MARCHF9

Summary

MARCHF9 (membrane associated ring-CH-type finger 9, HGNC:25139) is a protein-coding gene on chromosome 12q14.1, encoding E3 ubiquitin-protein ligase MARCHF9 (Q86YJ5). E3 ubiquitin-protein ligase that may mediate ubiquitination of MHC-I, CD4 and ICAM1, and promote their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. It is a selective cancer dependency (DepMap: 20.8% of cell lines).

MARCH9 is a member of the MARCH family of membrane-bound E3 ubiquitin ligases (EC 6.3.2.19). MARCH enzymes add ubiquitin (see MIM 191339) to target lysines in substrate proteins, thereby signaling their vesicular transport between membrane compartments. MARCH9 induces internalization of several membrane glycoproteins and directs them to the endosomal compartment (Bartee et al., 2004 [PubMed 14722266]; Hoer et al., 2007 [PubMed 17174307]).

Source: NCBI Gene 92979 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 49 total
• Cancer dependency (DepMap): dependent in 20.8% of screened cell lines
• MANE Select transcript: NM_138396

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25139
Approved symbol	MARCHF9
Name	membrane associated ring-CH-type finger 9
Location	12q14.1
Locus type	gene with protein product
Status	Approved
Aliases	RNF179, FLJ36578
Ensembl gene	ENSG00000139266
Ensembl biotype	protein_coding
OMIM	613336
Entrez	92979

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000266643, ENST00000548358, ENST00000552279

RefSeq mRNA: 1 — MANE Select: NM_138396 NM_138396

CCDS: CCDS31847

Canonical transcript exons

ENST00000266643 — 4 exons

Exon	Start	End
ENSE00001249036	57758563	57760411
ENSE00001336991	57756929	57757084
ENSE00001336994	57755103	57755885
ENSE00001667716	57758108	57758300

Expression profiles

Bgee: expression breadth ubiquitous, 196 present calls, max score 92.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.0070 / max 90.4550, expressed in 1659 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
126325	8.5719	1625
126324	1.1677	745
126326	0.2674	99

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adenohypophysis	UBERON:0002196	92.02	gold quality
cortical plate	UBERON:0005343	90.84	gold quality
cerebellar hemisphere	UBERON:0002245	90.76	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.66	gold quality
pituitary gland	UBERON:0000007	90.65	gold quality
cerebellar cortex	UBERON:0002129	90.64	gold quality
granulocyte	CL:0000094	90.32	gold quality
metanephros cortex	UBERON:0010533	90.14	gold quality
left lobe of thyroid gland	UBERON:0001120	89.76	gold quality
right lobe of thyroid gland	UBERON:0001119	89.62	gold quality
cerebellum	UBERON:0002037	89.53	gold quality
spleen	UBERON:0002106	88.56	gold quality
lower esophagus mucosa	UBERON:0035834	88.07	gold quality
thyroid gland	UBERON:0002046	88.01	gold quality
apex of heart	UBERON:0002098	87.42	gold quality
cortex of kidney	UBERON:0001225	87.19	gold quality
left adrenal gland cortex	UBERON:0035825	87.02	gold quality
right adrenal gland	UBERON:0001233	86.66	gold quality
right frontal lobe	UBERON:0002810	86.59	gold quality
right adrenal gland cortex	UBERON:0035827	86.41	gold quality
left adrenal gland	UBERON:0001234	86.19	gold quality
small intestine Peyer’s patch	UBERON:0003454	86.12	gold quality
upper lobe of left lung	UBERON:0008952	86.08	gold quality
ganglionic eminence	UBERON:0004023	86.04	gold quality
right lung	UBERON:0002167	85.98	gold quality
ventricular zone	UBERON:0003053	85.91	gold quality
skin of abdomen	UBERON:0001416	85.87	gold quality
adult mammalian kidney	UBERON:0000082	85.83	gold quality
adrenal cortex	UBERON:0001235	85.75	gold quality
right uterine tube	UBERON:0001302	85.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

84 targeting MARCHF9, 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-1252-5P	100.00	69.80	2774
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-370-5P	99.78	66.81	706
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-3136-3P	99.57	66.59	781
HSA-MIR-7155-3P	99.57	66.48	794
HSA-MIR-6758-3P	99.57	67.55	1078

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 20.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 7)

• MARCH-IX expression causes ubiquitination and downregulation of ICAM-1 (PMID:17174307)
• Downregulation of Mult1 by MARCH9 was reversed by heat-shock treatment, which resulted in the dissociation of the two proteins and increased the amount of Mult1 at the cell surface. (PMID:20870941)
• this study shows that MARCH9-mediated ubiquitination regulates MHC I export from the trans Golgi network (PMID:28559542)
• analysis of glioblastoma alterations such as IDH mutation, NF1 inactivation, and CDK4-MARCH9 locus amplification (PMID:29921698)
• Overexpression of MARCH9 was found to attenuate the oncogenic effect of ICAM-1, suggesting that MARCH9 may inhibit tumor progression by downregulating ICAM-1 signaling. (PMID:30278450)
• biochemical and structural findings demonstrate that specific sequences in the alpha-helical MARCH9 TM domains make crucial contributions to its ability to down-regulate its protein substrates. (PMID:30554144)
• Investigating the Prognostic and Oncogenic Roles of Membrane-Associated Ring-CH-Type Finger 9 in Colorectal Cancer. (PMID:39185021)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	marchf9	ENSDARG00000055740
mus_musculus	Marchf9	ENSMUSG00000040502
rattus_norvegicus	Marchf9	ENSRNOG00000046245

Paralogs (6): MARCHF2 (ENSG00000099785), MARCHF4 (ENSG00000144583), MARCHF1 (ENSG00000145416), MARCHF8 (ENSG00000165406), MARCHF3 (ENSG00000173926), MARCHF11 (ENSG00000183654)

Protein

Protein identifiers

E3 ubiquitin-protein ligase MARCHF9 — Q86YJ5 (reviewed: Q86YJ5)

Alternative names: Membrane-associated RING finger protein 9, Membrane-associated RING-CH protein IX, RING finger protein 179, RING-type E3 ubiquitin transferase MARCHF9

All UniProt accessions (1): Q86YJ5

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin-protein ligase that may mediate ubiquitination of MHC-I, CD4 and ICAM1, and promote their subsequent endocytosis and sorting to lysosomes via multivesicular bodies. E3 ubiquitin ligases accept ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfer the ubiquitin to targeted substrates.

Subunit / interactions. Homodimer.

Subcellular location. Golgi apparatus membrane. Lysosome membrane.

Tissue specificity. Ubiquitously expressed.

Domain organisation. The RING-CH-type zinc finger domain is required for E3 ligase activity.

Pathway. Protein modification; protein ubiquitination.

Miscellaneous. Has no E3 activity due to lack of RINGv-type zinc finger domain but is able to dimerize with and stabilize isoform 1.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86YJ5-1	1	yes
Q86YJ5-2	2, RINGless

RefSeq proteins (1): NP_612405* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011016	Znf_RING-CH	Domain
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR046356	MARCHF4/9/11	Family
IPR047904	MARCHF9_RING_CH-C4HC3	Domain

Pfam: PF12906

UniProt features (23 total): binding site 8, region of interest 4, compositionally biased region 3, transmembrane region 2, sequence variant 2, chain 1, splice variant 1, mutagenesis site 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86YJ5-F1	65.75	0.12

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 (8): 110; 113; 126; 128; 136; 139; 152; 155

Mutagenesis-validated functional residues (1):

Position	Phenotype
231	diminishes ability to promote mhc-i internalization.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 60 (showing top): GOCC_VACUOLAR_MEMBRANE, GOCC_TRANS_GOLGI_NETWORK, NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOCC_GOLGI_STACK, MARSON_BOUND_BY_FOXP3_STIMULATED, GARY_CD5_TARGETS_UP, GOCC_ORGANELLE_SUBCOMPARTMENT, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_AMINOACYLTRANSFERASE_ACTIVITY, GOMF_UBIQUITIN_LIKE_PROTEIN_LIGASE_ACTIVITY, MEISSNER_NPC_HCP_WITH_H3K4ME2, KRIEG_HYPOXIA_NOT_VIA_KDM3A, ZWANG_EGF_INTERVAL_DN, ESC_V6.5_UP_EARLY.V1_UP

GO Biological Process (1): protein ubiquitination (GO:0016567)

GO Molecular Function (5): ubiquitin-protein transferase activity (GO:0004842), zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (7): Golgi membrane (GO:0000139), lysosomal membrane (GO:0005765), Golgi stack (GO:0005795), trans-Golgi network (GO:0005802), lysosome (GO:0005764), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
Golgi apparatus subcompartment	2
protein modification by small protein conjugation	1
ubiquitin-like protein transferase activity	1
transition metal ion binding	1
ubiquitin-protein transferase activity	1
ubiquitin-like protein ligase activity	1
catalytic activity	1
cation binding	1
Golgi apparatus	1
bounding membrane of organelle	1
lysosome	1
lytic vacuole membrane	1
lytic vacuole	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

430 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MARCHF9	UBE2H	P37286	740
MARCHF9	AP1M1	Q9BXS5	648
MARCHF9	MARCHF10	Q8NA82	643
MARCHF9	UBE2E1	P51965	614
MARCHF9	CDC34	P49427	553
MARCHF9	UBA1	P22314	476
MARCHF9	CD4	P01730	467
MARCHF9	UBE2D1	P51668	465
MARCHF9	MARCHF7	Q9H992	459
MARCHF9	ICAM1	P05362	445
MARCHF9	IFFO1	Q0D2I5	441
MARCHF9	UBE2S	Q16763	440
MARCHF9	NEK11	Q8NG66	429
MARCHF9	GLOD5	A6NK44	426
MARCHF9	MAP7D3	Q8IWC1	424

IntAct

120 interactions, top by confidence:

A	B	Type	Score
MARCHF9	LNX2	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	MAST2	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	GORASP2	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	PATJ	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	SNX27	psi-mi:“MI:0407”(direct interaction)	0.440
DLG1	MARCHF9	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	SNTB1	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	SNTA1	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	DLG1	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	PDZD7	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	DLG3	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	DLG2	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	MAGI3	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	MAGI2	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	PTPN3	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	GOPC	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	SNTG1	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	MAGI1	psi-mi:“MI:0407”(direct interaction)	0.440
HTRA1	MARCHF9	psi-mi:“MI:0407”(direct interaction)	0.440
SYNJ2BP	MARCHF9	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	ARHGEF12	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	SCRIB	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	RADIL	psi-mi:“MI:0407”(direct interaction)	0.440
MARCHF9	MAST1	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (9): POTEI (Affinity Capture-MS), ATG9A (Affinity Capture-MS), ICAM1 (Affinity Capture-Western), ATG9A (Affinity Capture-MS), POTEI (Affinity Capture-MS), ATG9A (Affinity Capture-Western), HLA-A (Affinity Capture-Western), MARCH9 (Affinity Capture-Western), MARCH9 (Affinity Capture-Luminescence)

ESM2 similar proteins: A2A7Q9, F1LXF1, O08873, O14795, O35274, O46606, P11274, P12755, P22681, P22682, P49797, P50636, Q08B84, Q0VGY8, Q1L8L6, Q2VJ60, Q3UR85, Q3YEC7, Q4KUS2, Q60698, Q62768, Q69ZT9, Q6PAJ1, Q6R891, Q6T4P5, Q6ZMZ0, Q6ZWB6, Q7TMB0, Q7TPB0, Q80U28, Q86YJ5, Q8HXH0, Q8NEL9, Q8TEK3, Q8WXG6, Q8WXH2, Q92622, Q92625, Q96SB3, Q9CXG9

Diamond homologs: A0JN69, A6NNE9, A6P320, F4JKK0, O60103, O60337, P40318, P90489, P90495, Q0IH10, Q0P496, Q0VD59, Q1LVZ2, Q28EX7, Q32L65, Q3TZ87, Q5I0I2, Q5PQ35, Q5R9W1, Q5T0T0, Q5XIE5, Q5XIV2, Q68FA7, Q6NZQ8, Q6ZQ89, Q80TE3, Q86UD3, Q86YJ5, Q8BRX9, Q8CBH7, Q8TCQ1, Q99M02, Q9DBD2, Q9P0N8, Q9P2E8, Q0X0A5, Q28IK8, Q3KNM2, Q3ZC24, Q5R9W2

SIGNOR signaling

16 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	MARCHF9	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	PVR	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	VAMP8	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	PLXNC1	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	CEMIP2	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	LILRB1	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	PTPRJ	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	PTPRF	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	SLAMF1	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	HLA-DQA1	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	HLA-DQB1	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	PTPRA	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	FCGR2B	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	IGHD	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	FCRL2	ubiquitination
MARCHF9	“down-regulates quantity by destabilization”	ICAM1	ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 77 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
Ras activation upon Ca2+ influx through NMDA receptor	5	58.3×	9e-07
Unblocking of NMDA receptors, glutamate binding and activation	5	55.5×	9e-07
Negative regulation of NMDA receptor-mediated neuronal transmission	5	55.5×	9e-07
Long-term potentiation	5	48.5×	1e-06
Assembly and cell surface presentation of NMDA receptors	8	41.4×	1e-09
Neurexins and neuroligins	9	36.2×	4e-10
Protein-protein interactions at synapses	6	32.5×	9e-07
RAF/MAP kinase cascade	5	6.2×	9e-03

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	10	78.5×	1e-14
protein localization to synapse	6	62.1×	6e-08
receptor clustering	7	59.0×	4e-09
regulation of postsynaptic membrane neurotransmitter receptor levels	6	40.2×	5e-07
cell-cell adhesion	10	13.7×	2e-07
protein-containing complex assembly	7	10.8×	2e-04
protein localization to plasma membrane	5	7.3×	8e-03
chemical synaptic transmission	7	7.3×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

798 predictions. Top by Δscore:

Variant	Effect	Δscore
12:57756925:CCAGG:C	acceptor_loss	1.0000
12:57756926:CAG:C	acceptor_loss	1.0000
12:57756927:A:AG	acceptor_gain	1.0000
12:57756927:AG:A	acceptor_gain	1.0000
12:57756927:AGG:A	acceptor_gain	1.0000
12:57756927:AGGG:A	acceptor_gain	1.0000
12:57756927:AGGGG:A	acceptor_gain	1.0000
12:57756928:G:GA	acceptor_gain	1.0000
12:57756928:GG:G	acceptor_gain	1.0000
12:57756928:GGG:G	acceptor_gain	1.0000
12:57756928:GGGG:G	acceptor_gain	1.0000
12:57756928:GGGGG:G	acceptor_gain	1.0000
12:57757082:CAG:C	donor_loss	1.0000
12:57757084:GG:G	donor_loss	1.0000
12:57755974:G:GT	donor_gain	0.9900
12:57757081:GCAG:G	donor_gain	0.9900
12:57757091:TGC:T	donor_gain	0.9900
12:57757155:G:GT	donor_gain	0.9900
12:57758076:T:A	acceptor_gain	0.9900
12:57758077:G:A	acceptor_gain	0.9900
12:57758104:ACAGT:A	acceptor_gain	0.9900
12:57758106:A:AG	acceptor_gain	0.9900
12:57758106:AGT:A	acceptor_gain	0.9900
12:57758106:AGTG:A	acceptor_gain	0.9900
12:57758107:G:GA	acceptor_gain	0.9900
12:57758107:GT:G	acceptor_gain	0.9900
12:57758107:GTG:G	acceptor_gain	0.9900
12:57758107:GTGG:G	acceptor_gain	0.9900
12:57758107:GTGGC:G	acceptor_gain	0.9900
12:57758301:G:A	donor_loss	0.9900

AlphaMissense

2197 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:57755856:T:A	C110S	1.000
12:57755856:T:C	C110R	1.000
12:57755857:G:A	C110Y	1.000
12:57755857:G:C	C110S	1.000
12:57755858:C:G	C110W	1.000
12:57755863:T:A	I112N	1.000
12:57755863:T:C	I112T	1.000
12:57755863:T:G	I112S	1.000
12:57755865:T:A	C113S	1.000
12:57755865:T:C	C113R	1.000
12:57755866:G:A	C113Y	1.000
12:57755866:G:C	C113S	1.000
12:57755867:C:G	C113W	1.000
12:57755868:T:A	F114I	1.000
12:57755868:T:C	F114L	1.000
12:57755870:C:A	F114L	1.000
12:57755870:C:G	F114L	1.000
12:57756945:C:A	P125H	1.000
12:57756947:T:A	C126S	1.000
12:57756947:T:C	C126R	1.000
12:57756948:G:A	C126Y	1.000
12:57756948:G:C	C126S	1.000
12:57756948:G:T	C126F	1.000
12:57756949:C:G	C126W	1.000
12:57756953:T:A	C128S	1.000
12:57756953:T:C	C128R	1.000
12:57756954:G:A	C128Y	1.000
12:57756954:G:C	C128S	1.000
12:57756954:G:T	C128F	1.000
12:57756955:C:G	C128W	1.000

dbSNP variants (sampled 300 via entrez): RS1000017904 (12:57756619 T>C), RS1000170434 (12:57755895 G>A,T), RS1000224122 (12:57754933 G>A), RS1000505886 (12:57757618 G>T), RS1002018434 (12:57757024 C>A), RS1002410631 (12:57759010 C>T), RS1002559611 (12:57760754 G>A), RS1002746140 (12:57760553 C>T), RS1002797436 (12:57760164 G>A), RS1002814184 (12:57753200 C>A,G), RS1002943409 (12:57753214 T>G), RS1003313681 (12:57755171 G>A), RS1003386519 (12:57753451 G>A), RS1003693741 (12:57754902 C>T), RS1003973206 (12:57756255 G>C)

Disease associations

OMIM: gene MIM:613336 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010703_209	Brain morphology (MOSTest)	2.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs2069502	AGAP2, CDK4, MARCHF9, TSPAN31	3	2.00	1	somatropin recombinant

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	5
aristolochic acid I	increases expression	1
di-n-butylphosphoric acid	affects expression	1
entinostat	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Leflunomide	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Lead	affects expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Thiram	decreases expression	1
Tretinoin	decreases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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