GRMD) dogs with rAAVrh74.MHCK7.GALGT2 induces muscle glycosylation and utrophin expression but has no significant effect on muscle strength. (PMID:33770101)
• Glycosyltransferase B4GALNT2 as a Predictor of Good Prognosis in Colon Cancer: Lessons from Databases. (PMID:33919332)
• B4GALNT2 Controls Sd(a) and SLe(x) Antigen Biosynthesis in Healthy and Cancer Human Colon. (PMID:34397142)
• Analysis of the proximal promoter of the human colon-specific B4GALNT2 (Sd(a) synthase) gene: B4GALNT2 is transcriptionally regulated by ETS1. (PMID:34500083)
• Glycoproteomic and Phenotypic Elucidation of B4GALNT2 Expression Variants in the SID Histo-Blood Group System. (PMID:35409292)
• N-Glycan on the Non-Consensus N-X-C Glycosylation Site Impacts Activity, Stability, and Localization of the Sd[a] Synthase B4GALNT2. (PMID:36835549)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	b4galnt2.2	ENSDARG00000070605
danio_rerio	zmp:0000001331	ENSDARG00000076361
danio_rerio	b4galnt2.1	ENSDARG00000094579
mus_musculus	B4galnt2	ENSMUSG00000013418
rattus_norvegicus	B4galnt2	ENSRNOG00000067203

Paralogs (1): B4GALNT1 (ENSG00000135454)

Protein

Protein identifiers

Beta-1,4 N-acetylgalactosaminyltransferase 2 — Q8NHY0 (reviewed: Q8NHY0)

Alternative names: Sd(a) beta-1,4-GalNAc transferase, UDP-GalNAc:Neu5Aca2-3Galb-R b1,4-N-acetylgalactosaminyltransferase

All UniProt accessions (1): Q8NHY0

UniProt curated annotations — full annotation on UniProt →

Function. Beta-1,4 N-acetylgalactosaminyltransferase involved in the biosynthesis of Sd(a) histo-blood group antigen. Catalyzes the transfer of N-acetylgalactosamine (GalNAc) group in a beta-1,4-linkage from UDP-GalNAc to the galactose residue of NeuAcalpha2->3Gal-R to form Sd(a) glycan epitope GalNAcbeta1->4(NeuAcalpha2->3)Gal-R. The Sd(a) epitope is carried in O- and N-linked glycoproteins and glycolipids, including O-linked core 1 structures on GYPA/glycophorin, SLC4A1 and SLC29A1 in erythrocytes, N-linked glycans attached to the Tamm-Horsfall glycoprotein UMOD/uromodulin in renal fluids, O-linked core 3 glycans on mucins in colon and neolactosides in gastric mucosa. Confers protection against influenza A virus strains that attach to NeuAcalpha2->3-carrying host receptors. Modifies N-glycan chains on host receptors and prevents virus entry into cells.

Subunit / interactions. Homodimer; disulfide-linked.

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

Tissue specificity. Widely expressed. Highly expressed in colon and to a lesser extent in kidney, stomach, ileum and rectum.

Disease relevance. Sd(a) polyagglutination syndrome (SDPS) [MIM:615018] A condition characterized by red blood cells agglutination upon exposure to almost all human sera, but not to autologous serum or the sera of newborns. The condition becomes apparent during blood typing and cross-matching in the laboratory. SDPS depends on the strength of expression of the Sd(a) antigen on red blood cells. Most people have weak anti-Sd(a) antibodies in their serum, which is usually of no clinical importance, but can result in red cell agglutination if they are transfused with cells showing strong Sd(a) expression. The gene represented in this entry is involved in disease pathogenesis.

Pathway. Protein modification; protein glycosylation. Glycolipid biosynthesis.

Polymorphism. The Sd(a) antigen on red blood cells defines the SID blood group system. There is considerable variability in the strength of antigen expression, ranging from ordinary Sd(a+) to strong Sd(a++) expression [MIM:615018]. Lack of Sd(a) antigen results in the Sd(a-) phenotype, due to genetic variants in B4GALNT2.

Similarity. Belongs to the glycosyltransferase 2 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8NHY0-1	1	yes
Q8NHY0-2	2
Q8NHY0-3	3

RefSeq proteins (3): NP_001152859, NP_001152860, NP_703147 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001173	Glyco_trans_2-like	Domain
IPR011143	GM2_synthase	Family
IPR029044	Nucleotide-diphossugar_trans	Homologous_superfamily

Pfam: PF00535

Enzyme classification (BRENDA):

• EC 2.4.1.165 — N-acetylneuraminylgalactosylglucosyl-glucoside beta-1,4-N-acetylgalactosaminyltransferase (BRENDA: 4 organisms, 25 substrates, 3 inhibitors, 7 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

5 substrates with measured Km, best-characterized 5. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
FETUIN	0.222–0.94	2
UDP-N-ACETYLGALACTOSAMINE	0.055–0.064	2
N-ACETYLNEURAMINYL-2,3-ALPHA-D-GALACTOSYL-1,4-BE	1.1	1
NEU5AC-ALPHA(2-3)GAL-BETA(1-3)GLCNAC-BETA-1-O-BE	0.38	1
UDP-N-ACETYL-D-GALACTOSAMINE	0.11	1

Catalyzed reactions (Rhea), 4 shown:

• an N-acetyl-alpha-neuraminyl-(2->3)-beta-D-galactosyl derivative + UDP-N-acetyl-alpha-D-galactosamine = an N-acetyl-beta-D-galactosaminyl-(1->4)-[N-acetyl-alpha-neuraminyl-(2->3)]-beta-D-galactosyl derivative + UDP + H(+) (RHEA:81947)
• a 3-O-{alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-[alpha-Neu5Ac-(2->6)]-alpha-D-GalNAc}-L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = a 3-O-{[alpha-Neu5Ac-(2->3)]-beta-D-GalNAc-(1->4)-beta-D-Gal-(1->3)-[alpha-Neu5Ac-(2->6)]-alpha-D-GalNAc}-L-seryl-[protein] + UDP + H(+) (RHEA:81955)
• a 3-O-{alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-[alpha-Neu5Ac-(2->6)]-alpha-D-GalNAc}-L-threonyl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = a 3-O-{[alpha-Neu5Ac-(2->3)]-beta-D-GalNAc-(1->4)-beta-D-Gal-(1->3)-[alpha-Neu5Ac-(2->6)]-alpha-D-GalNAc}-L-threonyl-[protein] + UDP + H(+) (RHEA:81971)
• a neolactoside IV(3)-alpha-NeuAc-nLc4Cer + UDP-N-acetyl-alpha-D-galactosamine = a neolactoside IV(4)-GalNAc,IV(3)-alpha-NeuAc-nLc4Cer + UDP + H(+) (RHEA:82011)

UniProt features (13 total): sequence variant 5, topological domain 2, splice variant 2, chain 1, transmembrane region 1, region of interest 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NHY0-F1	84.66	0.71

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-446203	Asparagine N-linked glycosylation
R-HSA-9037629	Lewis blood group biosynthesis
R-HSA-1430728	Metabolism
R-HSA-392499	Metabolism of proteins
R-HSA-597592	Post-translational protein modification
R-HSA-71387	Metabolism of carbohydrates and carbohydrate derivatives
R-HSA-9033658	Blood group systems biosynthesis

MSigDB gene sets: 512 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, GSE45365_NK_CELL_VS_CD8A_DC_UP, GSE45365_NK_CELL_VS_BCELL_UP, GOBP_OLIGOSACCHARIDE_METABOLIC_PROCESS, GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_HEPATICOBILIARY_SYSTEM_DEVELOPMENT, GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS, GOBP_MUSCLE_TISSUE_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, GOBP_SKELETAL_MUSCLE_TISSUE_REGENERATION, GOBP_RESPONSE_TO_AMINE, GOBP_RESPONSE_TO_CORTICOSTEROID, GOBP_PROTEIN_N_LINKED_GLYCOSYLATION, GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, MATTIOLI_MGUS_VS_PCL

GO Biological Process (11): UDP-N-acetylglucosamine metabolic process (GO:0006047), oligosaccharide biosynthetic process (GO:0009312), protein import (GO:0017038), obsolete protein N-linked glycosylation via asparagine (GO:0018279), UDP-N-acetylgalactosamine metabolic process (GO:0019276), negative regulation of cell-cell adhesion (GO:0022408), skeletal muscle tissue regeneration (GO:0043403), skeletal muscle fiber differentiation (GO:0098528), obsolete protein glycosylation (GO:0006486), obsolete lipid glycosylation (GO:0030259), carbohydrate derivative biosynthetic process (GO:1901137)

GO Molecular Function (6): acetylgalactosaminyltransferase activity (GO:0008376), N-acetylneuraminylgalactosylglucosylceramide beta-1,4-N-acetylgalactosaminyltransferase activity (GO:0047233), protein binding (GO:0005515), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757), hexosyltransferase activity (GO:0016758)

GO Cellular Component (5): Golgi membrane (GO:0000139), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), Golgi apparatus (GO:0005794), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
Post-translational protein modification	1
Blood group systems biosynthesis	1
Metabolism of proteins	1
Metabolism	1
Metabolism of carbohydrates and carbohydrate derivatives	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
amino sugar metabolic process	2
nucleotide-sugar metabolic process	2
cytoplasm	2
oligosaccharide metabolic process	1
carbohydrate biosynthetic process	1
protein transport	1
negative regulation of cell adhesion	1
regulation of cell-cell adhesion	1
cell-cell adhesion	1
tissue regeneration	1
myotube differentiation	1
skeletal muscle cell differentiation	1
biosynthetic process	1
carbohydrate derivative metabolic process	1
UDP-glycosyltransferase activity	1
hexosyltransferase activity	1
acetylgalactosaminyltransferase activity	1
binding	1
catalytic activity	1
transferase activity	1
glycosyltransferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cellular anatomical structure	1
vesicle membrane	1
cytoplasmic vesicle	1
endomembrane system	1
intracellular membrane-bounded organelle	1
intracellular vesicle	1

Protein interactions and networks

STRING

512 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
B4GALNT2	B4GALT1	P15291	924
B4GALNT2	B4GALT2	O60909	879
B4GALNT2	B3GALT1	Q9Y5Z6	846
B4GALNT2	B4GALT3	O60512	839
B4GALNT2	VWF	P04275	725
B4GALNT2	HOXB9	P17482	662
B4GALNT2	FUT6	P51993	651
B4GALNT2	LALBA	P00709	610
B4GALNT2	UTRN	P46939	583
B4GALNT2	B4GALT4	O60513	544
B4GALNT2	B4GALT5	O43286	527
B4GALNT2	DAG1	Q14118	511
B4GALNT2	B3GALT5	Q9Y2C3	507
B4GALNT2	B3GNT2	Q9NY97	483
B4GALNT2	C1GALT1	Q9NS00	479

IntAct

15 interactions, top by confidence:

A	B	Type	Score
BSCL2	B4GALNT2	psi-mi:“MI:0915”(physical association)	0.560
OTX2	B4GALNT2	psi-mi:“MI:0915”(physical association)	0.560
FAM209A	B4GALNT2	psi-mi:“MI:0915”(physical association)	0.560
ARL13B	B4GALNT2	psi-mi:“MI:0915”(physical association)	0.560
M		psi-mi:“MI:0914”(association)	0.350
	B4GALNT2	psi-mi:“MI:0915”(physical association)	0.000
B4GALNT2	BSCL2	psi-mi:“MI:0915”(physical association)	0.000
B4GALNT2	OTX2	psi-mi:“MI:0915”(physical association)	0.000
B4GALNT2	FAM209A	psi-mi:“MI:0915”(physical association)	0.000
B4GALNT2	ARL13B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): B4GALNT2 (Two-hybrid), B4GALNT2 (Two-hybrid), BSCL2 (Two-hybrid), ARL13B (Two-hybrid), B4GALNT2 (Affinity Capture-RNA), B4GALNT2 (Affinity Capture-MS)

ESM2 similar proteins: A0JMH0, A2ARP1, A5PK74, A7Z050, A9JTG5, B5DE73, B5DFG1, D3YY23, D3ZU57, O00562, O35954, O43304, P0C644, P0CB42, P16386, Q01433, Q02356, Q09200, Q10468, Q32P28, Q3SZL5, Q3U308, Q3V1T4, Q4KLM6, Q5HZW3, Q5RDF1, Q5RF50, Q5U2N3, Q5ZMM1, Q68J42, Q6ICH7, Q6JHU7, Q6PD26, Q6PFW1, Q6YRM6, Q80VP9, Q86TL0, Q8BGV9, Q8BGW1, Q8CG71

Diamond homologs: Q00973, Q09199, Q09200, Q10468, Q8NHY0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	88
Likely benign	8
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

1867 predictions. Top by Δscore:

Variant	Effect	Δscore
17:49133063:TGG:T	donor_gain	1.0000
17:49133065:G:GT	donor_gain	1.0000
17:49133217:GGG:G	donor_gain	1.0000
17:49133218:GGG:G	donor_gain	1.0000
17:49141234:T:TA	acceptor_gain	1.0000
17:49141236:T:TA	acceptor_gain	1.0000
17:49141245:A:AC	acceptor_loss	1.0000
17:49141245:A:AG	acceptor_gain	1.0000
17:49141245:AGCTC:A	acceptor_gain	1.0000
17:49141246:G:GT	acceptor_gain	1.0000
17:49141246:GC:G	acceptor_gain	1.0000
17:49141246:GCT:G	acceptor_gain	1.0000
17:49141246:GCTC:G	acceptor_gain	1.0000
17:49141246:GCTCG:G	acceptor_gain	1.0000
17:49141444:TCTG:T	donor_gain	1.0000
17:49141445:CTGGT:C	donor_loss	1.0000
17:49141447:GGTGA:G	donor_loss	1.0000
17:49141448:G:GG	donor_gain	1.0000
17:49141448:GTGA:G	donor_loss	1.0000
17:49141449:T:G	donor_loss	1.0000
17:49152798:A:AG	acceptor_gain	1.0000
17:49152799:G:GG	acceptor_gain	1.0000
17:49152799:GA:G	acceptor_gain	1.0000
17:49152799:GAGAA:G	acceptor_gain	1.0000
17:49156554:T:TA	acceptor_gain	1.0000
17:49160553:A:AG	acceptor_gain	1.0000
17:49160554:G:GG	acceptor_gain	1.0000
17:49160554:GTGA:G	acceptor_gain	1.0000
17:49164145:A:G	acceptor_gain	1.0000
17:49164247:TG:T	donor_gain	1.0000

AlphaMissense

3305 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:49164109:T:A	V323D	0.994
17:49166120:T:C	F381L	0.989
17:49166122:T:A	F381L	0.989
17:49166122:T:G	F381L	0.989
17:49166169:T:C	L397P	0.989
17:49168867:T:C	F488L	0.989
17:49168869:T:A	F488L	0.989
17:49168869:T:G	F488L	0.989
17:49169561:T:C	S512P	0.985
17:49166171:T:A	W398R	0.984
17:49166171:T:C	W398R	0.984
17:49168835:T:C	L477P	0.984
17:49164118:C:A	A326D	0.983
17:49164205:C:A	A355D	0.983
17:49166139:C:A	A387D	0.983
17:49166193:T:C	F405S	0.981
17:49168801:T:A	C466S	0.981
17:49168802:G:C	C466S	0.981
17:49169559:G:A	G511E	0.981
17:49168813:A:C	S470R	0.980
17:49168815:T:A	S470R	0.980
17:49168815:T:G	S470R	0.980
17:49168831:T:C	F476L	0.980
17:49168833:C:A	F476L	0.980
17:49168833:C:G	F476L	0.980
17:49168838:C:A	A478D	0.980
17:49168685:G:A	G427D	0.979
17:49168802:G:A	C466Y	0.979
17:49166136:T:C	L386P	0.978
17:49168801:T:C	C466R	0.978

dbSNP variants (sampled 300 via entrez): RS1000039560 (17:49163410 C>T), RS1000064632 (17:49176980 A>G), RS1000088906 (17:49131211 T>C), RS1000093102 (17:49120859 A>G), RS1000114625 (17:49147105 T>C,G), RS1000231097 (17:49164689 G>A), RS1000262295 (17:49165021 C>A), RS1000367171 (17:49135686 C>T), RS1000367846 (17:49136323 A>G), RS1000441676 (17:49118486 T>A), RS1000450057 (17:49145945 G>A,C), RS1000536741 (17:49126605 G>T), RS1000560537 (17:49166379 G>A,T), RS1000583259 (17:49145652 T>C), RS1000593290 (17:49166899 G>A)

Disease associations

OMIM: gene MIM:111730 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001942_17	Prostate cancer	2.000000e-09
GCST005194_179	Coronary artery disease	4.000000e-09
GCST006291_66	Spherical equivalent or myopia (age of diagnosis)	3.000000e-10
GCST010002_125	Refractive error	1.000000e-44
GCST90002394_404	Monocyte percentage of white cells	4.000000e-11

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004847	age at onset
EFO:0007989	monocyte percentage of leukocytes

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
sodium arsenite	affects cotreatment, increases abundance, decreases expression	2
terbufos	increases methylation	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, decreases reaction	1
Aerosols	decreases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Vehicle Emissions	decreases expression, decreases reaction	1
Benzo(a)pyrene	increases methylation	1
Fonofos	increases methylation	1
Parathion	increases methylation	1
Smoke	increases expression	1
Tobacco Smoke Pollution	affects expression	1
Valproic Acid	increases methylation	1
Particulate Matter	decreases expression, decreases reaction	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_EI10	Hep-G2 SimpleCell O-GalNAc KO GalNAc-T2	Cancer cell line	Male
CVCL_SE49	HAP1 B4GALNT2 (-) 1	Cancer cell line	Male
CVCL_XL89	HAP1 B4GALNT2 (-) 2	Cancer cell line	Male
CVCL_XL90	HAP1 B4GALNT2 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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