ST6GALNAC6

Summary

ST6GALNAC6 (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6, HGNC:23364) is a protein-coding gene on chromosome 9q34.11, encoding Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6 (Q969X2). Transfers the sialyl group (N-acetyl-alpha-neuraminyl or NeuAc) from CMP-NeuAc onto glycoproteins and glycolipids, forming an alpha-2,6-linkage.

ST6GALNAC6 belongs to a family of sialyltransferases that modify proteins and ceramides on the cell surface to alter cell-cell or cell-extracellular matrix interactions (Tsuchida et al., 2003 [PubMed 12668675]).

Source: NCBI Gene 30815 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_013443

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23364
Approved symbol	ST6GALNAC6
Name	ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6
Location	9q34.11
Locus type	gene with protein product
Status	Approved
Aliases	ST6GALNACVI
Ensembl gene	ENSG00000160408
Ensembl biotype	protein_coding
OMIM	610135
Entrez	30815

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 19 protein_coding, 6 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000291839, ENST00000373141, ENST00000373142, ENST00000373144, ENST00000373146, ENST00000463086, ENST00000478319, ENST00000480417, ENST00000481355, ENST00000483353, ENST00000494541, ENST00000494611, ENST00000542456, ENST00000622357, ENST00000852793, ENST00000852794, ENST00000852795, ENST00000852796, ENST00000852797, ENST00000916402, ENST00000916403, ENST00000916404, ENST00000916405, ENST00000967698, ENST00000967699, ENST00000967700

RefSeq mRNA: 13 — MANE Select: NM_013443 NM_001286999, NM_001287000, NM_001287001, NM_001287002, NM_001287003, NM_001388489, NM_001400830, NM_001400831, NM_001400832, NM_001400833, NM_001400834, NM_001400835, NM_013443

CCDS: CCDS6882, CCDS69668, CCDS69669, CCDS75908

Canonical transcript exons

ENST00000373146 — 7 exons

Exon	Start	End
ENSE00001146860	127885321	127886788
ENSE00001459657	127899503	127899603
ENSE00003566138	127896242	127896332
ENSE00003630060	127897956	127898010
ENSE00003715084	127887484	127887591
ENSE00003722915	127894512	127894691
ENSE00003788754	127890637	127891043

Expression profiles

Bgee: expression breadth ubiquitous, 144 present calls, max score 98.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.5116 / max 339.4932, expressed in 1807 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
102611	22.5235	1794
102612	3.5071	1456
102613	2.1220	293
102610	0.2286	117
102609	0.1304	54

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
amygdala	UBERON:0001876	98.50	gold quality
temporal lobe	UBERON:0001871	98.48	gold quality
nucleus accumbens	UBERON:0001882	98.32	gold quality
putamen	UBERON:0001874	98.29	gold quality
caudate nucleus	UBERON:0001873	98.23	gold quality
anterior cingulate cortex	UBERON:0009835	98.23	gold quality
right frontal lobe	UBERON:0002810	98.21	gold quality
Ammon’s horn	UBERON:0001954	98.12	gold quality
rectum	UBERON:0001052	97.79	gold quality
right coronary artery	UBERON:0001625	97.74	gold quality
frontal cortex	UBERON:0001870	97.63	gold quality
frontal lobe	UBERON:0016525	97.63	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.62	gold quality
cerebral cortex	UBERON:0000956	97.55	gold quality
popliteal artery	UBERON:0002250	97.50	gold quality
tibial artery	UBERON:0007610	97.50	gold quality
artery	UBERON:0001637	97.48	gold quality
prefrontal cortex	UBERON:0000451	97.39	gold quality
mucosa of stomach	UBERON:0001199	97.30	gold quality
left coronary artery	UBERON:0001626	97.28	gold quality
subcutaneous adipose tissue	UBERON:0002190	97.18	gold quality
descending thoracic aorta	UBERON:0002345	97.05	gold quality
superior frontal gyrus	UBERON:0002661	97.05	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.01	gold quality
adipose tissue	UBERON:0001013	96.91	gold quality
thoracic aorta	UBERON:0001515	96.88	gold quality
ascending aorta	UBERON:0001496	96.84	gold quality
left ovary	UBERON:0002119	96.78	gold quality
peripheral nervous system	UBERON:0000010	96.75	gold quality
nerve	UBERON:0001021	96.75	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	15.22
E-ANND-3	yes	4.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

52 targeting ST6GALNAC6, 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-5193	100.00	67.26	1744
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-486-5P	99.51	70.39	707
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-4489	99.50	65.56	785
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-3922-5P	98.77	66.53	1059
HSA-MIR-423-5P	98.69	67.48	1522
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-504-5P	98.67	65.40	631
HSA-MIR-4725-5P	98.67	65.42	628
HSA-MIR-3184-5P	98.56	67.13	1491

Literature-anchored findings (GeneRIF, showing 2)

• novel substrate specificity of ST6GalNAc VI, which is responsible for the synthesis of disialyl Lea but not for alpha-series gangliosides in human colon tissues (PMID:12668675)
• ST6GalNAc-VI and disialylgalactosylgloboside were found in proximal tubule epithelial cells in normal kidney tissues (PMID:17123352)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	st6galnac6	ENSDARG00000036913
mus_musculus	St6galnac6	ENSMUSG00000026811
rattus_norvegicus	St6galnac6	ENSRNOG00000046984

Paralogs (14): ST3GAL1 (ENSG00000008513), ST3GAL6 (ENSG00000064225), ST6GALNAC1 (ENSG00000070526), ST6GALNAC2 (ENSG00000070731), ST6GAL1 (ENSG00000073849), ST3GAL4 (ENSG00000110080), ST3GAL5 (ENSG00000115525), ST6GALNAC5 (ENSG00000117069), C20orf173 (ENSG00000125975), ST3GAL3 (ENSG00000126091), ST6GALNAC4 (ENSG00000136840), ST6GAL2 (ENSG00000144057), ST3GAL2 (ENSG00000157350), ST6GALNAC3 (ENSG00000184005)

Protein

Protein identifiers

Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6 — Q969X2 (reviewed: Q969X2)

Alternative names: GalNAc alpha-2,6-sialyltransferase VI, ST6GalNAc VI, Sialyltransferase 7F

All UniProt accessions (4): Q969X2, A0A0S2Z5G9, A0A0S2Z653, F6SGE3

UniProt curated annotations — full annotation on UniProt →

Function. Transfers the sialyl group (N-acetyl-alpha-neuraminyl or NeuAc) from CMP-NeuAc onto glycoproteins and glycolipids, forming an alpha-2,6-linkage. Produces branched type disialyl structures by transfer of a sialyl group onto the GalNAc or GlcNAc residue inside backbone core chains having a terminal sialic acid with an alpha-2,3-linkage on Gal. ST6GalNAcVI prefers glycolipids to glycoproteins, predominantly catalyzing the biosynthesis of ganglioside GD1alpha from GM1b. Besides GMb1, MSGG and other glycolipids, it shows activity towards sialyl Lc4Cer generating disialyl Lc4Cer, which can lead to the synthesis of disialyl Lewis a (Le(a)), suggested to be a cancer-associated antigen. Also has activity toward GD1a and GT1b, and can generate DSGG (disialylgalactosylgloboside) from MSGG (monosialylgalactosylgloboside).

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Expressed in kidney, in proximal tubule epithelial cells. Expressed in colon cell lines.

Induction. Down-regulated in renal cancers.

Miscellaneous. The carbohydrate antigen disialyl Lewis a, which is at least partly synthesized by ST6GALNAC6, is a normal counterpart of sialyl Lewis a, better known as CA19-9, an antigen widely used as a serum marker for diagnosis of cancers in the digestive track. Disialyl Lewis a is predominantly expressed in non-malignant epithelial cells of the digestive organs, while sialyl Lewis a is preferentially expressed in cancers. Disialyl Lewis a in normal epithelial cells serves as a ligand for immunosuppressive receptors, such as SIGLEC7 and SIGLEC9, expressed on resident monocytes/macrophages and maintains immunological homeostasis of mucosal membranes in digestive organs. Sialyl Lewis a, as well as its positional isomer sialyl Lewis x, serves as a ligand for vascular cell adhesion molecule E-selectin and facilitates hematogenous metastasis through mediating adhesion of circulating cancer cells to vascular endothelium.

Similarity. Belongs to the glycosyltransferase 29 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q969X2-1	1	yes
Q969X2-2	2
Q969X2-3	3

RefSeq proteins (13): NP_001273928, NP_001273929, NP_001273930, NP_001273931, NP_001273932, NP_001375418, NP_001387759, NP_001387760, NP_001387761, NP_001387762, NP_001387763, NP_001387764, NP_038471* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001675	Glyco_trans_29	Family
IPR038578	GT29-like_sf	Homologous_superfamily

Pfam: PF00777

Enzyme classification (BRENDA):

• EC 2.4.99.7 — alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3-N-acetylgalactosaminide 6-alpha-sialyltransferase (BRENDA: 0 organisms, 0 substrates, 0 inhibitors, 0 Km, 0 kcat entries)

Catalyzed reactions (Rhea), 7 shown:

• a ganglioside GM1b (d18:1(4E)) + CMP-N-acetyl-beta-neuraminate = a ganglioside GD1alpha (d18:1(4E)) + CMP + H(+) (RHEA:41968)
• a ganglioside GD1a (d18:1(4E)) + CMP-N-acetyl-beta-neuraminate = a ganglioside GT1aalpha (d18:1(4E)) + CMP + H(+) (RHEA:41972)
• a ganglioside GT1b (d18:1(4E)) + CMP-N-acetyl-beta-neuraminate = a ganglioside GQ1balpha (d18:1(4E)) + CMP + H(+) (RHEA:41976)
• N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->3)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1’)-N-acyl-sphing-4-enine + CMP-N-acetyl-beta-neuraminate = N-acetyl-alpha-neuraminosyl-(2->3)-beta-D-galactosyl-(1->3)-[N-acetyl-alpha-neuraminosyl-(2->6)]-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1’)-N-acyl-sphing-4-enine + CMP + H(+) (RHEA:47884)
• a globoside MSGG + CMP-N-acetyl-beta-neuraminate = a globoside DSGG + CMP + H(+) (RHEA:56088)
• 3-O-[alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-alpha-D-GalNAc]-L-Ser-[protein] + CMP-N-acetyl-beta-neuraminate = a 3-O-{alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-[alpha-Neu5Ac-(2->6)]-alpha-D-GalNAc}-L-seryl-[protein] + CMP + H(+) (RHEA:65280)
• 3-O-[alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-alpha-D-GalNAc]-L-Thr-[protein] + CMP-N-acetyl-beta-neuraminate = a 3-O-{alpha-Neu5Ac-(2->3)-beta-D-Gal-(1->3)-[alpha-Neu5Ac-(2->6)]-alpha-D-GalNAc}-L-threonyl-[protein] + CMP + H(+) (RHEA:65284)

UniProt features (14 total): sequence conflict 4, topological domain 2, splice variant 2, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1, glycosylation site 1, disulfide bond 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q969X2-F1	85.61	0.64

Functional residue map

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

Disulfide bonds (1): 108–256

Glycosylation sites (1): 98

Function

Pathways and Gene Ontology

Reactome pathways

14 pathways

ID	Pathway
R-HSA-4085001	Sialic acid metabolism
R-HSA-9037629	Lewis blood group biosynthesis
R-HSA-9840309	Glycosphingolipid biosynthesis
R-HSA-1430728	Metabolism
R-HSA-1660662	Glycosphingolipid metabolism
R-HSA-392499	Metabolism of proteins
R-HSA-428157	Sphingolipid metabolism
R-HSA-446193	Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
R-HSA-446203	Asparagine N-linked glycosylation
R-HSA-446219	Synthesis of substrates in N-glycan biosythesis
R-HSA-556833	Metabolism of lipids
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: 154 (showing top): GOBP_OLIGOSACCHARIDE_METABOLIC_PROCESS, GOBP_GLYCOLIPID_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CERAMIDE_BIOSYNTHETIC_PROCESS, GOBP_SPHINGOLIPID_METABOLIC_PROCESS, GOBP_AMIDE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_AMIDE_BIOSYNTHETIC_PROCESS, GOBP_GLYCOSPHINGOLIPID_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, GOBP_GANGLIOSIDE_BIOSYNTHETIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_OLIGOSACCHARIDE_BIOSYNTHETIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, GOBP_CERAMIDE_METABOLIC_PROCESS

GO Biological Process (11): ganglioside biosynthetic process (GO:0001574), glycosylceramide metabolic process (GO:0006677), glycosphingolipid metabolic process (GO:0006687), glycosphingolipid biosynthetic process (GO:0006688), glycoprotein metabolic process (GO:0009100), oligosaccharide metabolic process (GO:0009311), oligosaccharide biosynthetic process (GO:0009312), cell-cell recognition (GO:0009988), obsolete protein glycosylation (GO:0006486), lipid metabolic process (GO:0006629), ceramide metabolic process (GO:0006672)

GO Molecular Function (5): alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665), sialyltransferase activity (GO:0008373), protein binding (GO:0005515), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (5): Golgi membrane (GO:0000139), cytoplasm (GO:0005737), plasma membrane (GO:0005886), membrane (GO:0016020), Golgi apparatus (GO:0005794)

Reactome top-level categories

Rollup of top-11 pathways:

Category	Pathways
Metabolism	2
Synthesis of substrates in N-glycan biosythesis	1
Blood group systems biosynthesis	1
Glycosphingolipid metabolism	1
Sphingolipid metabolism	1
Metabolism of lipids	1
Asparagine N-linked glycosylation	1
Post-translational protein modification	1
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein	1
Metabolism of proteins	1
Metabolism of carbohydrates and carbohydrate derivatives	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
glycosphingolipid metabolic process	2
sphingolipid metabolic process	2
cellular anatomical structure	2
ganglioside metabolic process	1
glycosphingolipid biosynthetic process	1
ceramide biosynthetic process	1
ceramide metabolic process	1
glycolipid metabolic process	1
glycolipid biosynthetic process	1
sphingolipid biosynthetic process	1
protein metabolic process	1
carbohydrate derivative metabolic process	1
carbohydrate metabolic process	1
oligosaccharide metabolic process	1
carbohydrate biosynthetic process	1
cell recognition	1
primary metabolic process	1
sialyltransferase activity	1
glycosyltransferase activity	1
binding	1
catalytic activity	1
transferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

704 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ST6GALNAC6	ST8SIA6	P61647	634
ST6GALNAC6	ST8SIA5	O15466	618
ST6GALNAC6	ST6GALNAC1	Q9NSC7	611
ST6GALNAC6	ST8SIA1	Q92185	564
ST6GALNAC6	ST6GALNAC2	Q9UJ37	558
ST6GALNAC6	B3GALT5	Q9Y2C3	551
ST6GALNAC6	C1GALT1	Q9NS00	519
ST6GALNAC6	B3GNT5	Q9BYG0	518
ST6GALNAC6	B3GALT1	Q9Y5Z6	492
ST6GALNAC6	ST3GAL3	Q11203	483
ST6GALNAC6	B3GALT2	O43825	481
ST6GALNAC6	SELE	P16111	469
ST6GALNAC6	SIGLEC7	Q9Y286	445
ST6GALNAC6	SLC26A2	P50443	436
ST6GALNAC6	B3GNT3	Q9Y2A9	434

IntAct

18 interactions, top by confidence:

A	B	Type	Score
ATXN1	ST6GALNAC6	psi-mi:“MI:0915”(physical association)	0.670
LRP10	ST6GALNAC6	psi-mi:“MI:0915”(physical association)	0.560
ANKRD46	ST6GALNAC6	psi-mi:“MI:0915”(physical association)	0.560
ST6GALNAC6	SERBP1	psi-mi:“MI:0915”(physical association)	0.400
MYC		psi-mi:“MI:0914”(association)	0.350
ST6GALNAC6	A2ML1	psi-mi:“MI:0914”(association)	0.350
ST6GALNAC6	HSPA5	psi-mi:“MI:0914”(association)	0.350
ANKRD46	ST6GALNAC6	psi-mi:“MI:0915”(physical association)	0.000
LRP10	ST6GALNAC6	psi-mi:“MI:0915”(physical association)	0.000
ATXN1	ST6GALNAC6	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (106): ST6GALNAC6 (Reconstituted Complex), ANKRD46 (Two-hybrid), LRP10 (Two-hybrid), ST6GALNAC6 (Proximity Label-MS), PKP1 (Affinity Capture-MS), ANXA1 (Affinity Capture-MS), ANXA3 (Affinity Capture-MS), ALDH1A3 (Affinity Capture-MS), CDH1 (Affinity Capture-MS), NDRG1 (Affinity Capture-MS), CRYAB (Affinity Capture-MS), HPX (Affinity Capture-MS), IGLC6 (Affinity Capture-MS), FGB (Affinity Capture-MS), ME1 (Affinity Capture-MS)

ESM2 similar proteins: A7RX69, O15466, O35696, O43173, P38566, P48794, P54751, P61130, P61131, P61643, P61644, P61645, P61646, P61647, P61648, P70126, P70277, Q02745, Q07977, Q08E15, Q11200, Q11201, Q11204, Q11205, Q11206, Q16842, Q4V8F8, Q64686, Q64689, Q64690, Q64692, Q68G12, Q6KB55, Q6KB58, Q6KB59, Q6ZXC8, Q6ZXC9, Q70D51, Q812F3, Q8K4T1

Diamond homologs: A2WX64, A2XVC2, A2ZI41, A5D7T4, O35696, O43173, P13721, P15907, P61130, P61131, P61643, P61644, P61645, P61943, P70277, Q02745, Q07977, Q08E15, Q11200, Q11201, Q11204, Q11205, Q11206, Q16842, Q2QXM3, Q2R2B1, Q5K027, Q5QQ37, Q5RE85, Q64685, Q64689, Q64690, Q6H8M7, Q6KB54, Q6KB58, Q6KB59, Q6ZH45, Q6ZXC9, Q701R0, Q701R1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

985 predictions. Top by Δscore:

Variant	Effect	Δscore
9:127886789:C:CC	acceptor_gain	1.0000
9:127887478:GCTCA:G	donor_loss	1.0000
9:127887479:CTCA:C	donor_loss	1.0000
9:127887480:TCAC:T	donor_loss	1.0000
9:127887481:CA:C	donor_loss	1.0000
9:127887482:A:T	donor_loss	1.0000
9:127887483:C:T	donor_loss	1.0000
9:127887590:CCCT:C	acceptor_loss	1.0000
9:127887591:CCTG:C	acceptor_loss	1.0000
9:127890709:T:TA	donor_gain	1.0000
9:127894506:CGCTA:C	donor_loss	1.0000
9:127894507:GCTAC:G	donor_loss	1.0000
9:127894508:CTA:C	donor_loss	1.0000
9:127894509:TA:T	donor_loss	1.0000
9:127894510:A:AT	donor_loss	1.0000
9:127894556:T:TA	donor_gain	1.0000
9:127896238:TTACT:T	donor_loss	1.0000
9:127896239:TACT:T	donor_loss	1.0000
9:127896240:A:AC	donor_gain	1.0000
9:127896241:C:CT	donor_gain	1.0000
9:127896241:CT:C	donor_gain	1.0000
9:127896241:CTT:C	donor_gain	1.0000
9:127896241:CTTT:C	donor_gain	1.0000
9:127896241:CTTTG:C	donor_gain	1.0000
9:127886785:CTGG:C	acceptor_gain	0.9900
9:127886786:TGG:T	acceptor_gain	0.9900
9:127887588:CTCC:C	acceptor_gain	0.9900
9:127887590:CC:C	acceptor_gain	0.9900
9:127887591:CC:C	acceptor_gain	0.9900
9:127887592:C:CC	acceptor_gain	0.9900

AlphaMissense

2185 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:127886644:C:A	W319C	1.000
9:127886644:C:G	W319C	1.000
9:127886663:T:A	K313I	1.000
9:127886665:C:A	E312D	1.000
9:127886665:C:G	E312D	1.000
9:127886666:T:A	E312V	1.000
9:127886674:G:C	F309L	1.000
9:127886674:G:T	F309L	1.000
9:127886675:A:C	F309C	1.000
9:127886675:A:G	F309S	1.000
9:127886676:A:G	F309L	1.000
9:127886678:C:G	R308P	1.000
9:127886679:G:T	R308S	1.000
9:127886682:G:C	H307D	1.000
9:127886757:G:C	H282D	1.000
9:127887529:C:T	C256Y	1.000
9:127887560:A:G	W246R	1.000
9:127887560:A:T	W246R	1.000
9:127887567:G:C	S243R	1.000
9:127887567:G:T	S243R	1.000
9:127887568:C:A	S243I	1.000
9:127887569:T:G	S243R	1.000
9:127887571:A:G	L242S	1.000
9:127890794:A:G	W183R	1.000
9:127890794:A:T	W183R	1.000
9:127890880:C:G	R154P	1.000
9:127890933:A:C	N136K	1.000
9:127890933:A:T	N136K	1.000
9:127886607:A:G	W332R	0.999
9:127886607:A:T	W332R	0.999

dbSNP variants (sampled 300 via entrez): RS1000209056 (9:127897743 C>T), RS1000224713 (9:127900931 C>A,T), RS1000452293 (9:127895293 C>T), RS1000456356 (9:127902319 C>A,T), RS1000560336 (9:127902139 T>A,C), RS1000795432 (9:127900752 G>A), RS1000812869 (9:127896716 C>T), RS1000830230 (9:127889060 T>A,C), RS1000885183 (9:127895478 C>A), RS1000945446 (9:127895274 G>A), RS1000986608 (9:127891030 C>A,T), RS1001182789 (9:127896430 C>T), RS1001453106 (9:127906037 C>T), RS1001559125 (9:127905898 C>G,T), RS1001630640 (9:127904788 G>A)

Disease associations

OMIM: gene MIM:610135 | disease phenotypes: MIM:615042

GenCC curated gene-disease

Mondo (1): congenital muscular dystrophy with intellectual disability and severe epilepsy (MONDO:0014023)

Orphanet (1): Congenital muscular dystrophy with intellectual disability and severe epilepsy (Orphanet:329178)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005951_65	Body mass index	5.000000e-09
GCST006585_1508	Blood protein levels	3.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression, affects cotreatment	2
bisphenol F	affects cotreatment, increases expression	1
potassium perchlorate	decreases expression	1
M-VAC protocol	decreases response to substance	1
perfluoro-n-nonanoic acid	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
Sunitinib	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	decreases expression	1
Cytarabine	decreases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Dexamethasone	increases expression, affects cotreatment	1
Doxorubicin	decreases expression	1
Gallic Acid	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	increases expression, affects cotreatment	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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