◎ Sugi Atlas
Send feedback

Atlas / Gene / CSGALNACT2

CSGALNACT2

gene
On this page

Also known as GALNACT2MGC40204PRO0082GALNACT-2

Summary

CSGALNACT2 (chondroitin sulfate N-acetylgalactosaminyltransferase 2, HGNC:24292) is a protein-coding gene on chromosome 10q11.21, encoding Chondroitin sulfate N-acetylgalactosaminyltransferase 2 (Q8N6G5). Transfers 1,4-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of glucuronic acid (GlcUA).

This gene encodes a member of the chondroitin N-acetylgalactosaminyltransferase family. The encoded protein is involved in elongation during chondroitin sulfate synthesis. Alternative splicing of this gene results in multiple transcript variants. Two related pseudogenes have been identified on chromosome X.

Source: NCBI Gene 55454 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 91 total
  • GTEx eGene: eQTL in 49 tissues, sQTL in 36 (q < 0.05)
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.89 (unconstrained)
  • MANE Select transcript: NM_018590
  • Notable: 91 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24292
Approved symbolCSGALNACT2
Namechondroitin sulfate N-acetylgalactosaminyltransferase 2
Location10q11.21
Locus typegene with protein product
StatusApproved
AliasesGALNACT2, MGC40204, PRO0082, GALNACT-2
Ensembl geneENSG00000169826
Ensembl biotypeprotein_coding
OMIM616616
Entrez55454

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 15 protein_coding, 12 nonsense_mediated_decay

MANE Select: ENST00000374466

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1

ENST00000374466, ENST00000908294, ENST00000908295, ENST00000908296, ENST00000908297, ENST00000943043, ENST00000943044, ENST00000943045, ENST00000943046, ENST00000990821, ENST00000990822, ENST00000990823, ENST00000990824, ENST00000990825, ENST00001038860, ENST00001038862, ENST00001038864, ENST00001038865, ENST00001038866, ENST00001038867, ENST00001038868, ENST00001038869, ENST00001038870, ENST00001088041, ENST00001088042, ENST00001123397, ENST00001143031

RefSeq mRNA: 3 — MANE Select: NM_018590 NM_001319654, NM_001319656, NM_018590

CCDS: CCDS7201

Canonical transcript exons

ENST00000374466 — 8 exons

ExonStartEnd
ENSE000011558344317595143176032
ENSE000011647044316700443167098
ENSE000011947694316049443160595
ENSE000011947764315871543158931
ENSE000011947814315489743155810
ENSE000011947884313844543138567
ENSE000011948014316386643164044
ENSE000014635914318325043185302

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 96.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.7063 / max 401.6199, expressed in 1771 samples.

Highest expression (Bgee): secondary oocyte, visceral pleura, tibia, bone marrow, monocyte.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CSGALNACT2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 49 tissues and its splicing (sQTL) in 36 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 85 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Nerve Tibialeqtl5.2e-167-1.1310:43162363:T:G
Thyroideqtl6.6e-127-0.8310:43162363:T:G
Testiseqtl2.6e-93-0.7810:43162363:T:G
Nerve Tibialsqtl5.3e-88+1.2110:43205531:C:G
Esophagus Musculariseqtl3.5e-74-0.5910:43170302:A:G
Breast Mammary Tissueeqtl9.8e-58-0.5010:43125875:C:G
Skin Not Sun Exposed Suprapubiceqtl1.2e-50-0.3810:43170302:A:G
Heart Atrial Appendageeqtl3.4e-50-0.5310:43162363:T:G
Esophagus Gastroesophageal Junctioneqtl5.4e-50-0.6710:43171319:G:T
Adipose Subcutaneouseqtl9.1e-50+0.4310:43200036:T:G
Colon Sigmoideqtl5.8e-49+0.5910:43194943:G:A
Colon Transverseeqtl1.4e-46+0.3510:43194943:G:A
Pituitaryeqtl5.8e-46-0.8210:43171319:G:T
Adipose Visceral Omentumeqtl1.8e-45+0.4210:43200036:T:G
Brain Cortexeqtl4.3e-44-0.8310:43162363:T:G
Skin Sun Exposed Lower legeqtl2.3e-42-0.3210:43170302:A:G
Brain Caudate basal gangliaeqtl6.0e-42-0.7910:43162363:T:G
Brain Nucleus accumbens basal gangliaeqtl1.8e-40-0.8410:43162363:T:G
Artery Tibialsqtl1.7e-39-0.8710:43162363:T:G
Artery Tibialeqtl3.3e-39-0.3810:43170302:A:G

FANTOM5 promoters

5 alternative TSS:

Promoter IDTPM avgSamples expressed
10474115.47131748
1047425.40301526
1047431.8946839
1047451.5221564
1047440.4154205

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065596.38gold quality
visceral pleuraUBERON:000240195.98gold quality
tibiaUBERON:000097995.79gold quality
bone marrowUBERON:000237195.66gold quality
monocyteCL:000057695.41gold quality
mononuclear cellCL:000084295.39gold quality
leukocyteCL:000073895.02gold quality
endothelial cellCL:000011594.52gold quality
cartilage tissueUBERON:000241894.47gold quality
superficial temporal arteryUBERON:000161494.16gold quality
germinal epithelium of ovaryUBERON:000130493.88gold quality
synovial jointUBERON:000221793.78gold quality
bone marrow cellCL:000209293.56gold quality
pleuraUBERON:000097793.47gold quality
trabecular bone tissueUBERON:000248393.05gold quality
lower lobe of lungUBERON:000894993.05gold quality
parietal pleuraUBERON:000240092.98gold quality
oocyteCL:000002392.65gold quality
cortical plateUBERON:000534392.40gold quality
amniotic fluidUBERON:000017392.37gold quality
bloodUBERON:000017892.26gold quality
periodontal ligamentUBERON:000826692.01gold quality
calcaneal tendonUBERON:000370191.71gold quality
saphenous veinUBERON:000731891.60gold quality
mucosa of paranasal sinusUBERON:000503090.95gold quality
right lungUBERON:000216790.80gold quality
choroid plexus epitheliumUBERON:000391190.51gold quality
gall bladderUBERON:000211090.35gold quality
blood vessel layerUBERON:000479790.17gold quality
mammary ductUBERON:000176589.98gold quality
ganglionic eminenceUBERON:000402389.42gold quality
Brodmann (1909) area 23UBERON:001355489.31gold quality
skin of hipUBERON:000155489.30gold quality
urethraUBERON:000005789.25gold quality
vermiform appendixUBERON:000115489.21gold quality
epithelium of mammary glandUBERON:000324489.20gold quality
epithelium of nasopharynxUBERON:000195189.16gold quality
granulocyteCL:000009489.00gold quality
dorsal root ganglionUBERON:000004489.00gold quality
descending thoracic aortaUBERON:000234588.93gold quality
lungUBERON:000204888.91gold quality
pigmented layer of retinaUBERON:000178288.90gold quality
tibial nerveUBERON:000132388.89gold quality
tibial arteryUBERON:000761088.84gold quality
layer of synovial tissueUBERON:000761688.84gold quality
popliteal arteryUBERON:000225088.83gold quality
tendonUBERON:000004388.82gold quality
upper lobe of lungUBERON:000894888.75gold quality
corpus callosumUBERON:000233688.74gold quality
aortaUBERON:000094788.59gold quality
caecumUBERON:000115388.57gold quality
lymph nodeUBERON:000002988.48gold quality
trigeminal ganglionUBERON:000167588.48gold quality
upper lobe of left lungUBERON:000895288.44gold quality
subthalamic nucleusUBERON:000190688.41gold quality
penisUBERON:000098988.33gold quality
cauda epididymisUBERON:000436088.24gold quality
thoracic aortaUBERON:000151588.22gold quality
ascending aortaUBERON:000149688.16gold quality
upper leg skinUBERON:000426287.99gold quality
left coronary arteryUBERON:000162687.89gold quality
spleenUBERON:000210687.88gold quality
coronary arteryUBERON:000162187.79gold quality
myometriumUBERON:000129687.74gold quality
stromal cell of endometriumCL:000225587.61gold quality
pericardiumUBERON:000240787.44gold quality
smooth muscle tissueUBERON:000113587.37gold quality
subcutaneous adipose tissueUBERON:000219087.35gold quality
islet of LangerhansUBERON:000000687.33gold quality
endometriumUBERON:000129587.26gold quality
left uterine tubeUBERON:000130387.26gold quality
connective tissueUBERON:000238487.09gold quality
substantia nigra pars reticulataUBERON:000196687.05gold quality
mammary glandUBERON:000191187.03gold quality
urinary bladderUBERON:000125587.00gold quality
thoracic mammary glandUBERON:000520086.95gold quality
adipose tissueUBERON:000101386.87gold quality
lower esophagus muscularis layerUBERON:003583386.84gold quality
right coronary arteryUBERON:000162586.82gold quality
lower esophagusUBERON:001347386.77gold quality
ovaryUBERON:000099286.59gold quality
mucosa of stomachUBERON:000119986.57gold quality
pylorusUBERON:000116686.46gold quality
adipose tissue of abdominal regionUBERON:000780886.40gold quality
omental fat padUBERON:001041486.39gold quality
peritoneumUBERON:000235886.38gold quality
esophagogastric junction muscularis propriaUBERON:003584186.38gold quality
left ovaryUBERON:000211986.28gold quality
uterusUBERON:000099586.16gold quality
vena cavaUBERON:000408786.10gold quality
biceps brachiiUBERON:000150786.03gold quality
right ovaryUBERON:000211885.89gold quality
colonic epitheliumUBERON:000039785.85gold quality
ventricular zoneUBERON:000305385.72gold quality
primary visual cortexUBERON:000243685.71gold quality
lateral globus pallidusUBERON:000247685.70gold quality
superior vestibular nucleusUBERON:000722785.70gold quality
body of uterusUBERON:000985385.70gold quality
substantia nigra pars compactaUBERON:000196585.68gold quality
spinal cordUBERON:000224085.62gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes17.55

HPA expression

RNA tissue specificity: Tissue enriched

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Bone marrowtissue126.5medium
Choroid plexustissue28.5
Thymustissue26.0
Spleentissue25.0medium
Placentatissue24.7high
Gallbladdertissue23.7high
Appendixtissue22.8high
Urinary bladdertissue22.5high
Lymph nodetissue21.1high
Nucleus accumbenstissue20.0
Smooth muscletissue19.4medium
Locus coeruleustissue18.6
Hippocampustissue18.5medium
Adipose tissuetissue18.4low
Endometrium 1tissue18.3high
Postcentral gyrustissue18.2
Lungtissue18.1medium
Tonsiltissue16.3high
Tonguetissue16.0
Ovarytissue14.9low
Livertissue13.0medium
Cervixtissue12.9medium
Prostatetissue12.6high
Skeletal muscletissue12.3low
Breasttissue11.3medium
Vaginatissue11.3medium
Rectumtissue10.9high
Pituitary glandtissue10.8
Cerebellumtissue10.8high
Skin 1tissue10.4medium
Seminal vesicletissue10.3high
Adrenal glandtissue10.0high
Esophagustissue9.9medium
Heart muscletissue9.8medium
Stomach 1tissue9.5medium
Olfactory bulbtissue9.4
Spinal cordtissue9.2
Retinatissue9.1
Small intestinetissue9.1medium
Testistissue8.6high
Cerebral cortextissue8.6high
Motor cortextissue8.6
Substantia nigratissue8.6
Duodenumtissue8.6medium
Thyroid glandtissue8.5medium
Caudate putamentissue8.5
Colontissue8.4high
Corpus callosumtissue8.3
Retrosplenial and cingulate cortextissue8.3
Kidneytissue8.2high
Hippocampal formationtissue8.2
Frontal cortextissue8.1
Somatosensory cortextissue8.1
Prefrontal cortextissue8.0
Epididymistissue8.0high
Entorhinal cortextissue8.0
Retrosplenial cortextissue8.0
Superior colliculitissue7.9
Ponstissue7.8
Temporal cortextissue7.8

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Cerebellar cortex (33.2), Flocculonodular lobe (32.3), Area parastriata, superior (30.2), Temporal white matter (29.6), Corpus callosum, genu (white matter) (29.0).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CSGALNACT2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 137 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692A100.0074.406850
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-3163100.0077.238605
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-569699.9872.364487
HSA-MIR-480399.9871.993117
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-512-3P99.9767.351049
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-9-3P99.9670.882068
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426

Functional genomics

gnomAD constraint: pLI 4.57e-06, LOEUF 0.886, missense Z 1.93 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000374466 splits into 2 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)Missense obs / expo/eConstrained
10:43,155,150–43,163,903374 / 401.30.93no
10:43,163,904–43,183,539170 / 256.20.66no

Literature-anchored findings (GeneRIF, showing 3)

  • plays a role in the initiation and elongation in the synthesis of chondroitin sulfate (PMID:12446672)
  • Chondroitin sulfate N-acetylgalactosaminyltransferase 2 is functionally involved in the progression of atherosclerosis both in its early and advanced stages. (PMID:30579596)
  • CSGALNACT2 restricts ovarian cancer migration and invasion by modulating MAPK/ERK pathway through DUSP1. (PMID:38082211)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriocsgalnact2ENSDARG00000061400
mus_musculusCsgalnact2ENSMUSG00000042042
rattus_norvegicusCsgalnact2ENSRNOG00000014713
drosophila_melanogasterCsgalnactFBGN0033500

Paralogs (7): CHPF2 (ENSG00000033100), CHPF (ENSG00000123989), CHSY1 (ENSG00000131873), B4GALNT3 (ENSG00000139044), CSGALNACT1 (ENSG00000147408), B4GALNT4 (ENSG00000182272), CHSY3 (ENSG00000198108)

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
RASGEF1Aprotein-coding221002
LINC02633ncRNA105378270
HNRNPFprotein-coding3185
FXYD4protein-coding53828
MIR5100ncRNA100847014
LINC01264ncRNA104266963
CSGALNACT2-DTncRNA118568825
RETprotein-coding5979

Protein

Protein identifiers

Chondroitin sulfate N-acetylgalactosaminyltransferase 2 — Q8N6G5 (reviewed: Q8N6G5)

Alternative names: Chondroitin beta-1,4-N-acetylgalactosaminyltransferase 2

All UniProt accessions (4): A0A0S2Z5F5, A0A0S2Z5F9, A0A0S2Z5K4, Q8N6G5

UniProt curated annotations — full annotation on UniProt →

Function. Transfers 1,4-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of glucuronic acid (GlcUA). Required for addition of the first GalNAc to the core tetrasaccharide linker and for elongation of chondroitin chains.

Subcellular location. Golgi apparatus. Golgi stack membrane.

Tissue specificity. Ubiquitous.

Similarity. Belongs to the chondroitin N-acetylgalactosaminyltransferase family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N6G5-11yes
Q8N6G5-22

RefSeq proteins (3): NP_001306583, NP_001306585, NP_061060* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008428Chond_GalNAcFamily
IPR029044Nucleotide-diphossugar_transHomologous_superfamily
IPR051227CS_glycosyltransferaseFamily

Pfam: PF05679

Enzyme classification (BRENDA)

  • EC 2.4.1.174 — glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase (BRENDA: 5 organisms, 22 substrates, 39 inhibitors, 0 Km, 0 kcat entries)
  • EC 2.4.1.175 — glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase (BRENDA: 8 organisms, 92 substrates, 7 inhibitors, 8 Km, 1 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
UDP-N-ACETYL-BETA-D-GALACTOSAMINE0.0059–0.053
UDP-GALNAC0.221–9.2752
CHONDROITIN SULFATE CS-110.361
UDP-N-ACETYL-ALPHA-D-GLUCOSAMINE0.00591

Catalyzed reactions (Rhea)

  • 3-O-(beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + UDP-N-acetyl-alpha-D-galactosamine = 3-O-(beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + UDP + H(+) (RHEA:23464)

UniProt features (14 total): topological domain 2, splice variant 2, sequence variant 2, binding site 2, glycosylation site 2, chain 1, sequence conflict 1, transmembrane region 1, coiled-coil region 1

Structure

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N6G5-F187.160.63

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Transferases, Metabolic proteins, Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): endoplasmic reticulum

Antibody reliability (HPA): IH approved · IF approved

Functional residue map

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

Ligand- & substrate-binding residues (2)

PositionRole
369a divalent metal cation
486a divalent metal cation

Glycosylation sites (2)

TypePositions
N-linked (glcnac…) asparagine41, 333

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 5; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

5 pathways:

IDPathwayEvidence
R-HSA-2022870CS-GAG biosynthesiscurated
R-HSA-1793185Chondroitin sulfate/dermatan sulfate metabolism—
R-HSA-1630316Glycosaminoglycan metabolism—
R-HSA-1430728Metabolism—
R-HSA-71387Metabolism of carbohydrates and carbohydrate derivatives—

MSigDB gene sets: 213 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_BIOSYNTHETIC_PROCESS, GNF2_MCL1, WANG_LMO4_TARGETS_DN, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, BROWN_MYELOID_CELL_DEVELOPMENT_DN, NRF2_01, SENESE_HDAC1_TARGETS_UP, LIU_CMYB_TARGETS_UP, CUI_TCF21_TARGETS_2_DN, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_METABOLIC_PROCESS, MODULE_207, LIU_VMYB_TARGETS_UP

GO Biological Process (3): proteoglycan biosynthetic process (GO:0030166), chondroitin sulfate proteoglycan biosynthetic process (GO:0050650), dermatan sulfate proteoglycan biosynthetic process (GO:0050651)

GO Molecular Function (8): acetylgalactosaminyltransferase activity (GO:0008376), metal ion binding (GO:0046872), glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237), glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238), protein binding (GO:0005515), UDP-glycosyltransferase activity (GO:0008194), transferase activity (GO:0016740), hexosyltransferase activity (GO:0016758)

GO Cellular Component (4): Golgi membrane (GO:0000139), membrane (GO:0016020), Golgi cisterna membrane (GO:0032580), Golgi apparatus (GO:0005794)

Reactome top-level categories

4 top-level categories:

CategoryPathways
Chondroitin sulfate/dermatan sulfate metabolism1
Metabolism of carbohydrates and carbohydrate derivatives1
Glycosaminoglycan metabolism1
Metabolism1

GO top-level categories

21 GO namespaces:

CategoryTerms
proteoglycan biosynthetic process2
protein O-linked glycosylation via xylose2
acetylgalactosaminyltransferase activity2
glycosyltransferase activity2
proteoglycan metabolic process1
glycoprotein biosynthetic process1
chondroitin sulfate proteoglycan metabolic process1
dermatan sulfate proteoglycan metabolic process1
UDP-glycosyltransferase activity1
hexosyltransferase activity1
cation binding1
binding1
catalytic activity1
Golgi apparatus1
bounding membrane of organelle1
cellular anatomical structure1
organelle membrane1
Golgi cisterna1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 5 of 15 annotations. The rest are phylogenetic / computational / electronic (IEA).

5 experimentally-supported GO terms:

GO termNSEvidence
chondroitin sulfate proteoglycan biosynthetic processBPdirect assay
dermatan sulfate proteoglycan biosynthetic processBPdirect assay
proteoglycan biosynthetic processBPdirect assay
membraneCChigh-throughput assay
acetylgalactosaminyltransferase activityMFdirect assay

Protein interactions and networks

STRING

showing 15 of 584 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
CSGALNACT2CHST11Q9NPF2724
CSGALNACT2B3GAT3O94766717
CSGALNACT2CHST12Q9NRB3717
CSGALNACT2CHST7Q9NS84700
CSGALNACT2CHST13Q8NET6693
CSGALNACT2EXT2Q93063667
CSGALNACT2B4GALT7Q9UBV7649
CSGALNACT2CHST15Q7LFX5641
CSGALNACT2EXT1Q16394621
CSGALNACT2EXTL2Q9UBQ6611
CSGALNACT2NDST2P52849602
CSGALNACT2CHST14Q8NCH0593
CSGALNACT2EXTL3O43909589
CSGALNACT2DSEQ9UL01576
CSGALNACT2CHST3Q7LGC8567

IntAct

Human interaction partners of CSGALNACT2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

27 partners by confidence:

PartnerInteraction typeMIscoreRecords
SYNE4physical association0.6703
ARL13Bphysical association0.5603
ATP1B4physical association0.5603
BSNDphysical association0.5603
CLDN2physical association0.5603
CREB3L1physical association0.5603
CYB5R3physical association0.5603
FCGR2Aphysical association0.5603
GPR152physical association0.5603
GTT3physical association0.5603
HSD17B11physical association0.5603
MFSD14Bphysical association0.5603
MUC1physical association0.5603
RETREG3physical association0.5603
SLC35E3physical association0.5603
SSMEM1physical association0.5603
SYT1physical association0.5603
TMEM143physical association0.5603
TMEM52Bphysical association0.5603
UBE2Iphysical association0.5603
TPST1association0.5302
GOLIM4association0.5301
CREB3physical association0.3702
BCL2L13physical association0.3701
BPNT2association0.3501
CLASP2association0.3501
GOSR2association0.3501

BioGRID (181 interactions; top human partners by supporting records): SYNE4 (Two-hybrid; 5 records), CSGALNACT1 (Affinity Capture-MS; 3 records), FUT1 (Affinity Capture-MS; 3 records), GINM1 (Affinity Capture-MS; 3 records), LPAR1 (Affinity Capture-MS; 3 records), POGLUT1 (Affinity Capture-MS; 3 records), SLC30A1 (Affinity Capture-MS; 3 records), SLC30A5 (Affinity Capture-MS; 3 records), SLC35A5 (Affinity Capture-MS; 3 records), SLC8A3 (Affinity Capture-MS; 3 records), ST3GAL4 (Affinity Capture-MS; 3 records), ADPGK (Affinity Capture-MS; 2 records), B3GAT3 (Affinity Capture-MS; 2 records), CCDC8 (Affinity Capture-MS; 2 records), CHSY1 (Affinity Capture-MS; 2 records)

Disease & clinical

Genetic variants

Variant evidence for CSGALNACT2: 91 ClinVar records (0 pathogenic / likely pathogenic); 7 GWAS associations.

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance76
Likely benign4
Benign0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 28 predictions of 778):

Position(s)EffectΔscoreSites
10:43138568–43138569donor_loss1.00004
10:43167002–43167003acceptor_loss1.00004
10:43167120donor_gain1.0000
10:43175945acceptor_gain1.0000
10:43175949acceptor_gain1.0000
10:43175949–43175950acceptor_loss1.00004
10:43176033–43176034donor_loss1.00005
10:43138568donor_loss0.9900
10:43155632acceptor_gain0.9900
10:43158932–43158933donor_loss0.99006

AlphaMissense

1,344 missense substitutions predicted likely pathogenic (of 3,602 scored), across 325 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M43490.9000.995
M50190.8510.987
D45980.9970.999
H48380.9910.999
D36780.9890.998
H48680.9870.996
D36980.9820.995
D42980.9750.993
F28880.9710.997
F52180.9700.997
S39780.9670.999
F43080.9660.999
D17580.9620.995
F34380.9620.998
F39680.9610.999
D44180.9560.990
F28580.9440.988
F36480.9420.995
F25480.9410.992
F15180.9400.995

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Disease associations

OMIM: gene MIM:616616 | disease phenotypes:

GWAS associations

7 associations:

StudyTraitp-value
GCST006585_1239Blood protein levels6e-57
GCST002658_5Hirschsprung disease6e-19
GCST000334_2Hirschsprung disease4e-18
GCST012227_253Hip circumference adjusted for BMI8e-9
GCST90000654_17Central corneal thickness2e-8
GCST005531_126Multiple sclerosis3e-7
GCST009391_885Metabolite levels6e-6

EFO canonical traits (from GWAS)

3 canonical traits:

EFO IDTrait name
EFO:0010533sorbitol measurement
EFO:0008039BMI-adjusted hip circumference
EFO:0005213central corneal thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Air Pollutantsincreases expression, increases abundance, decreases expression4
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
Acetaminophenincreases expression3
bisphenol Aaffects expression, decreases expression2
Arsenicaffects cotreatment, increases abundance, increases expression2
Benzo(a)pyreneincreases expression, increases methylation2
Silicon Dioxideincreases expression2
Tretinoinincreases expression2
Cyclosporineincreases expression2
Aflatoxin B1increases expression2
Asbestos, Crocidoliteaffects expression, increases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
GSK-J4increases expression1
pyrimidin-2-one beta-ribofuranosideincreases expression1
sodium arsenateincreases abundance, increases expression1
tris(2-butoxyethyl) phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
cobaltous chlorideincreases expression1
butyraldehydeincreases expression1
pentanalincreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608increases reaction, affects binding1
abrineincreases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
bisphenol Sincreases methylation1
jinfukangaffects cotreatment, decreases expression1
(+)-JQ1 compoundincreases expression1
Leflunomideincreases expression1
Amphotericin Bincreases expression1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Hirschsprung disease

About this page

Built deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source. Provided for research and reference, not medical advice or a diagnosis. Data may be incomplete, especially for rare conditions. Consult a qualified clinician.

Generated
Atlas version
v1.12.2
BioBTree
v2.16.1

Sources 94

This page pulls from 94 datasets indexed by BioBTree:

alliance_phenotypealphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruscellphonedbchembl_activitychembl_mechanismchembl_moleculechembl_targetciviccivic_assertioncivic_evidencecivic_variantclingen_dosageclingen_gene_validityclingen_variantclinical_trialsclinvarcollectricorumctd_gene_interactiondepmapdepmap_dependencydiamond_similarityefoensemblentrezexonfantom5_genefantom5_promotergenccgenerifgnomad_constraintgnomad_rmcgogoparentgtex_egenegtopdbgwasgwas_studyhgnchpahpa_expressionhpa_pathologyhpointactinterprointogenjasparmeshmgimimmirdbmondomsigdbneighborentrezorphanetorthologorthologentrezpanelapp_geneparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_var_annotationpharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontaxonomytranscriptufeatureuniprot