SYNM

Summary

SYNM (synemin, HGNC:24466) is a protein-coding gene on chromosome 15q26.3, encoding Synemin (O15061). Type-VI intermediate filament (IF) which plays an important cytoskeletal role within the muscle cell cytoskeleton.

The protein encoded by this gene is an intermediate filament (IF) family member. IF proteins are cytoskeletal proteins that confer resistance to mechanical stress and are encoded by a dispersed multigene family. This protein has been found to form a linkage between desmin, which is a subunit of the IF network, and the extracellular matrix, and provides an important structural support in muscle. Two alternatively spliced variants encoding different isoforms have been described for this gene.

Source: NCBI Gene 23336 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 169 total
• MANE Select transcript: NM_145728

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24466
Approved symbol	SYNM
Name	synemin
Location	15q26.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0353, SYN
Ensembl gene	ENSG00000182253
Ensembl biotype	protein_coding
OMIM	606087
Entrez	23336

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000328642, ENST00000336292, ENST00000560674, ENST00000594047

RefSeq mRNA: 2 — MANE Select: NM_145728 NM_015286, NM_145728

CCDS: CCDS73786, CCDS73787

Canonical transcript exons

ENST00000336292 — 4 exons

Exon	Start	End
ENSE00001390297	99129367	99135593
ENSE00003181765	99105080	99106009
ENSE00003738018	99113591	99113715
ENSE00003752585	99126722	99126792

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 99.78.

FANTOM5 (CAGE): breadth broad, TPM avg 6.5716 / max 860.3968, expressed in 808 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
148854	5.9639	707
148853	0.6077	307

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
seminal vesicle	UBERON:0000998	99.78	gold quality
saphenous vein	UBERON:0007318	99.68	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	99.64	gold quality
gluteal muscle	UBERON:0002000	99.60	gold quality
vastus lateralis	UBERON:0001379	99.54	gold quality
cauda epididymis	UBERON:0004360	99.52	gold quality
cranial nerve II	UBERON:0000941	99.51	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	99.51	gold quality
quadriceps femoris	UBERON:0001377	99.50	gold quality
biceps brachii	UBERON:0001507	99.50	gold quality
heart right ventricle	UBERON:0002080	99.45	gold quality
deltoid	UBERON:0001476	99.41	gold quality
diaphragm	UBERON:0001103	99.39	gold quality
lower esophagus muscularis layer	UBERON:0035833	99.38	gold quality
lower esophagus	UBERON:0013473	99.36	gold quality
skeletal muscle tissue	UBERON:0001134	99.34	gold quality
triceps brachii	UBERON:0001509	99.31	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	99.29	gold quality
inferior olivary complex	UBERON:0002127	99.25	gold quality
left ventricle myocardium	UBERON:0006566	99.15	gold quality
urethra	UBERON:0000057	99.14	gold quality
nipple	UBERON:0002030	99.11	gold quality
tibialis anterior	UBERON:0001385	99.09	gold quality
mucosa of stomach	UBERON:0001199	99.04	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	98.99	gold quality
hindlimb stylopod muscle	UBERON:0004252	98.98	gold quality
choroid plexus epithelium	UBERON:0003911	98.95	gold quality
epithelium of mammary gland	UBERON:0003244	98.94	gold quality
mammary duct	UBERON:0001765	98.88	gold quality
body of tongue	UBERON:0011876	98.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.78
E-ENAD-27	no	25.47

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GLI1

miRNA regulators (miRDB)

136 targeting SYNM, 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-3646	100.00	73.56	5283
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488

Literature-anchored findings (GeneRIF, showing 26)

• Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3. (PMID:11454237)
• Expression of the intermediate filament protein synemin in myofibrillar myopathies and other muscle diseases. (PMID:12669240)
• the default of KIAA0353 gene may play a role in the occurrence and development of varicose great saphenous vein in PDVI patients. (PMID:12887813)
• The colocalization of Synemin [syn] with vimentin, GFAP, or neurofilament supports the idea that Syn is a key cross-linking protein in morphogenesis that connects different cytoskeletal structures (PMID:14552890)
• Based on its localization and its expression pattern, beta-synemin functions as a structural protein involved in maintaining muscle integrity through its interactions with alpha-dystrobrevin, desmin, and other structural proteins. (PMID:15318345)
• synemin is associated with ruffled membranes in addition to being distributed along the intermediate filament network (PMID:15657940)
• Desmuslin is down-regulated in incompetent saphenous veins. (PMID:16476617)
• Mammalian synemin is also shown to colocalize with dystrophin within muscle cell cultures (PMID:16777071)
• The stability of DMN was analyzed under the action of low-level laser therapy. (PMID:17564317)
• alpha-synemin, but not beta-synemin, interacts with both vinculin and metavinculin (PMID:18028034)
• results revealed that synemin was modulated nearly in all human human hepatocellular carcinoma cases (PMID:18084875)
• Results suggest human alpha-synemin plays an essential role in linking the heteropolymeric intermediate filament to adherens-type junctions, such as the costameres within mammalian striated muscle cells, via its interaction with talin. (PMID:18342854)
• The LIM domain protein zyxin was identified as an interaction partner for human synemin. (PMID:19853601)
• The differences in human syncoilin and beta-synemin mRNA ratios between Duchenne muscular dystrophy and normal muscles were not statistically significant (PMID:20199207)
• SYNM could represent a novel putative breast tumor suppressor gene that is prone to epigenetic silencing. SYNM promoter methylation may become a useful predictive biomarker to stratify breast cancer patients’ risk for tumor relapse. (PMID:20543860)
• Desmuslin expression is required for the maintenance of vascular smooth muscle phenotype. Decreased desmuslin expression may affect differentiation of VSMCs and ultimately contribute to the development of varicose veins. (PMID:20573469)
• Synemin knock-down did not influence the cytoskeleton expression and organization of human Chang liver cells (PMID:21144834)
• synemin positively regulates glioblastoma cell proliferation by helping sequester PP2A away from Akt, thereby favoring Akt activation. (PMID:22337773)
• Immunohistochemistry of synemin in reactive astrocytes and Rosenthal fibers in two patients with Alexander disease. There was an abundance of GFAP-positive Rosenthal fibers and widespread reactive gliosis in the white matter and subpial regions. (PMID:23594359)
• alpha-Synemin localizes to the M-band of the sarcomere through interaction with the M10 region of titin (PMID:25447537)
• LMOD1, SYNPO2, PDLIM7, PLN, and SYNM down-regulation reflect the altered phenotype of smooth muscle cells in vascular disease and could be early sensitive markers of SMC dedifferentiation. (PMID:27470516)
• a novel heterozygous missense mutation p.(Trp538Arg) of SYNM was identified and cosegregated with the affected members in a Chinese family (PMID:30276801)
• Synemin is a target of myocardin family coactivators. (PMID:31461342)
• c-Abl Tyrosine Kinase Is Regulated Downstream of the Cytoskeletal Protein Synemin in Head and Neck Squamous Cell Carcinoma Radioresistance and DNA Repair. (PMID:33019757)
• A risk model of gene signatures for predicting platinum response and survival in ovarian cancer. (PMID:35361267)
• Synemin promotes pulmonary artery smooth muscle cell phenotypic switch in shunt-induced pulmonary arterial hypertension. (PMID:35769011)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	synm	ENSDARG00000062350
mus_musculus	Synm	ENSMUSG00000030554
rattus_norvegicus	Synm	ENSRNOG00000014030

Paralogs (68): KRT33A (ENSG00000006059), VIM (ENSG00000026025), KRT31 (ENSG00000094796), NEFM (ENSG00000104722), KRT23 (ENSG00000108244), KRT37 (ENSG00000108417), KRT32 (ENSG00000108759), KRT18 (ENSG00000111057), LMNB1 (ENSG00000113368), KRT36 (ENSG00000126337), KRT17 (ENSG00000128422), GFAP (ENSG00000131095), KRT34 (ENSG00000131737), KRT33B (ENSG00000131738), NES (ENSG00000132688), PRPH (ENSG00000135406), KRT85 (ENSG00000135443), KRT7 (ENSG00000135480), KRT71 (ENSG00000139648), INA (ENSG00000148798), LMNTD1 (ENSG00000152936), LMNA (ENSG00000160789), KRT84 (ENSG00000161849), KRT82 (ENSG00000161850), KRT80 (ENSG00000167767), KRT1 (ENSG00000167768), KRT24 (ENSG00000167916), KRT8 (ENSG00000170421), KRT78 (ENSG00000170423), KRT86 (ENSG00000170442), KRT75 (ENSG00000170454), KRT6C (ENSG00000170465), KRT4 (ENSG00000170477), KRT74 (ENSG00000170484), KRT72 (ENSG00000170486), KRT83 (ENSG00000170523), BFSP2 (ENSG00000170819), KRT19 (ENSG00000171345), KRT15 (ENSG00000171346), KRT38 (ENSG00000171360)

Protein

Protein identifiers

Synemin — O15061 (reviewed: O15061)

Alternative names: Desmuslin

All UniProt accessions (4): O15061, A0A075B7B1, C9JIE4, H0YL34

UniProt curated annotations — full annotation on UniProt →

Function. Type-VI intermediate filament (IF) which plays an important cytoskeletal role within the muscle cell cytoskeleton. It forms heteromeric IFs with desmin and/or vimentin, and via its interaction with cytoskeletal proteins alpha-dystrobrevin, dystrophin, talin-1, utrophin and vinculin, is able to link these heteromeric IFs to adherens-type junctions, such as to the costameres, neuromuscular junctions, and myotendinous junctions within striated muscle cells.

Subunit / interactions. Interacts with GFAP and VIM. Isoform 1 interacts with TLN1 and VCL. Isoform 2 interacts with DES and DTNA. Isoform 1 and isoform 2 interact with DMD and UTRN.

Subcellular location. Cytoplasm. Cytoskeleton. Cell junction. Adherens junction.

Tissue specificity. Isoform 2 is strongly detected in adult heart, fetal skeletal muscles and fetal heart. Isoform 1 is weakly detected in fetal heart and also in fetal skeletal muscle. Isoform 1 and isoform 2 are detected in adult bladder (at protein level). The mRNA is predominantly expressed in heart and muscle with some expression in brain which may be due to tissue-specific isoforms.

Similarity. Belongs to the intermediate filament family.

Isoforms (3)

UniProt ID	Names	Canonical?
O15061-1	1, Alpha	yes
O15061-2	2, Beta
O15061-3	3

RefSeq proteins (2): NP_056101, NP_663780* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018039	IF_conserved	Conserved_site
IPR030634	SYNM	Family
IPR039008	IF_rod_dom	Domain

Pfam: PF00038

UniProt features (85 total): sequence conflict 27, region of interest 17, sequence variant 17, modified residue 13, compositionally biased region 6, splice variant 3, chain 1, domain 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6EWO	X-RAY DIFFRACTION	2.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O15061-F1	50.06	0.15

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 (13): 429, 598, 651, 653, 777, 1044, 1049, 1077, 1087, 1181, 1184, 1435, 1487

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 177 (showing top): GOBP_INTERMEDIATE_FILAMENT_BASED_PROCESS, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, GOBP_MULTICELLULAR_ORGANISMAL_MOVEMENT, BROWNE_HCMV_INFECTION_12HR_UP, GOBP_SKELETAL_MUSCLE_CONTRACTION, GOBP_MUSCLE_CONTRACTION, BLALOCK_ALZHEIMERS_DISEASE_UP, BILD_E2F3_ONCOGENIC_SIGNATURE, DELYS_THYROID_CANCER_DN, NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON, ONDER_CDH1_TARGETS_2_UP, TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN, GOBP_MUSCLE_SYSTEM_PROCESS, GOMF_STRUCTURAL_CONSTITUENT_OF_MUSCLE, MODULE_6

GO Biological Process (2): fast-twitch skeletal muscle fiber contraction (GO:0031443), intermediate filament cytoskeleton organization (GO:0045104)

GO Molecular Function (5): structural constituent of cytoskeleton (GO:0005200), structural constituent of muscle (GO:0008307), vinculin binding (GO:0017166), intermediate filament binding (GO:0019215), protein binding (GO:0005515)

GO Cellular Component (10): intermediate filament (GO:0005882), adherens junction (GO:0005912), sarcolemma (GO:0042383), costamere (GO:0043034), intermediate filament cytoskeleton (GO:0045111), neurofilament cytoskeleton (GO:0060053), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), membrane (GO:0016020), anchoring junction (GO:0070161)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cytoskeleton organization	2
structural molecule activity	2
cytoskeleton	2
binding	2
intermediate filament cytoskeleton	2
twitch skeletal muscle contraction	1
intermediate filament-based process	1
cytoskeletal protein binding	1
polymeric cytoskeletal fiber	1
cell-cell junction	1
plasma membrane	1
myofibril	1
neurofilament	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
cell junction	1

Protein interactions and networks

STRING

1540 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SYNM	VCL	P18206	946
SYNM	NES	P48681	918
SYNM	TLN2	Q9Y4G6	902
SYNM	PLEC	Q15149	878
SYNM	ZYX	Q15942	875
SYNM	DTNA	Q9Y4J8	858
SYNM	TLN1	Q9Y490	856
SYNM	SYNC	Q9H7C4	781
SYNM	LHX4	Q969G2	771
SYNM	LHX3	Q9UBR4	750
SYNM	FLNC	Q14315	606
SYNM	MYOT	Q9UBF9	599
SYNM	GFAP	P14136	562
SYNM	TCAP	O15273	556
SYNM	MYOZ1	Q9NP98	554

IntAct

47 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
CT55	BLTP3B	psi-mi:“MI:0914”(association)	0.530
DNAJB4	SYNM	psi-mi:“MI:0914”(association)	0.530
SYNM	TTN	psi-mi:“MI:0915”(physical association)	0.510
DTNA	SYNM	psi-mi:“MI:0915”(physical association)	0.510
SYNM	DTNA	psi-mi:“MI:0915”(physical association)	0.510
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
FLNC	SYNM	psi-mi:“MI:0915”(physical association)	0.370
DISC1	SYNM	psi-mi:“MI:0915”(physical association)	0.370
ERBB2	SYNM	psi-mi:“MI:0915”(physical association)	0.370
ERBB3	SYNM	psi-mi:“MI:0915”(physical association)	0.370
ERBB4	SYNM	psi-mi:“MI:0915”(physical association)	0.370
Tuba3a	CCHCR1	psi-mi:“MI:0914”(association)	0.350
SKA1	ILVBL	psi-mi:“MI:0914”(association)	0.350
CEP43	CCHCR1	psi-mi:“MI:0914”(association)	0.350
CSNK2A2	WDR46	psi-mi:“MI:0914”(association)	0.350
Bach1	SYNM	psi-mi:“MI:0914”(association)	0.350
CUL4A	HAX1	psi-mi:“MI:0914”(association)	0.350
COPS6	DDX3X	psi-mi:“MI:0914”(association)	0.350
SYNC	NDC80	psi-mi:“MI:0914”(association)	0.350

BioGRID (77): SYNM (Affinity Capture-MS), SYNM (Affinity Capture-MS), SYNM (Proximity Label-MS), SYNM (Affinity Capture-MS), SYNM (Affinity Capture-MS), SYNM (Affinity Capture-MS), SYNM (Affinity Capture-MS), SYNM (Affinity Capture-MS), PPP2R2B (Affinity Capture-Western), PPP2R1A (Affinity Capture-Western), SYNM (Affinity Capture-Western), SYNM (Affinity Capture-Western), SYNM (Affinity Capture-MS), SYNM (Affinity Capture-MS), SYNM (Affinity Capture-MS)

ESM2 similar proteins: A2AHC3, A2AMT1, A6NCC3, A6NN73, D3Z8E6, D6RF30, E7F5E1, H3BPF8, H3BQL2, H3BSY2, O15061, O35668, P0DX52, P0DX53, P53814, P54256, P54257, P62025, P97434, Q02435, Q06002, Q06637, Q0D2H9, Q0VF96, Q12934, Q3UHU5, Q3V0F0, Q5DU05, Q5T5Y3, Q5TF21, Q60664, Q62627, Q63312, Q6AW69, Q6NZL0, Q6PHN1, Q6WCQ1, Q70IV5, Q80VC9, Q80Y56

Diamond homologs: O15061, O77788, P02533, P02542, P05786, P07196, P07197, P08552, P08553, P08779, P12036, P12839, P14136, P19246, P23565, P23729, P35616, P46660, P48671, P48672, P48673, Q01550, Q02916, Q28115, Q5R408, Q6IFU7, Q6IFV1, Q6IFX2, Q6NWF6, Q70IV5, Q9Z1Q1, Q9Z2K1, P16053, P21263, P48681, P86839, Q6P5H2, A0A8C0N8E3, A0JND2, A1L595

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	36
Benign	41

Top pathogenic / likely-pathogenic (0)

SpliceAI

942 predictions. Top by Δscore:

Variant	Effect	Δscore
15:99113587:TTA:T	acceptor_loss	1.0000
15:99113588:TAGA:T	acceptor_loss	1.0000
15:99113588:TAGAG:T	acceptor_gain	1.0000
15:99113589:A:AG	acceptor_gain	1.0000
15:99113589:A:T	acceptor_loss	1.0000
15:99113589:AGAGA:A	acceptor_gain	1.0000
15:99113590:G:GG	acceptor_gain	1.0000
15:99113590:GA:G	acceptor_gain	1.0000
15:99113590:GAGA:G	acceptor_gain	1.0000
15:99113590:GAGAG:G	acceptor_gain	1.0000
15:99113712:ACCGG:A	donor_loss	1.0000
15:99113714:CGGTA:C	donor_loss	1.0000
15:99113716:G:GG	donor_gain	1.0000
15:99113716:GTA:G	donor_loss	1.0000
15:99113717:TAA:T	donor_loss	1.0000
15:99126716:TTACA:T	acceptor_loss	1.0000
15:99126717:TACAG:T	acceptor_loss	1.0000
15:99126720:A:AC	acceptor_loss	1.0000
15:99126720:A:AG	acceptor_gain	1.0000
15:99126720:AG:A	acceptor_gain	1.0000
15:99126720:AGG:A	acceptor_gain	1.0000
15:99126721:G:GG	acceptor_gain	1.0000
15:99126721:GG:G	acceptor_gain	1.0000
15:99126721:GGG:G	acceptor_gain	1.0000
15:99126721:GGGC:G	acceptor_gain	1.0000
15:99126788:GTCAG:G	donor_gain	1.0000
15:99126790:CAGG:C	donor_loss	1.0000
15:99126791:AGGTA:A	donor_loss	1.0000
15:99126793:G:C	donor_loss	1.0000
15:99126793:G:GG	donor_gain	1.0000

AlphaMissense

10138 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:99113715:G:C	R312P	0.994
15:99129977:G:C	W539C	0.994
15:99129977:G:T	W539C	0.994
15:99105294:T:C	L32P	0.993
15:99105252:T:C	L18P	0.992
15:99105264:T:C	L22P	0.992
15:99105282:G:C	R28P	0.990
15:99105243:T:C	L15P	0.987
15:99130955:G:C	W865C	0.987
15:99130955:G:T	W865C	0.987
15:99113705:G:C	A309P	0.986
15:99130953:T:A	W865R	0.986
15:99130953:T:C	W865R	0.986
15:99105261:G:C	R21P	0.984
15:99129975:T:A	W539R	0.983
15:99129975:T:C	W539R	0.983
15:99126723:G:C	A313P	0.982
15:99131362:C:A	A1001D	0.981
15:99113670:T:C	L297P	0.980
15:99105288:G:C	R30P	0.979
15:99113711:T:G	Y311D	0.978
15:99131361:G:C	A1001P	0.978
15:99105264:T:A	L22H	0.977
15:99130288:T:A	V643D	0.976
15:99113691:T:C	L304P	0.974
15:99105257:G:C	A20P	0.971
15:99105300:G:C	R34P	0.969
15:99105305:A:G	N36D	0.969
15:99113683:G:C	K301N	0.968
15:99113683:G:T	K301N	0.968

dbSNP variants (sampled 300 via entrez): RS1000075766 (15:99106284 C>G), RS1000119573 (15:99125789 T>C), RS1000350384 (15:99125240 C>T), RS1000426806 (15:99141734 G>C), RS1000621611 (15:99120116 T>A), RS1000678069 (15:99126507 G>A), RS1000789989 (15:99132272 C>G), RS1000864065 (15:99131163 A>G), RS1000995957 (15:99111401 G>A), RS1001037302 (15:99116492 T>G), RS1001194089 (15:99141314 A>G), RS1001260018 (15:99111708 T>A,C), RS1001302160 (15:99141118 A>G), RS1001442934 (15:99111008 A>G), RS1001508772 (15:99121564 T>C)

Disease associations

OMIM: gene MIM:606087 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003391_10	Low high density lipoprotein cholesterol levels	8.000000e-06
GCST004162_1	Carotid plaque burden	7.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0006501	carotid plaque build

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression, increases methylation	6
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	4
bisphenol A	decreases expression	3
sodium arsenite	increases expression	3
entinostat	increases expression, affects cotreatment	2
Acetaminophen	increases expression	2
Air Pollutants	increases abundance, increases oxidation, decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
FR900359	affects phosphorylation	1
bisphenol F	increases expression	1
dicrotophos	increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
trichostatin A	increases expression	1
arsenite	affects binding, decreases reaction	1
potassium chromate(VI)	decreases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
diallyl trisulfide	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
belinostat	decreases expression	1
bisphenol B	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
bisphenol S	increases expression, affects cotreatment	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	decreases expression, affects binding	1
(+)-JQ1 compound	increases expression	1
bisphenol AF	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 induced pluripotent stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_D0MY	TMOi001-A-11	Induced pluripotent stem cell	Female

Clinical trials (associated diseases)

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