APOBEC1

Summary

APOBEC1 (apolipoprotein B mRNA editing enzyme catalytic subunit 1, HGNC:604) is a protein-coding gene on chromosome 12p13.31, encoding C->U-editing enzyme APOBEC-1 (P41238). Cytidine deaminase catalyzing the cytidine to uridine postranscriptional editing of a variety of mRNAs.

This gene encodes a member of the cytidine deaminase enzyme family. The encoded protein forms a multiple-protein editing holoenzyme with APOBEC1 complementation factor (ACF) and APOBEC1 stimulating protein (ASP). This holoenzyme is involved in the editing of C-to-U nucleotide bases in apolipoprotein B and neurofibromatosis-1 mRNAs. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 339 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 25 total
• MANE Select transcript: NM_001644

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:604
Approved symbol	APOBEC1
Name	apolipoprotein B mRNA editing enzyme catalytic subunit 1
Location	12p13.31
Locus type	gene with protein product
Status	Approved
Aliases	BEDP, CDAR1, APOBEC-1, HEPR
Ensembl gene	ENSG00000111701
Ensembl biotype	protein_coding
OMIM	600130
Entrez	339

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000229304, ENST00000467171

RefSeq mRNA: 3 — MANE Select: NM_001644 NM_001304566, NM_001644, NM_005889

CCDS: CCDS8579

Canonical transcript exons

ENST00000229304 — 5 exons

Exon	Start	End
ENSE00001045681	7654605	7654632
ENSE00002144808	7665857	7665908
ENSE00003502836	7651023	7651141
ENSE00003633937	7649400	7649696
ENSE00003677322	7652438	7652835

Expression profiles

Bgee: expression breadth broad, 38 present calls, max score 97.00.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1192 / max 103.5570, expressed in 12 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
129275	0.0690	9
129276	0.0502	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
jejunal mucosa	UBERON:0000399	97.00	gold quality
duodenum	UBERON:0002114	93.31	gold quality
ileal mucosa	UBERON:0000331	92.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.10	gold quality
small intestine	UBERON:0002108	80.09	gold quality
mucosa of transverse colon	UBERON:0004991	79.73	gold quality
small intestine Peyer’s patch	UBERON:0003454	79.72	gold quality
jejunum	UBERON:0002115	75.73	gold quality
olfactory bulb	UBERON:0002264	62.07	gold quality
mucosa of stomach	UBERON:0001199	61.98	gold quality
oocyte	CL:0000023	60.86	gold quality
colonic mucosa	UBERON:0000317	59.14	gold quality
pancreatic ductal cell	CL:0002079	58.89	silver quality
transverse colon	UBERON:0001157	58.82	gold quality
islet of Langerhans	UBERON:0000006	58.00	gold quality
decidua	UBERON:0002450	56.55	gold quality
tibialis anterior	UBERON:0001385	56.28	silver quality
intestine	UBERON:0000160	55.89	gold quality
endometrium epithelium	UBERON:0004811	55.16	gold quality
cerebellar vermis	UBERON:0004720	54.34	gold quality
epithelial cell of pancreas	CL:0000083	52.77	gold quality
mucosa of sigmoid colon	UBERON:0004993	52.64	silver quality
deltoid	UBERON:0001476	52.56	gold quality
hair follicle	UBERON:0002073	52.43	gold quality
rectum	UBERON:0001052	51.83	gold quality
quadriceps femoris	UBERON:0001377	51.11	gold quality
male germ cell	CL:0000015	50.68	gold quality
gall bladder	UBERON:0002110	50.42	gold quality
frontal pole	UBERON:0002795	50.41	gold quality
sperm	CL:0000019	50.38	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

7 targeting APOBEC1, 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-3941	99.86	70.54	2735
HSA-MIR-4797-5P	99.39	68.01	1354
HSA-MIR-4777-5P	99.33	67.53	1148
HSA-MIR-548V	99.29	69.47	1157
HSA-MIR-6794-3P	98.76	66.99	894
HSA-MIR-1912-5P	97.94	67.98	832
HSA-MIR-4727-3P	96.75	64.97	415

Literature-anchored findings (GeneRIF, showing 24)

• C–>U editing of neurofibromatosis 1 mRNA occurs in tumors that express both the type II transcript and apobec-1, the catalytic subunit of the apolipoprotein B mRNA-editing enzyme (PMID:11727199)
• expression of two proteins essential for apolipoprotein B mRNA editing from a single gene through alternative splicing (PMID:11815617)
• determination of multifunctional cycle and suppression of nonsense-mediated decay (PMID:12881431)
• apobec-1 complementation factor has a role in regulating nucleocytoplasmic import and shuttling (PMID:12896982)
• apobec-1-mediated apoB mRNA editing is regulated by BAG-4 (PMID:14559896)
• Expression of Apobec1 in HepG2 cells resulted in apoB mRNA editing, leading to decreased apoB100 abundance (to 6% of control) and the appearance of apoB48. (PMID:15979078)
• APOBEC3G is not a nucleo-cytoplasmic shuttling protein like APOBEC-1 and activation-induced cytidine deaminase (PMID:16999936)
• No evidence of association of APOBEC1 and PPARG with gallstone susceptibility was detected. (PMID:17696929)
• Studies indicate the APOBEC family consists of 11 members: APOBEC-1 (Apo1), APOBEC-2 (Apo2), activation induced cytidine deaminase (AID), APOBEC- 3A, -3B, -3C, -3DE, -3F, -3H (Apo3A-H) and APOBEC- 4 (Apo4). (PMID:19911124)
• The data presented in this report suggested that similar regulatory mechanisms controlling the functional interaction of APOBEC-1 with ACF might be operational during enterocyte differentiation. (PMID:19932086)
• Identified two novel variants, rs1349411 (APOBEC1) and rs1424032, for serum apoB levels in Mexicans. (PMID:19965785)
• The hypermutation activity of APOBEC-1 was decreased to background levels by a single point APOBEC-1 mutation of P29F or E181Q, while 50% of wild-type control editing at the normal site was retained. (PMID:20348446)
• Results show that expression of APOBEC1 induces a mutator phenotype in 2 different cellular models. (PMID:25085003)
• hnRNPQ6 is required for APOBEC1-enhanced IL8 production. (PMID:25100733)
• An APOBEC-mediated mutational signature in 47% of 192 tumors suggests that APOBEC-catalyzed deamination provides a source of DNA damage in esophageal squamous cell carcinoma. (PMID:25839328)
• AICDA/APOBEC family of cytidine deaminases is significant in innate immunity, as it restricts numerous viruses, including HBV, through hypermutationdependent and independent mechanisms. (Review) (PMID:26398702)
• Luciferase-fused 3’ untranslated region of human Dickkopf1 activity was highly upregulated in A1CF-overexpressed MCF7 cells, but this upregulation can be inhibited by mutating conserved binding motifs of Dickkopf1 3’ untranslated region. A1CF played a crucial role in cell migration and survival through affecting 3’ untranslated region of Dickkopf1 to upregulate its expression in MCF7 cells. (PMID:28639893)
• Our findings propose APOBEC1 and isoform b as the potential endogenous mutators implicated in cancer in-frame indels and pave the way for their use as novel prognostic tumor markers. (PMID:29346513)
• APOBEC1 cytosine deaminase activity on single-stranded DNA is suppressed by replication protein A. (PMID:33330905)
• Harnessing A3G for efficient and selective C-to-T conversion at C-rich sequences. (PMID:33602235)
• The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness. (PMID:36100631)
• APOBEC mutagenesis is a common process in normal human small intestine. (PMID:36702998)
• Identification of RBM46 as a novel APOBEC1 cofactor for C-to-U RNA-editing activity. (PMID:38708190)
• Demonstrates the presence of a 36-aa peptide (isoform 2) derived from this gene in adult small intestinal villi using immunocytochemical analysis. (PMID:9186903)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Apobec1	ENSMUSG00000040613
rattus_norvegicus	Apobec1	ENSRNOG00000015411

Paralogs (9): APOBEC3H (ENSG00000100298), AICDA (ENSG00000111732), APOBEC2 (ENSG00000124701), APOBEC3A (ENSG00000128383), APOBEC3F (ENSG00000128394), APOBEC3B (ENSG00000179750), APOBEC3G (ENSG00000239713), APOBEC3D (ENSG00000243811), APOBEC3C (ENSG00000244509)

Protein

Protein identifiers

C->U-editing enzyme APOBEC-1 — P41238 (reviewed: P41238)

Alternative names: Apolipoprotein B mRNA-editing enzyme catalytic subunit 1, HEPR, mRNA(cytosine(6666)) deaminase 1

All UniProt accessions (2): P41238, A0A0B4J232

UniProt curated annotations — full annotation on UniProt →

Function. Cytidine deaminase catalyzing the cytidine to uridine postranscriptional editing of a variety of mRNAs. Form complexes with cofactors that confer differential editing activity and selectivity. Responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in the apolipoprotein B mRNA. Also involved in CGA (Arg) to UGA (Stop) editing in the NF1 mRNA. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation.

Subunit / interactions. Homodimer. Interacts with A1CF; form an mRNA editing complex. Interacts with RBM47; form an mRNA editing complex. Found in a complex with CELF2/CUGBP2 and A1CF. Interacts with HNRPAB. Interacts with SYNCRIP.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Expressed exclusively in the small intestine.

Cofactor. Binds 1 Zn(2+) ion per subunit.

Similarity. Belongs to the cytidine and deoxycytidylate deaminase family.

RefSeq proteins (3): NP_001291495, NP_001635, NP_005880 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002125	CMP_dCMP_dom	Domain
IPR016192	APOBEC/CMP_deaminase_Zn-bd	Binding_site
IPR016193	Cytidine_deaminase-like	Homologous_superfamily
IPR041547	APOBEC1	Family
IPR050610	APOBEC_Cyt_Deaminase	Family

Pfam: PF18774

Enzyme classification (BRENDA):

• EC 3.5.4.36 — mRNA(cytosine6666) deaminase (BRENDA: 7 organisms, 26 substrates, 2 inhibitors, 4 Km, 0 kcat entries)
• EC 3.5.4.37 — double-stranded RNA adenine deaminase (BRENDA: 11 organisms, 31 substrates, 15 inhibitors, 0 Km, 2 kcat entries)

Substrate kinetics (BRENDA)

3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
CYTOSINE6666 IN APOLIPOPROTEIN B MRNA	—	4
8-AZAADENINE IN DOUBLE-STRANDED RNA	—	0
ADENINE IN DOUBLE-STRANDED RNA	—	0

Catalyzed reactions (Rhea), 2 shown:

• cytidine(6666) in apoB mRNA + H2O + H(+) = uridine(6666) in apoB mRNA + NH4(+) (RHEA:21772)
• a cytidine in mRNA + H2O + H(+) = a uridine in mRNA + NH4(+) (RHEA:74355)

UniProt features (10 total): binding site 3, sequence variant 2, sequence conflict 2, chain 1, domain 1, active site 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6X91	X-RAY DIFFRACTION	3.51

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P41238-F1	88.16	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.

Catalytic / active sites (1): 63 (proton donor)

Ligand- & substrate-binding residues (3): 61; 93; 96

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-72200	mRNA Editing: C to U Conversion
R-HSA-75094	Formation of the Editosome
R-HSA-75072	mRNA Editing
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 263 (showing top): MORF_ITGA2, BROWNE_HCMV_INFECTION_4HR_UP, AP1_01, GOBP_RESPONSE_TO_IONIZING_RADIATION, GOBP_REGULATION_OF_TRIGLYCERIDE_METABOLIC_PROCESS, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOBP_LIPOPROTEIN_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_LIPID_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MORF_RAD51L3, GOBP_MRNA_MODIFICATION, GOBP_GLYCEROLIPID_METABOLIC_PROCESS

GO Biological Process (20): mRNA processing (GO:0006397), lipid metabolic process (GO:0006629), triglyceride metabolic process (GO:0006641), response to gamma radiation (GO:0010332), cytidine to uridine editing (GO:0016554), mRNA modification (GO:0016556), regulation of cell population proliferation (GO:0042127), lipoprotein biosynthetic process (GO:0042158), lipoprotein transport (GO:0042953), positive regulation of gene expression via chromosomal CpG island demethylation (GO:0044029), mRNA stabilization (GO:0048255), establishment of localization in cell (GO:0051649), negative regulation of triglyceride metabolic process (GO:0090209), chromosomal 5-methylcytosine DNA demethylation pathway (GO:0141166), negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623), regulation of macromolecule biosynthetic process (GO:0010556), positive regulation of macromolecule metabolic process (GO:0010604), low-density lipoprotein particle clearance (GO:0034383), lipoprotein metabolic process (GO:0042157), regulation of mRNA metabolic process (GO:1903311)

GO Molecular Function (8): RNA binding (GO:0003723), cytidine deaminase activity (GO:0004126), zinc ion binding (GO:0008270), mRNA 3’-UTR AU-rich region binding (GO:0035925), catalytic activity (GO:0003824), protein binding (GO:0005515), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), apolipoprotein B mRNA editing enzyme complex (GO:0030895), mRNA editing complex (GO:0045293)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
mRNA Editing	1
mRNA Editing: C to U Conversion	1
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mRNA metabolic process	3
macromolecule biosynthetic process	2
negative regulation of mRNA catabolic process	2
regulation of macromolecule metabolic process	2
cellular anatomical structure	2
RNA processing	1
primary metabolic process	1
acylglycerol metabolic process	1
response to ionizing radiation	1
base conversion or substitution editing	1
RNA modification	1
cell population proliferation	1
regulation of cellular process	1
lipoprotein metabolic process	1
protein transport	1
lipoprotein localization	1
transcription initiation-coupled chromatin remodeling	1
regulation of mRNA stability	1
RNA stabilization	1
establishment of localization	1
cellular localization	1
triglyceride metabolic process	1
negative regulation of lipid metabolic process	1
regulation of triglyceride metabolic process	1
DNA metabolic process	1
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1
regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	1
regulation of biosynthetic process	1
positive regulation of metabolic process	1
macromolecule metabolic process	1
plasma lipoprotein particle clearance	1
low-density lipoprotein particle disassembly	1
protein metabolic process	1
regulation of RNA metabolic process	1
nucleic acid binding	1
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines	1
deaminase activity	1
transition metal ion binding	1
mRNA 3’-UTR binding	1
molecular_function	1

Protein interactions and networks

STRING

718 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
APOBEC1	A1CF	Q9NQ94	995
APOBEC1	CDA	P32320	967
APOBEC1	APOBEC4	Q8WW27	964
APOBEC1	APOB	P04114	962
APOBEC1	UNG	P13051	794
APOBEC1	TDG	Q13569	689
APOBEC1	RBM47	A0AV96	684
APOBEC1	CUL5	Q93034	677
APOBEC1	HNRNPAB	Q99729	661
APOBEC1	DNAJB11	Q9UBS4	643
APOBEC1	ADAR	P55265	623
APOBEC1	NF1	P21359	573
APOBEC1	EIF4G2	P78344	563
APOBEC1	CLEC4A	Q9UMR7	548
APOBEC1	SLCO6A1	Q86UG4	520

IntAct

25 interactions, top by confidence:

A	B	Type	Score
NOTO	APOBEC1	psi-mi:“MI:0915”(physical association)	0.560
APOBEC1	HNRNPK	psi-mi:“MI:0915”(physical association)	0.560
APOBEC1	CDK6	psi-mi:“MI:0915”(physical association)	0.560
APOBEC1	UFSP2	psi-mi:“MI:0915”(physical association)	0.560
APOBEC1	HNRNPF	psi-mi:“MI:0915”(physical association)	0.560
APOBEC1	KRTAP19-5	psi-mi:“MI:0915”(physical association)	0.560
APOBEC1	KRTAP6-2	psi-mi:“MI:0915”(physical association)	0.560
APOBEC1	KRTAP6-1	psi-mi:“MI:0915”(physical association)	0.560
APOBEC1	NOTO	psi-mi:“MI:0915”(physical association)	0.000
UFSP2	APOBEC1	psi-mi:“MI:0915”(physical association)	0.000
HNRNPF	APOBEC1	psi-mi:“MI:0915”(physical association)	0.000
APOBEC1	HNRNPK	psi-mi:“MI:0915”(physical association)	0.000
CDK6	APOBEC1	psi-mi:“MI:0915”(physical association)	0.000
APOBEC1	KRTAP19-5	psi-mi:“MI:0915”(physical association)	0.000
APOBEC1	KRTAP6-2	psi-mi:“MI:0915”(physical association)	0.000
APOBEC1	KRTAP6-1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (24): APOBEC1 (Reconstituted Complex), APOBEC1 (Reconstituted Complex), APOBEC1 (Affinity Capture-Western), BAG4 (Two-hybrid), KPNA2 (Two-hybrid), APOBEC1 (Synthetic Lethality), APOBEC1 (Two-hybrid), APOBEC1 (Two-hybrid), HNRNPK (Two-hybrid), HNRNPF (Two-hybrid), KRTAP6-1 (Two-hybrid), KRTAP6-2 (Two-hybrid), KRTAP19-5 (Two-hybrid), NOTO (Two-hybrid), SYNCRIP (Two-hybrid)

ESM2 similar proteins: A1BPI0, A2BD94, B0ZE70, B2GV47, C3VD30, D3ZSP7, O35892, O35893, O88196, P03079, P38483, P41238, P47855, P51908, P59025, P60704, P60705, Q1ZYL8, Q2PT36, Q497M3, Q4R739, Q4R9F7, Q5QGT7, Q694B3, Q6AXX9, Q75W64, Q7Z2W4, Q80VH0, Q86WZ0, Q8C779, Q8C8C1, Q8ND61, Q8WP22, Q8WW27, Q95JK0, Q99J72, Q9CWH0, Q9D494, Q9EQP0, Q9GZX7

Diamond homologs: A9QA56, P31941, P38483, P41238, P47855, P60704, P60705, Q19Q52, Q1WBT4, Q2PT36, Q4VDN5, Q694B3, Q694B5, Q694B6, Q694B7, Q694B8, Q694B9, Q694C0, Q694C1, Q694C2, Q694C4, Q694C5, Q6NTF7, Q75W64, Q7YR23, Q7YR24, Q7YR25, Q8IUX4, Q99J72, Q9EQP0, Q9GZX7, Q9HC16, Q9NRW3, Q9TUI7, Q9UH17, Q9WVE0, P51908, Q96AK3, Q9WV35, Q3SYR3

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
APOBEC1	“form complex”	“C-to-U editosome complex”	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

617 predictions. Top by Δscore:

Variant	Effect	Δscore
12:7649694:ACTC:A	acceptor_loss	1.0000
12:7649695:CT:C	acceptor_gain	1.0000
12:7649696:TC:T	acceptor_loss	1.0000
12:7649697:C:CC	acceptor_gain	1.0000
12:7649697:C:CG	acceptor_loss	1.0000
12:7649698:T:A	acceptor_loss	1.0000
12:7652689:A:C	donor_gain	1.0000
12:7652692:T:TA	donor_gain	1.0000
12:7652693:C:A	donor_gain	1.0000
12:7649692:AGACT:A	acceptor_gain	0.9900
12:7649693:GACT:G	acceptor_gain	0.9900
12:7651021:A:AC	donor_gain	0.9900
12:7651022:C:CC	donor_gain	0.9900
12:7651022:CTAGA:C	donor_gain	0.9900
12:7651140:CT:C	acceptor_gain	0.9900
12:7651142:C:CC	acceptor_gain	0.9900
12:7652465:CTCCA:C	donor_gain	0.9900
12:7652691:TTC:T	donor_gain	0.9900
12:7652692:TCC:T	donor_gain	0.9900
12:7652735:T:TA	donor_gain	0.9900
12:7649702:A:AC	acceptor_gain	0.9800
12:7652466:TC:T	donor_gain	0.9800
12:7652467:CC:C	donor_gain	0.9800
12:7652495:G:A	donor_gain	0.9800
12:7652688:AACTT:A	donor_gain	0.9800
12:7652721:G:C	donor_gain	0.9800
12:7652836:C:CC	acceptor_gain	0.9800
12:7665855:A:G	donor_loss	0.9800
12:7665856:C:CA	donor_loss	0.9800
12:7651022:CT:C	donor_gain	0.9700

AlphaMissense

1560 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:7652607:A:C	S91R	0.994
12:7652607:A:T	S91R	0.994
12:7652609:T:G	S91R	0.994
12:7651116:A:C	F156L	0.981
12:7651116:A:T	F156L	0.981
12:7651118:A:G	F156L	0.981
12:7652624:A:G	W86R	0.977
12:7652624:A:T	W86R	0.977
12:7652619:G:C	F87L	0.975
12:7652619:G:T	F87L	0.975
12:7652621:A:G	F87L	0.975
12:7652811:A:C	F23L	0.974
12:7652811:A:T	F23L	0.974
12:7652813:A:G	F23L	0.974
12:7652520:A:C	F120L	0.973
12:7652520:A:T	F120L	0.973
12:7652522:A:G	F120L	0.973
12:7652527:C:G	R118P	0.967
12:7652612:A:G	W90R	0.964
12:7652612:A:T	W90R	0.964
12:7652571:A:C	F103L	0.963
12:7652571:A:T	F103L	0.963
12:7652573:A:G	F103L	0.963
12:7652497:C:G	R128P	0.961
12:7652697:G:C	H61Q	0.953
12:7652697:G:T	H61Q	0.953
12:7651042:T:A	E181V	0.952
12:7651114:A:T	V157D	0.949
12:7652614:G:A	S89F	0.946
12:7652691:T:A	E63D	0.942

dbSNP variants (sampled 300 via entrez): RS1000086155 (12:7663265 T>C), RS1000349979 (12:7668035 A>G), RS1000408388 (12:7654366 C>T), RS1000439946 (12:7662867 TGCAATGGAGGGAGATGA>T), RS1000926561 (12:7656993 T>C), RS1000950399 (12:7666510 T>A), RS1001140694 (12:7670142 C>T), RS1001193072 (12:7669837 T>C), RS1001308309 (12:7662080 AAAAAC>A,AAAAACAAAAC), RS1001336525 (12:7668717 A>T), RS1001452559 (12:7668468 G>A), RS1001481582 (12:7657395 C>G), RS1001680520 (12:7662314 G>T), RS1001716436 (12:7655652 T>C), RS1001748985 (12:7655267 T>C)

Disease associations

OMIM: gene MIM:600130 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004232_90	HDL cholesterol levels	1.000000e-08
GCST006014_35	Creatine kinase levels	4.000000e-273
GCST008158_111	Body mass index	2.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004534	creatine kinase measurement
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

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
kojic acid	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Estradiol	affects binding, increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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