VMA12

Summary

VMA12 (vacuolar ATPase assembly factor VMA12, HGNC:18085) is a protein-coding gene on chromosome 17q11.2, encoding Vacuolar ATPase assembly protein VMA12 (Q8N511). Accessory component of the proton-transporting vacuolar (V)-ATPase protein pump involved in intracellular iron homeostasis. It is a selective cancer dependency (DepMap: 77.0% of cell lines).

The protein encoded by this gene has been observed to localize to the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC) and coat protein complex I (COPI) in some human cells. The encoded protein shares some homology with the yeast protein Vma12. Defects in this gene are a cause of congenital disorder of glycosylation, type IIp.

Source: NCBI Gene 147007 — RefSeq curated summary.

At a glance

• Gene–disease (curated): TMEM199-CDG (Strong, GenCC)
• GWAS associations: 7
• Clinical variants (ClinVar): 79 total — 3 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 23
• Cancer dependency (DepMap): dependent in 77.0% of screened cell lines
• MANE Select transcript: NM_152464

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18085
Approved symbol	VMA12
Name	vacuolar ATPase assembly factor VMA12
Location	17q11.2
Locus type	gene with protein product
Status	Approved
Aliases	VPH2, MGC45714
Ensembl gene	ENSG00000244045
Ensembl biotype	protein_coding
OMIM	616815
Entrez	147007

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 3 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000292114, ENST00000395404, ENST00000483505, ENST00000509083, ENST00000555264, ENST00000579762, ENST00000580868, ENST00000581386, ENST00000585027, ENST00000971958

RefSeq mRNA: 1 — MANE Select: NM_152464 NM_152464

CCDS: CCDS11228

Canonical transcript exons

ENST00000292114 — 6 exons

Exon	Start	End
ENSE00001234014	28361157	28363683
ENSE00002687446	28357647	28357881
ENSE00003458426	28359315	28359404
ENSE00003514308	28360529	28360571
ENSE00003573203	28358916	28358989
ENSE00003580565	28360735	28360847

Expression profiles

Bgee: expression breadth ubiquitous, 197 present calls, max score 89.63.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.3472 / max 141.7951, expressed in 1826 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
160009	32.3472	1826

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	89.63	gold quality
leukocyte	CL:0000738	89.53	gold quality
granulocyte	CL:0000094	89.22	gold quality
mucosa of transverse colon	UBERON:0004991	87.51	gold quality
right adrenal gland	UBERON:0001233	87.19	gold quality
metanephros cortex	UBERON:0010533	87.00	gold quality
left adrenal gland	UBERON:0001234	86.97	gold quality
right adrenal gland cortex	UBERON:0035827	86.81	gold quality
left adrenal gland cortex	UBERON:0035825	86.74	gold quality
cortical plate	UBERON:0005343	86.65	gold quality
islet of Langerhans	UBERON:0000006	86.41	gold quality
vermiform appendix	UBERON:0001154	86.36	gold quality
prefrontal cortex	UBERON:0000451	86.25	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.04	gold quality
right lobe of thyroid gland	UBERON:0001119	86.01	gold quality
ganglionic eminence	UBERON:0004023	85.97	gold quality
embryo	UBERON:0000922	85.96	gold quality
right lobe of liver	UBERON:0001114	85.95	gold quality
adenohypophysis	UBERON:0002196	85.61	gold quality
left lobe of thyroid gland	UBERON:0001120	85.26	gold quality
spleen	UBERON:0002106	85.24	gold quality
adrenal gland	UBERON:0002369	85.06	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.04	gold quality
adrenal cortex	UBERON:0001235	84.88	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.78	gold quality
body of uterus	UBERON:0009853	84.71	gold quality
bone marrow cell	CL:0002092	84.68	gold quality
cerebellar hemisphere	UBERON:0002245	84.63	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.59	gold quality
cerebellar cortex	UBERON:0002129	84.57	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

123 targeting VMA12, 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-513A-5P	100.00	69.77	2465
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 77.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

• We have identified TMEM199 as a protein involved in Golgi homeostasis and show that TMEM199 deficiency results in a hepatic phenotype with abnormal glycosylation. (PMID:26833330)
• Vacuolar H+ ATPase (V-ATPase), the key proton pump for endo-lysosomal acidification, and two previously uncharacterised V-ATPase assembly factors, TMEM199 and CCDC115, stabilise HIF1alpha in aerobic conditions. (PMID:28296633)
• Defective Lipid Droplet-Lysosome Interaction Causes Fatty Liver Disease as Evidenced by Human Mutations in TMEM199 and CCDC115. (PMID:34626841)
• Higher frequency of TMEM199-CDG in the southern mediterranean area is associated with c.92G>C (p.Arg31Pro) mutation. (PMID:36706865)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	tmem199	ENSDARG00000069314
mus_musculus	Tmem199	ENSMUSG00000051232
rattus_norvegicus	Tmem199	ENSRNOG00000009896
drosophila_melanogaster	CG7071	FBGN0260467
caenorhabditis_elegans		WBGENE00017289

Protein

Protein identifiers

Vacuolar ATPase assembly protein VMA12 — Q8N511 (reviewed: Q8N511)

Alternative names: Transmembrane protein 199

All UniProt accessions (4): J3KRW7, J3KS81, K7EJL8, Q8N511

UniProt curated annotations — full annotation on UniProt →

Function. Accessory component of the proton-transporting vacuolar (V)-ATPase protein pump involved in intracellular iron homeostasis. In aerobic conditions, required for intracellular iron homeostasis, thus triggering the activity of Fe(2+) prolyl hydroxylase (PHD) enzymes, and leading to HIF1A hydroxylation and subsequent proteasomal degradation. Necessary for endolysosomal acidification and lysosomal degradation. May be involved in Golgi homeostasis. Binds 20(S)-hydroxycholesterol (20(S)-OHC).

Subunit / interactions. Accessory component of the multisubunit proton-transporting vacuolar (V)-ATPase protein pump.

Subcellular location. Cytoplasmic vesicle. COPI-coated vesicle membrane. Endoplasmic reticulum-Golgi intermediate compartment membrane. Endoplasmic reticulum membrane.

Disease relevance. Congenital disorder of glycosylation 2P (CDG2P) [MIM:616829] A form of congenital disorder of glycosylation, a genetically heterogeneous group of autosomal recessive, multisystem disorders caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. CDG2P is characterized by mild metabolic dysfunction, primarily affecting the liver. Psychomotor development is normal. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (1): NP_689677* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021013	ATPase_Vma12	Family

Pfam: PF11712

UniProt features (10 total): sequence variant 5, transmembrane region 2, initiator methionine 1, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N511-F1	80.82	0.24

Functional residue map

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

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 202 (showing top): GOBP_VACUOLE_ORGANIZATION, GOCC_VACUOLAR_MEMBRANE, GOBP_INTRACELLULAR_IRON_ION_HOMEOSTASIS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, CHANDRAN_METASTASIS_DN, chr17q11, GOBP_RESPONSE_TO_INCREASED_OXYGEN_LEVELS, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_LEVELS, WANG_LMO4_TARGETS_DN, GOBP_RESPONSE_TO_OXYGEN_LEVELS, GOCC_COATED_VESICLE, GOBP_VACUOLAR_ACIDIFICATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, GOCC_GOLGI_ASSOCIATED_VESICLE, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS

GO Biological Process (5): intracellular iron ion homeostasis (GO:0006879), lysosomal lumen acidification (GO:0007042), cellular response to increased oxygen levels (GO:0036295), vacuolar proton-transporting V-type ATPase complex assembly (GO:0070072), lysosomal protein catabolic process (GO:1905146)

GO Molecular Function (2): oxysterol binding (GO:0008142), protein binding (GO:0005515)

GO Cellular Component (9): lysosome (GO:0005764), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), endomembrane system (GO:0012505), vacuolar proton-transporting V-type ATPase complex (GO:0016471), COPI-coated vesicle membrane (GO:0030663), endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	2
cellular anatomical structure	2
intracellular monoatomic cation homeostasis	1
inorganic ion homeostasis	1
vacuolar acidification	1
response to increased oxygen levels	1
cellular response to oxygen levels	1
proton-transporting V-type ATPase complex assembly	1
lysosome	1
protein catabolic process in the vacuole	1
sterol binding	1
binding	1
lytic vacuole	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
vacuole	1
plasma membrane	1
vacuolar membrane	1
proton-transporting V-type ATPase complex	1
COPI-coated vesicle	1
Golgi-associated vesicle membrane	1
coated vesicle membrane	1
endoplasmic reticulum-Golgi intermediate compartment	1
bounding membrane of organelle	1
intracellular vesicle	1

Protein interactions and networks

STRING

694 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VMA12	VMA22	Q96NT0	883
VMA12	ATP6V1E1	P36543	759
VMA12	ATP6AP1	Q15904	621
VMA12	ATP6V0A4	Q9HBG4	607
VMA12	ATP6V0A2	Q9Y487	606
VMA12	ATP6V1C1	P21283	604
VMA12	ATP6V0D1	P12953	603
VMA12	ATP6V1E2	Q96A05	587
VMA12	ATP6V0A1	Q93050	581
VMA12	TCIRG1	Q13488	579
VMA12	ATP6V1H	Q9UI12	573
VMA12	ATP6V1A	P38606	536
VMA12	ATP6V1G1	O75348	504
VMA12	SLC10A3	P09131	477
VMA12	ATP6V0B	Q99437	477

IntAct

111 interactions, top by confidence:

A	B	Type	Score
ATP6AP2	ATP6V0C	psi-mi:“MI:0914”(association)	0.730
ATP6V0A2	ATP6AP2	psi-mi:“MI:0914”(association)	0.730
VMA12	ATP6AP2	psi-mi:“MI:0914”(association)	0.640
TCIRG1	ATP6AP2	psi-mi:“MI:0914”(association)	0.640
VMA12	ERLIN1	psi-mi:“MI:0915”(physical association)	0.560
KASH5	VMA12	psi-mi:“MI:0915”(physical association)	0.560
ERLIN1	VMA12	psi-mi:“MI:0915”(physical association)	0.560
VMA12	KASH5	psi-mi:“MI:0915”(physical association)	0.560
VMA12	TIMMDC1	psi-mi:“MI:0915”(physical association)	0.560
VMA12	SLC10A4	psi-mi:“MI:0915”(physical association)	0.560
VMA12	EBP	psi-mi:“MI:0915”(physical association)	0.560
VMA12	JAGN1	psi-mi:“MI:0915”(physical association)	0.560
STX1A	VMA12	psi-mi:“MI:0915”(physical association)	0.560
STX4	VMA12	psi-mi:“MI:0915”(physical association)	0.560
BIK	VMA12	psi-mi:“MI:0915”(physical association)	0.560
EBP	VMA12	psi-mi:“MI:0915”(physical association)	0.560
VMA12	ELOVL4	psi-mi:“MI:0915”(physical association)	0.560
IFNGR2	VMA12	psi-mi:“MI:0915”(physical association)	0.560
AQP6	VMA12	psi-mi:“MI:0915”(physical association)	0.560
VMA12	CD300A	psi-mi:“MI:0915”(physical association)	0.560
VMA12	REEP4	psi-mi:“MI:0915”(physical association)	0.560
VMA12	TMEM14B	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (201): TMEM199 (Two-hybrid), CCDC155 (Two-hybrid), TMEM199 (Affinity Capture-MS), TMEM199 (Affinity Capture-MS), TMEM199 (Proximity Label-MS), TMEM199 (Proximity Label-MS), TMEM199 (Proximity Label-MS), TMEM199 (Proximity Label-MS), TMEM199 (Proximity Label-MS), TMEM199 (Proximity Label-MS), TMEM199 (Affinity Capture-MS), TMEM199 (Affinity Capture-MS), TMEM199 (Affinity Capture-MS), TMEM199 (Proximity Label-MS), ATP6V0A2 (Affinity Capture-MS)

ESM2 similar proteins: A2BD92, A4FV45, A5D7N3, A7S641, B0BN86, D3Z2R5, F1Q930, O76024, O95870, P17152, P97587, Q0IJ20, Q17QW2, Q1JPD2, Q1JPG0, Q2HJ63, Q3B8H3, Q4QQM5, Q5BK13, Q5BLE2, Q5RAS8, Q5RJQ8, Q5SWK7, Q5SYH2, Q5ZLD4, Q66H44, Q6DC66, Q6DF19, Q6GR21, Q6MG55, Q6NRI4, Q6NUQ4, Q6NWH5, Q6ZQE4, Q7L4E1, Q7SZC5, Q7ZW11, Q7ZWF4, Q7ZYA0, Q810L4

Diamond homologs: Q5BK13, Q5RAS8, Q5SYH2, Q8N511

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 88 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy	6	70.7×	1e-08
Insulin receptor recycling	10	66.8×	3e-14
Transferrin endocytosis and recycling	10	64.6×	3e-14
ROS and RNS production in phagocytes	9	53.0×	6e-12
Amino acids regulate mTORC1	6	21.1×	2e-05
Ion channel transport	10	16.8×	2e-08
Signaling by Interleukins	6	6.8×	6e-03
Cytokine Signaling in Immune system	8	5.7×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
vacuolar acidification	9	87.9×	2e-13
synaptic vesicle lumen acidification	6	74.9×	2e-08
lysosomal lumen acidification	6	53.9×	1e-07
proton transmembrane transport	8	33.3×	2e-08
regulation of macroautophagy	6	23.6×	2e-05
ERAD pathway	6	14.5×	2e-04
exocytosis	5	10.1×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	1
Uncertain significance	41
Likely benign	15
Benign	10

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
2200444	NM_152464.3(VMA12):c.13_14del (p.Leu5fs)	Pathogenic
223000	NM_152464.3(VMA12):c.40G>C (p.Ala14Pro)	Pathogenic
223001	NM_152464.3(VMA12):c.376-1G>A	Pathogenic
218965	NM_152464.3(VMA12):c.20C>A (p.Ala7Glu)	Likely pathogenic

SpliceAI

946 predictions. Top by Δscore:

Variant	Effect	Δscore
17:28357807:A:AG	donor_gain	1.0000
17:28359295:ATTT:A	acceptor_gain	1.0000
17:28359307:T:A	acceptor_gain	1.0000
17:28359311:TCAG:T	acceptor_loss	1.0000
17:28359311:TCAGA:T	acceptor_gain	1.0000
17:28359312:CAG:C	acceptor_gain	1.0000
17:28359313:A:AG	acceptor_gain	1.0000
17:28359313:A:C	acceptor_gain	1.0000
17:28359314:G:C	acceptor_gain	1.0000
17:28359314:G:GT	acceptor_gain	1.0000
17:28359314:GA:G	acceptor_gain	1.0000
17:28359314:GAA:G	acceptor_gain	1.0000
17:28359314:GAAC:G	acceptor_gain	1.0000
17:28359400:GTCAG:G	donor_gain	1.0000
17:28359401:TCAG:T	donor_gain	1.0000
17:28359403:AGG:A	donor_loss	1.0000
17:28359404:GGTAA:G	donor_loss	1.0000
17:28359405:G:GG	donor_gain	1.0000
17:28360524:CCCAG:C	acceptor_loss	1.0000
17:28360527:A:AC	acceptor_loss	1.0000
17:28360527:A:AG	acceptor_gain	1.0000
17:28360527:AG:A	acceptor_gain	1.0000
17:28360528:G:A	acceptor_gain	1.0000
17:28360528:G:GA	acceptor_gain	1.0000
17:28360528:GGAT:G	acceptor_gain	1.0000
17:28360731:A:AG	acceptor_gain	1.0000
17:28360731:AAAGT:A	acceptor_gain	1.0000
17:28360733:A:G	acceptor_gain	1.0000
17:28360734:G:GG	acceptor_gain	1.0000
17:28360734:GTGA:G	acceptor_gain	1.0000

AlphaMissense

1313 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:28360803:T:C	C163R	0.994
17:28360818:A:C	S168R	0.994
17:28360820:C:A	S168R	0.994
17:28360820:C:G	S168R	0.994
17:28359334:G:C	R102P	0.987
17:28361193:G:C	G190R	0.987
17:28361200:C:A	A192D	0.987
17:28360772:T:A	N152K	0.984
17:28360772:T:G	N152K	0.984
17:28360792:C:A	A159D	0.984
17:28359372:T:C	Y115H	0.983
17:28359373:A:C	Y115S	0.983
17:28360783:C:A	T156K	0.983
17:28359360:G:C	A111P	0.982
17:28361194:G:A	G190D	0.981
17:28360783:C:G	T156R	0.980
17:28361170:C:A	A182E	0.980
17:28360780:T:A	V155D	0.979
17:28359337:T:C	L103P	0.977
17:28361206:T:C	L194P	0.977
17:28359325:T:C	L99P	0.976
17:28359358:T:C	L110P	0.976
17:28360815:G:A	G167R	0.976
17:28360815:G:C	G167R	0.976
17:28360816:G:A	G167E	0.976
17:28360797:T:C	F161L	0.975
17:28360799:C:A	F161L	0.975
17:28360799:C:G	F161L	0.975
17:28358951:A:C	S83R	0.974
17:28358953:T:A	S83R	0.974

dbSNP variants (sampled 300 via entrez): RS1000063356 (17:28364109 G>C), RS1001298884 (17:28355934 C>T), RS1002074935 (17:28361159 G>A,C), RS1002550879 (17:28360263 G>A), RS1002674437 (17:28362804 C>T), RS1004025644 (17:28360304 G>C,T), RS1005999349 (17:28357489 G>A,C,T), RS1007525775 (17:28362479 T>C), RS1007715709 (17:28356545 A>C), RS1008013523 (17:28362006 C>T), RS1008123200 (17:28356881 G>A), RS1008344242 (17:28359416 C>G,T), RS1008680682 (17:28357959 C>T), RS1009674483 (17:28356934 C>T), RS1009930542 (17:28361097 C>T)

Disease associations

OMIM: gene MIM:616815 | disease phenotypes: MIM:616829

GenCC curated gene-disease

Disease	Classification	Inheritance
TMEM199-CDG	Strong	Autosomal recessive

Mondo (1): TMEM199-CDG (MONDO:0014790)

Orphanet (1): TMEM199-CDG (Orphanet:466703)

HPO phenotypes

23 total (23 of 23 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0001252	Hypotonia
HP:0001263	Global developmental delay
HP:0001395	Hepatic fibrosis
HP:0001397	Hepatic steatosis
HP:0001410	Decreased liver function
HP:0002240	Hepatomegaly
HP:0002910	Elevated circulating hepatic transaminase concentration
HP:0003124	Hypercholesterolemia
HP:0003141	Increased LDL cholesterol concentration
HP:0003155	Elevated circulating alkaline phosphatase concentration
HP:0003236	Elevated circulating creatine kinase concentration
HP:0003593	Infantile onset
HP:0003621	Juvenile onset
HP:0010837	Decreased circulating ceruloplasmin concentration
HP:0011463	Childhood onset
HP:0011967	Decreased circulating copper concentration
HP:0012301	Type II transferrin isoform profile
HP:0012347	Abnormal protein N-linked glycosylation
HP:0012358	Abnormal protein O-linked glycosylation
HP:0025321	Copper accumulation in liver
HP:0031956	Elevated circulating aspartate aminotransferase concentration
HP:0031964	Elevated circulating alanine aminotransferase concentration

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST002546_2	Osteoprotegerin levels	1.000000e-09
GCST010204_209	Low density lipoprotein cholesterol levels	3.000000e-15
GCST010241_191	Apolipoprotein A1 levels	1.000000e-26
GCST010242_147	HDL cholesterol levels	4.000000e-12
GCST010243_37	Apolipoprotein B levels	4.000000e-18
GCST010244_438	Triglyceride levels	2.000000e-09
GCST010245_117	LDL cholesterol levels	9.000000e-13

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004615	apolipoprotein B measurement
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol S	increases expression, affects cotreatment	2
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
diallyl trisulfide	decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
K 7174	increases expression	1
ICG 001	affects expression	1
Acetaminophen	affects response to substance	1
Atrazine	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	increases expression, affects cotreatment	1
Smoke	decreases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Sodium Selenite	increases expression	1
Antirheumatic Agents	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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