PIGM

Summary

PIGM (phosphatidylinositol glycan anchor biosynthesis class M, HGNC:18858) is a protein-coding gene on chromosome 1q23.2, encoding GPI alpha-1,4-mannosyltransferase I, catalytic subunit (Q9H3S5). Catalytic subunit of the glycosylphosphatidylinositol-mannosyltransferase I complex which catalyzes the transfer of the first mannose, via an alpha-1,4 bond from a dolichol-phosphate-mannose (Dol-P-Man) to a 2-acyl-6-alpha-D-glucosaminyl-1-(1-radyl,2-acyl-sn-glycero-3-phospho)-1….

This gene encodes a transmembrane protein that is located in the endoplasmic reticulum and is involved in GPI-anchor biosynthesis. The glycosylphosphatidylinositol (GPI)-anchor is a glycolipid which contains three mannose molecules in its core backbone. The GPI-anchor is found on many blood cells and serves to anchor proteins to the cell surface. This gene encodes a mannosyltransferase, GPI-MT-I, that transfers the first mannose to GPI on the lumenal side of the endoplasmic reticulum.

Source: NCBI Gene 93183 — RefSeq curated summary.

At a glance

• Gene–disease (curated): hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency (Moderate, GenCC)
• GWAS associations: 1
• Clinical variants (ClinVar): 162 total — 1 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 14
• MANE Select transcript: NM_145167

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18858
Approved symbol	PIGM
Name	phosphatidylinositol glycan anchor biosynthesis class M
Location	1q23.2
Locus type	gene with protein product
Status	Approved
Aliases	GPI-MT-I, PIG-M
Ensembl gene	ENSG00000143315
Ensembl biotype	protein_coding
OMIM	610273
Entrez	93183

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000368090

RefSeq mRNA: 1 — MANE Select: NM_145167 NM_145167

CCDS: CCDS1192

Canonical transcript exons

ENST00000368090 — 1 exons

Exon	Start	End
ENSE00001446298	160024953	160031990

Expression profiles

Bgee: expression breadth ubiquitous, 235 present calls, max score 89.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.9497 / max 47.2300, expressed in 1696 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15458	3.9015	1536
15457	3.0150	1063
15456	0.0332	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	89.00	gold quality
subthalamic nucleus	UBERON:0001906	87.65	gold quality
inferior vagus X ganglion	UBERON:0005363	87.51	gold quality
epithelial cell of pancreas	CL:0000083	86.78	gold quality
cardia of stomach	UBERON:0001162	86.16	silver quality
cardiac muscle of right atrium	UBERON:0003379	84.41	silver quality
dorsal plus ventral thalamus	UBERON:0001897	84.37	gold quality
pancreatic ductal cell	CL:0002079	84.35	silver quality
ventral tegmental area	UBERON:0002691	84.18	gold quality
medulla oblongata	UBERON:0001896	84.17	gold quality
epithelium of mammary gland	UBERON:0003244	84.09	gold quality
mammary duct	UBERON:0001765	84.08	gold quality
sperm	CL:0000019	83.99	gold quality
pylorus	UBERON:0001166	83.85	gold quality
kidney epithelium	UBERON:0004819	83.17	silver quality
pons	UBERON:0000988	83.16	silver quality
nipple	UBERON:0002030	82.81	gold quality
superior vestibular nucleus	UBERON:0007227	82.81	gold quality
lower lobe of lung	UBERON:0008949	82.04	silver quality
substantia nigra pars reticulata	UBERON:0001966	81.89	gold quality
pigmented layer of retina	UBERON:0001782	81.69	gold quality
mucosa of sigmoid colon	UBERON:0004993	81.40	gold quality
thymus	UBERON:0002370	80.94	gold quality
renal medulla	UBERON:0000362	80.86	gold quality
urethra	UBERON:0000057	80.64	gold quality
substantia nigra pars compacta	UBERON:0001965	80.44	silver quality
secondary oocyte	CL:0000655	80.14	gold quality
superior surface of tongue	UBERON:0007371	80.07	gold quality
corpus epididymis	UBERON:0004359	80.03	gold quality
epithelium of nasopharynx	UBERON:0001951	79.99	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.47
E-GEOD-124858	no	181.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

139 targeting PIGM, 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-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4668-3P	100.00	68.74	2635
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-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-651-3P	99.94	73.48	5177

Literature-anchored findings (GeneRIF, showing 4)

• Mutation substantially reduces transcription of PIGM and blocks mannosylation of glycosylphosphatidylinositol(GPI), leading to partial but severe deficiency of GPI. (PMID:16767100)
• Studies indicate that mutations in PGM1 by exome sequencing cause hypoglycemia and liver abnormalities. (PMID:23329837)
• B cells but not red cells are glycosylphosphatidylinositol deficient in PIGM-associated inherited glycosylphosphatidylinositol deficiency, caused by a core promoter mutation that abrogates Sp1 binding. (PMID:25293775)
• Function of a membrane-embedded domain evolutionarily multiplied in the GPI lipid anchor pathway proteins PIG-B, PIG-M, PIG-U, PIG-W, PIG-V, and PIG-Z has been described. (PMID:29764287)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pigm	ENSDARG00000024277
mus_musculus	Pigm	ENSMUSG00000050229
rattus_norvegicus	Pigm	ENSRNOG00000007735
drosophila_melanogaster	PIG-M	FBGN0034649
caenorhabditis_elegans		WBGENE00007189

Protein

Protein identifiers

GPI alpha-1,4-mannosyltransferase I, catalytic subunit — Q9H3S5 (reviewed: Q9H3S5)

Alternative names: GPI mannosyltransferase I, Phosphatidylinositol-glycan biosynthesis class M protein

All UniProt accessions (1): Q9H3S5

UniProt curated annotations — full annotation on UniProt →

Function. Catalytic subunit of the glycosylphosphatidylinositol-mannosyltransferase I complex which catalyzes the transfer of the first mannose, via an alpha-1,4 bond from a dolichol-phosphate-mannose (Dol-P-Man) to a 2-acyl-6-alpha-D-glucosaminyl-1-(1-radyl,2-acyl-sn-glycero-3-phospho)-1D-myo-inositol (glucosaminyl acyl phosphatidylinositol, GlcN-(acyl)PI) intermediate to generate 2-acyl-6-(alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl)-1-(1-radyl,2-acyl-sn-glycero-3-phospho)-1D-myo-inositol (also termed H2) and participates in the sixth step of the glycosylphosphatidylinositol-anchor biosynthesis.

Subunit / interactions. Part of the glycosylphosphatidylinositol-mannosyltransferase I complex that is composed of PIGM and PIGX. Interacts with PIGM; PIGX stabilizes PIGM.

Subcellular location. Endoplasmic reticulum membrane.

Disease relevance. Glycosylphosphatidylinositol biosynthesis defect 1 (GPIBD1) [MIM:610293] An autosomal recessive disorder characterized by portal vein thrombosis and portal hypertension, absence seizures, macrocephaly, splenomegaly, cytopenias and early-onset cerebral infarctions. The disease is caused by variants affecting the gene represented in this entry.

Pathway. Glycolipid biosynthesis; glycosylphosphatidylinositol-anchor biosynthesis.

Similarity. Belongs to the PIGM family.

RefSeq proteins (1): NP_660150* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007704	PIG-M	Family

Pfam: PF05007

Catalyzed reactions (Rhea), 1 shown:

• a 2-acyl-6-alpha-D-glucosaminyl-1-(1-radyl,2-acyl-sn-glycero-3-phospho)-1D-myo-inositol + a di-trans,poly-cis-dolichyl beta-D-mannosyl phosphate = a 2-acyl-6-(alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl)-1-(1-radyl,2-acyl-sn-glycero-3-phospho)-1D-myo-inositol + a di-trans,poly-cis-dolichyl phosphate + H(+) (RHEA:60500)

UniProt features (25 total): topological domain 11, transmembrane region 10, mutagenesis site 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H3S5-F1	90.10	0.76

Functional residue map

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

Mutagenesis-validated functional residues (2):

Position	Phenotype
49	almost abolishes enzyme activity.
51	abolishes enzyme activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-162710	Synthesis of glycosylphosphatidylinositol (GPI)

MSigDB gene sets: 155 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLINOSITOL_METABOLIC_PROCESS, GOBP_GLYCOLIPID_BIOSYNTHETIC_PROCESS, REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GOBP_PROTEIN_MATURATION, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, KEGG_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI_ANCHOR_BIOSYNTHESIS, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS

GO Biological Process (1): GPI anchor biosynthetic process (GO:0006506)

GO Molecular Function (7): mannosyltransferase activity (GO:0000030), dol-P-Man:GlcN-acyl-PI alpha-1,4-mannosyltransferase activity (GO:0180041), GPI mannosyltransferase activity (GO:0004376), protein binding (GO:0005515), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757), alpha-1,4-mannosyltransferase activity (GO:0051751)

GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), glycosylphosphatidylinositol-mannosyltransferase I complex (GO:1990529), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Post-translational modification: synthesis of GPI-anchored proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mannosyltransferase activity	2
GPI anchor metabolic process	1
glycolipid biosynthetic process	1
glycerophospholipid biosynthetic process	1
GPI anchored protein biosynthesis	1
hexosyltransferase activity	1
GPI mannosyltransferase activity	1
alpha-1,4-mannosyltransferase activity	1
binding	1
catalytic activity	1
transferase activity	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
mannosyltransferase complex	1
endoplasmic reticulum protein-containing complex	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

746 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PIGM	PIGX	Q8TBF5	954
PIGM	PIGA	P37287	934
PIGM	PIGV	Q9NUD9	879
PIGM	PIGL	Q9Y2B2	875
PIGM	PIGB	Q92521	854
PIGM	PIGO	Q8TEQ8	845
PIGM	PIGG	Q5H8A4	844
PIGM	PIGW	Q7Z7B1	822
PIGM	PIGH	Q14442	811
PIGM	PIGT	Q969N2	810
PIGM	PIGK	Q92643	806
PIGM	PIGC	Q92535	795
PIGM	PGAP2	Q9UHJ9	794
PIGM	PIGZ	Q86VD9	773
PIGM	PIGQ	Q9BRB3	767

IntAct

40 interactions, top by confidence:

A	B	Type	Score
PIGM	STARD7	psi-mi:“MI:0915”(physical association)	0.590
POMK	TMEM120B	psi-mi:“MI:0914”(association)	0.530
ADGRG5	KLRG2	psi-mi:“MI:0914”(association)	0.530
CNDP1	POTEF	psi-mi:“MI:0914”(association)	0.530
HAVCR2	TCAF2	psi-mi:“MI:0914”(association)	0.530
TM2D2	TMEM97	psi-mi:“MI:0914”(association)	0.530
SEMA7A	SGPL1	psi-mi:“MI:0914”(association)	0.530
PIGM	LTB4R2	psi-mi:“MI:0915”(physical association)	0.370
PIGM	CHEK1	psi-mi:“MI:0915”(physical association)	0.370
UPK1A	TMEM223	psi-mi:“MI:0914”(association)	0.350
HTR3C	TMEM223	psi-mi:“MI:0914”(association)	0.350
CHRM4	GEMIN2	psi-mi:“MI:0914”(association)	0.350
TTYH1	TMEM223	psi-mi:“MI:0914”(association)	0.350
AVPR2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
RAMP2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CMTM5	TMEM120B	psi-mi:“MI:0914”(association)	0.350
C5AR1	TCAF2	psi-mi:“MI:0914”(association)	0.350
OPALIN	GPR89A	psi-mi:“MI:0914”(association)	0.350
SPPL2B	GPR89A	psi-mi:“MI:0914”(association)	0.350
SLC5A4	GPR89A	psi-mi:“MI:0914”(association)	0.350
ATP13A3	GPR89A	psi-mi:“MI:0914”(association)	0.350
HTR3C	GET1	psi-mi:“MI:0914”(association)	0.350
SAAL1	QSOX1	psi-mi:“MI:0914”(association)	0.350
ABCA2	ABCD4	psi-mi:“MI:0914”(association)	0.350
CHRM4	TNPO2	psi-mi:“MI:0914”(association)	0.350
DRD4	TNPO2	psi-mi:“MI:0914”(association)	0.350

BioGRID (52): PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS), STARD7 (Affinity Capture-MS), PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS), STARD7 (Affinity Capture-MS), PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS), PIGM (Affinity Capture-MS)

ESM2 similar proteins: A0A8C2M425, A1L1J9, B0BNG2, O60725, O75908, O77759, O88269, O88908, O95255, Q0P4J9, Q290J8, Q3T1L5, Q3TAE8, Q3UV71, Q499P8, Q49LS7, Q4R4E1, Q4VV71, Q5F380, Q5KR61, Q5R8F6, Q5RAH7, Q5RKL5, Q6AZ83, Q6NVG1, Q7SXZ1, Q7T310, Q7TPN3, Q7TQM4, Q86VD9, Q8AVI9, Q8BTP0, Q8C0T0, Q8C3X8, Q8CI59, Q8IUR5, Q8K2A8, Q8L638, Q8R1J1, Q8R4P9

Diamond homologs: P47088, Q2TXB8, Q4I073, Q4R4E1, Q4WAH2, Q500W7, Q54IA4, Q5AMR5, Q5B7W0, Q5EA10, Q5F380, Q5RAH7, Q66IJ4, Q6BHI9, Q6CRE7, Q6FXQ5, Q75C82, Q7S4Z3, Q7T310, Q8C2R7, Q9BPQ5, Q9EQY6, Q9H3S5, Q9P6R5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	1
Uncertain significance	133
Likely benign	12
Benign	9

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
3362856	NM_145167.3(PIGM):c.401del (p.Asn134fs)	Pathogenic
520658	NM_145167.3(PIGM):c.2T>C (p.Met1Thr)	Likely pathogenic

SpliceAI

249 predictions. Top by Δscore:

Variant	Effect	Δscore
1:160031455:T:A	donor_gain	1.0000
1:160031437:G:C	donor_gain	0.9200
1:160031098:ACAAG:A	donor_gain	0.9100
1:160031099:CAAGC:C	donor_gain	0.9100
1:160027998:GAGCT:G	acceptor_gain	0.8500
1:160027999:AGCTA:A	acceptor_gain	0.8500
1:160031075:AG:A	donor_gain	0.8300
1:160031965:T:TA	donor_gain	0.8300
1:160028000:GCT:G	acceptor_gain	0.8200
1:160031792:TCTA:T	donor_gain	0.7800
1:160031000:T:C	donor_gain	0.7700
1:160031630:ACGCC:A	acceptor_gain	0.7700
1:160031961:G:A	donor_gain	0.7700
1:160027997:TGAGC:T	acceptor_gain	0.7400
1:160031044:TGC:T	donor_gain	0.7300
1:160031907:TGC:T	donor_gain	0.7200
1:160031632:GCCAT:G	acceptor_gain	0.7100
1:160030829:G:C	donor_gain	0.7000
1:160030888:G:A	donor_gain	0.7000
1:160028001:C:A	acceptor_gain	0.6800
1:160030881:TC:T	donor_gain	0.6800
1:160030882:CC:C	donor_gain	0.6800
1:160031102:G:A	donor_gain	0.6600
1:160031631:CGCC:C	acceptor_gain	0.6500
1:160031906:CTG:C	donor_gain	0.6500
1:160031909:C:CT	donor_gain	0.6500
1:160031910:T:TT	donor_gain	0.6500
1:160028000:G:C	acceptor_gain	0.6200
1:160030999:A:AC	donor_gain	0.6200
1:160031068:A:AC	donor_gain	0.6200

AlphaMissense

2742 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:160030930:G:C	N270K	0.998
1:160030930:G:T	N270K	0.998
1:160030728:A:G	W338R	0.996
1:160030728:A:T	W338R	0.996
1:160031314:G:C	S142R	0.996
1:160031314:G:T	S142R	0.996
1:160031316:T:G	S142R	0.996
1:160030629:A:G	W371R	0.995
1:160030629:A:T	W371R	0.995
1:160030949:C:A	R264M	0.995
1:160030650:A:G	W364R	0.994
1:160030650:A:T	W364R	0.994
1:160030915:G:C	F275L	0.994
1:160030915:G:T	F275L	0.994
1:160030917:A:G	F275L	0.994
1:160030738:C:A	Q334H	0.993
1:160030738:C:G	Q334H	0.993
1:160030756:G:C	N328K	0.993
1:160030756:G:T	N328K	0.993
1:160030943:T:G	D266A	0.992
1:160030944:C:G	D266H	0.992
1:160030949:C:G	R264T	0.992
1:160030616:G:T	A375D	0.991
1:160030935:G:C	H269D	0.991
1:160030927:A:C	F271L	0.990
1:160030927:A:T	F271L	0.990
1:160030929:A:G	F271L	0.990
1:160030732:A:C	F336L	0.989
1:160030732:A:T	F336L	0.989
1:160030734:A:G	F336L	0.989

dbSNP variants (sampled 300 via entrez): RS1000008313 (1:160032200 C>G), RS1000446356 (1:160032649 C>CTCACT), RS1000620831 (1:160025838 T>G), RS1001227283 (1:160032157 C>T), RS1002760436 (1:160033787 C>T), RS1003164015 (1:160029038 C>T), RS1003505334 (1:160027614 T>C), RS1003735029 (1:160028347 G>T), RS1004192861 (1:160027957 A>G), RS1004464694 (1:160024750 G>A,T), RS1004619252 (1:160032927 G>A,C), RS1004691344 (1:160031638 G>A,C), RS1005130020 (1:160025328 G>A), RS1005291576 (1:160030068 T>C), RS1005805649 (1:160028068 A>T)

Disease associations

OMIM: gene MIM:610273 | disease phenotypes: MIM:610293

GenCC curated gene-disease

Disease	Classification	Inheritance
hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency	Moderate	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency	Limited	AR

Mondo (1): hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency (MONDO:0012465)

Orphanet (1): Hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency (Orphanet:83639)

HPO phenotypes

14 total (14 of 14 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000750	Delayed speech and language development
HP:0001409	Portal hypertension
HP:0001744	Splenomegaly
HP:0002121	Generalized non-motor (absence) seizure
HP:0002240	Hepatomegaly
HP:0003593	Infantile onset
HP:0004936	Venous thrombosis
HP:0005561	Abnormal bone marrow cell morphology
HP:0010819	Atonic seizure
HP:0011463	Childhood onset
HP:0030242	Portal vein thrombosis
HP:0030243	Hepatic vein thrombosis
HP:0031555	Reduced granulocyte CD59 level

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008103_100	Bipolar disorder	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs12409352	Efficacy	3	methylphenidate	Attention Deficit Disorder with Hyperactivity

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs12409352	PIGM	3	0.00	1	methylphenidate

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
Benzo(a)pyrene	decreases expression, decreases methylation	3
Nickel	decreases expression, increases expression	3
Acetaminophen	increases expression, decreases expression	2
Tretinoin	decreases expression, increases expression	2
Cyclosporine	increases expression, decreases expression	2
Cadmium Chloride	decreases expression, increases expression	2
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
perfluorooctanoic acid	decreases expression	1
ferrous chloride	decreases expression	1
nickel sulfate	decreases expression	1
avobenzone	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Air Pollutants, Occupational	decreases expression	1
Atrazine	decreases expression	1
Doxorubicin	decreases expression	1
Endosulfan	decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Hydrogen Peroxide	increases expression	1
Methyl Methanesulfonate	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Thiram	decreases expression	1
Urethane	decreases expression	1
Copper Sulfate	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TD50	HAP1 PIGM (-) 1	Cancer cell line	Male
CVCL_TD51	HAP1 PIGM (-) 2	Cancer cell line	Male
CVCL_TD52	HAP1 PIGM (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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