SF3A2

Summary

SF3A2 (splicing factor 3a subunit 2, HGNC:10766) is a protein-coding gene on chromosome 19p13.3, encoding Splicing factor 3A subunit 2 (Q15428). Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs. It is a common-essential gene (DepMap: required in 99.9% of cancer cell lines).

This gene encodes subunit 2 of the splicing factor 3a protein complex. The splicing factor 3a heterotrimer includes subunits 1, 2 and 3 and is necessary for the in vitro conversion of 15S U2 snRNP into an active 17S particle that performs pre-mRNA splicing. Subunit 2 interacts with subunit 1 through its amino-terminus while the single zinc finger domain of subunit 2 plays a role in its binding to the 15S U2 snRNP. Subunit 2 may also function independently of its RNA splicing function as a microtubule-binding protein.

Source: NCBI Gene 8175 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 14 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 99.9% of screened cell lines (common-essential)
• MANE Select transcript: NM_007165

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10766
Approved symbol	SF3A2
Name	splicing factor 3a subunit 2
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Aliases	SF3a66, SAP62, PRPF11, Prp11
Ensembl gene	ENSG00000104897
Ensembl biotype	protein_coding
OMIM	600796
Entrez	8175

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 5 retained_intron

ENST00000221494, ENST00000586396, ENST00000587637, ENST00000589118, ENST00000590034, ENST00000592314, ENST00000592839, ENST00000866930, ENST00000866931, ENST00000866932, ENST00000866933, ENST00000911656, ENST00000911657, ENST00000911658

RefSeq mRNA: 1 — MANE Select: NM_007165 NM_007165

CCDS: CCDS12084

Canonical transcript exons

ENST00000221494 — 9 exons

Exon	Start	End
ENSE00000876643	2246882	2247022
ENSE00000876645	2247767	2248655
ENSE00002780869	2236824	2236901
ENSE00003558117	2247594	2247662
ENSE00003703087	2245446	2245555
ENSE00003707385	2244544	2244615
ENSE00003709163	2244733	2244779
ENSE00003710697	2243382	2243544
ENSE00003791536	2246753	2246802

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 97.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 103.4735 / max 556.1774, expressed in 1826 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173053	102.4290	1826
173054	1.0446	627

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	97.73	gold quality
left ovary	UBERON:0002119	97.67	gold quality
right testis	UBERON:0004534	97.65	gold quality
right uterine tube	UBERON:0001302	97.55	gold quality
right ovary	UBERON:0002118	97.42	gold quality
body of uterus	UBERON:0009853	97.42	gold quality
granulocyte	CL:0000094	97.19	gold quality
endocervix	UBERON:0000458	97.18	gold quality
skin of leg	UBERON:0001511	97.10	gold quality
skin of abdomen	UBERON:0001416	97.09	gold quality
ectocervix	UBERON:0012249	97.02	gold quality
lower esophagus mucosa	UBERON:0035834	97.02	gold quality
left uterine tube	UBERON:0001303	97.01	gold quality
ganglionic eminence	UBERON:0004023	96.71	gold quality
mucosa of stomach	UBERON:0001199	96.60	gold quality
nerve	UBERON:0001021	96.57	gold quality
tibial nerve	UBERON:0001323	96.57	gold quality
cortical plate	UBERON:0005343	96.41	gold quality
muscle layer of sigmoid colon	UBERON:0035805	96.37	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.33	gold quality
popliteal artery	UBERON:0002250	96.32	gold quality
tibial artery	UBERON:0007610	96.32	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	96.17	gold quality
small intestine Peyer’s patch	UBERON:0003454	96.15	gold quality
right lobe of thyroid gland	UBERON:0001119	96.10	gold quality
lower esophagus	UBERON:0013473	96.02	gold quality
lower esophagus muscularis layer	UBERON:0035833	96.02	gold quality
aorta	UBERON:0000947	96.01	gold quality
transverse colon	UBERON:0001157	95.96	gold quality
right coronary artery	UBERON:0001625	95.95	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting SF3A2, 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-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-194-3P	97.36	65.96	1027

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.9% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

• SF3a60, 66, and 120, but not SF1, are essential for pre-mRNA splicing (PMID:15647371)
• A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese (PMID:24916648)
• The results indicate that Sf3A2 and Prp31 directly regulate interactions among kinetochores, spindle microtubules and the Ndc80 complex in both Drosophila and human cells. (PMID:30475206)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	sf3a2	ENSDARG00000021107
mus_musculus	Sf3a2	ENSMUSG00000020211
rattus_norvegicus	Sf3a2	ENSRNOG00000019349
drosophila_melanogaster	Sf3a2	FBGN0036314
caenorhabditis_elegans		WBGENE00008683

Protein

Protein identifiers

Splicing factor 3A subunit 2 — Q15428 (reviewed: Q15428)

Alternative names: SF3a66, Spliceosome-associated protein 62

All UniProt accessions (2): Q15428, K7EMT0

UniProt curated annotations — full annotation on UniProt →

Function. Component of the 17S U2 SnRNP complex of the spliceosome, a large ribonucleoprotein complex that removes introns from transcribed pre-mRNAs. The 17S U2 SnRNP complex (1) directly participates in early spliceosome assembly and (2) mediates recognition of the intron branch site during pre-mRNA splicing by promoting the selection of the pre-mRNA branch-site adenosine, the nucleophile for the first step of splicing. Within the 17S U2 SnRNP complex, SF3A2 is part of the SF3A subcomplex that contributes to the assembly of the 17S U2 snRNP, and the subsequent assembly of the pre-spliceosome ‘E’ complex and the pre-catalytic spliceosome ‘A’ complex. Involved in pre-mRNA splicing as a component of pre-catalytic spliceosome ‘B’ complexes, including the Bact complex. Interacts directly with the duplex formed by U2 snRNA and the intron.

Subunit / interactions. Component of the 17S U2 SnRNP complex, a ribonucleoprotein complex that contains small nuclear RNA (snRNA) U2 and a number of specific proteins. Part of the SF3A subcomplex of the 17S U2 SnRNP complex which is composed of three subunits; SF3A3/SAP61, SF3A2/SAP62 and SF3A1/SAP114. SF3A associates with the splicing factor SF3B and a 12S RNA unit to form the mature 17S U2 small nuclear ribonucleoprotein complex (17S U2 snRNP). Identified in the spliceosome ‘E’ complex, a precursor of the spliceosome ‘A’ complex. Identified in the spliceosome ‘A’ and ‘B’ complexes. Identified in the spliceosome ‘C’ complex. Interacts with HTATSF1.

Subcellular location. Nucleus.

Similarity. Belongs to the SF3A2 family.

RefSeq proteins (1): NP_009096* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000690	Matrin/U1-C_Znf_C2H2	Domain
IPR003604	Matrin/U1-like-C_Znf_C2H2	Domain
IPR013087	Znf_C2H2_type	Domain
IPR031781	SF3A2_dom	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR052092	SF3A2	Family

Pfam: PF12874, PF16835

UniProt features (32 total): strand 12, compositionally biased region 5, helix 4, modified residue 3, turn 3, region of interest 2, chain 1, zinc finger region 1, sequence conflict 1

Structure

Experimental structures (PDB)

43 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
7Q4O	ELECTRON MICROSCOPY	2.1
7Q4P	ELECTRON MICROSCOPY	2.15
7EVO	ELECTRON MICROSCOPY	2.5
8H6L	ELECTRON MICROSCOPY	2.6
8H6K	ELECTRON MICROSCOPY	2.7
8HK1	ELECTRON MICROSCOPY	2.7
7VPX	ELECTRON MICROSCOPY	3
8I0R	ELECTRON MICROSCOPY	3
8I0T	ELECTRON MICROSCOPY	3
7ONB	ELECTRON MICROSCOPY	3.1
7QTT	ELECTRON MICROSCOPY	3.1
8H6E	ELECTRON MICROSCOPY	3.2
8H6J	ELECTRON MICROSCOPY	3.25
9ZE2	ELECTRON MICROSCOPY	3.26
6QX9	ELECTRON MICROSCOPY	3.28
6FF4	ELECTRON MICROSCOPY	3.4
8I0P	ELECTRON MICROSCOPY	3.4
9ZE0	ELECTRON MICROSCOPY	3.43
9ZEC	ELECTRON MICROSCOPY	3.61
6AHD	ELECTRON MICROSCOPY	3.8
9ZE3	ELECTRON MICROSCOPY	3.93
9ZED	ELECTRON MICROSCOPY	3.94
8QZS	ELECTRON MICROSCOPY	4.1
8I0S	ELECTRON MICROSCOPY	4.2
8R09	ELECTRON MICROSCOPY	4.3
8R0B	ELECTRON MICROSCOPY	4.4
6FF7	ELECTRON MICROSCOPY	4.5
7ABH	ELECTRON MICROSCOPY	4.5
5Z58	ELECTRON MICROSCOPY	4.9
5Z56	ELECTRON MICROSCOPY	5.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15428-F1	66.33	0.27

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 (3): 10, 153, 1

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-9770562	mRNA Polyadenylation
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-9943411	CHD1 and CHD2 subfamily
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854	Metabolism of RNA

MSigDB gene sets: 173 (showing top): HALMOS_CEBPA_TARGETS_UP, MORF_HDAC1, GOBP_NEUROGENESIS, MAYBURD_RESPONSE_TO_L663536_UP, MODULE_388, MARTINEZ_RB1_TARGETS_UP, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, BLALOCK_ALZHEIMERS_DISEASE_UP, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, MORF_BUB3, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, LIAO_METASTASIS, REACTOME_MRNA_SPLICING

GO Biological Process (7): spliceosomal complex assembly (GO:0000245), mRNA 3’-splice site recognition (GO:0000389), mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397), positive regulation of neuron projection development (GO:0010976), U2-type prespliceosome assembly (GO:1903241), RNA splicing (GO:0008380)

GO Molecular Function (5): RNA binding (GO:0003723), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (9): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U2-type spliceosomal complex (GO:0005684), U2 snRNP (GO:0005686), nuclear speck (GO:0016607), U2-type prespliceosome (GO:0071004), U2-type precatalytic spliceosome (GO:0071005), catalytic step 2 spliceosome (GO:0071013)

Reactome top-level categories

Rollup of top-6 pathways:

Category	Pathways
mRNA Splicing	1
mRNA 3’-end processing	1
Dengue Virus Infection	1
CHD chromatin remodelers	1
Processing of Capped Intron-Containing Pre-mRNA	1
Metabolism of RNA	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
binding	2
spliceosomal complex	2
U2-type spliceosomal complex	2
U1 snRNP	2
U2 snRNP	2
mRNA splicing, via spliceosome	1
protein-RNA complex assembly	1
mRNA splice site recognition	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
mRNA metabolic process	1
regulation of neuron projection development	1
neuron projection development	1
positive regulation of cell projection organization	1
spliceosomal complex assembly	1
nucleic acid binding	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
spliceosomal snRNP complex	1
nuclear ribonucleoprotein granule	1
prespliceosome	1
U4/U6 x U5 tri-snRNP complex	1
precatalytic spliceosome	1
Prp19 complex	1
U5 snRNP	1
catalytic complex	1

Protein interactions and networks

STRING

2193 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SF3A2	SF3A1	Q15459	999
SF3A2	SF3A3	Q12874	999
SF3A2	SF3B1	O75533	974
SF3A2	SF3B2	Q13435	951
SF3A2	SF3B3	Q15393	896
SF3A2	SFSWAP	Q12872	871
SF3A2	SF3B4	Q15427	851
SF3A2	DDX46	Q7L014	835
SF3A2	PHF5A	Q7RTV0	815
SF3A2	SF3B5	Q9BWJ5	807
SF3A2	SNRPA1	P09661	791
SF3A2	RNF113A	O15541	781
SF3A2	SF3B6	Q9Y3B4	676
SF3A2	AMH	P03971	665
SF3A2	PRPF31	Q8WWY3	645

IntAct

252 interactions, top by confidence:

A	B	Type	Score
SF1	U2AF2	psi-mi:“MI:0914”(association)	0.950
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
CSNK1A1	FAM83G	psi-mi:“MI:0914”(association)	0.900
PIK3CB	PIK3R2	psi-mi:“MI:0914”(association)	0.860
SF3A2	SF3A1	psi-mi:“MI:0915”(physical association)	0.800
SMNDC1	SF3B1	psi-mi:“MI:0914”(association)	0.790
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
PIGS	GPAA1	psi-mi:“MI:0914”(association)	0.760
HSPA8	GAK	psi-mi:“MI:0914”(association)	0.760
RBM17	U2SURP	psi-mi:“MI:0914”(association)	0.740
SF3A2	SNRPF	psi-mi:“MI:0915”(physical association)	0.740
SNRPA1	SF3A2	psi-mi:“MI:0915”(physical association)	0.740
SNRPB2	SF3A2	psi-mi:“MI:0915”(physical association)	0.740
CCDC97	SF3B1	psi-mi:“MI:0914”(association)	0.730
PHF5A	SF3B1	psi-mi:“MI:0914”(association)	0.730
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
SF3A2	SNRPB	psi-mi:“MI:0915”(physical association)	0.670
SF3A2	SNRPE	psi-mi:“MI:0915”(physical association)	0.670
SF3A2	SF3B1	psi-mi:“MI:0915”(physical association)	0.670
SF3A2	PHF5A	psi-mi:“MI:0915”(physical association)	0.670
RBM17	SF3A2	psi-mi:“MI:0915”(physical association)	0.670
QPRT	PIK3C2A	psi-mi:“MI:0914”(association)	0.640
SNRPA1	HTATSF1	psi-mi:“MI:0914”(association)	0.640
SF3B1	SAP18	psi-mi:“MI:0914”(association)	0.640

BioGRID (474): SF3A2 (Affinity Capture-MS), SF3A2 (Affinity Capture-MS), SF3A2 (Affinity Capture-MS), SF3A2 (Affinity Capture-MS), AQR (Co-fractionation), BUD31 (Co-fractionation), DDX46 (Co-fractionation), EIF4G1 (Co-fractionation), ISY1-RAB43 (Co-fractionation), ISY1 (Co-fractionation), PRPF19 (Co-fractionation), PRPF31 (Co-fractionation), PRPF4 (Co-fractionation), PSMD3 (Co-fractionation), SF3A1 (Co-fractionation)

ESM2 similar proteins: A2AJK6, A2VDB3, A5PJN8, C5XYW4, F1R5H6, F4NYQ2, G3CHK5, O55000, O60885, O95104, P0CB49, P49750, P51532, P75330, Q06A37, Q08D75, Q10124, Q15428, Q3TKT4, Q4R7I8, Q4V7X9, Q5TM61, Q5ZHZ4, Q62203, Q63623, Q63627, Q66KL9, Q6AXT8, Q6DFF2, Q6DID3, Q6DRG1, Q75N03, Q767K9, Q7TSH6, Q7YR38, Q80W00, Q8CFT2, Q8CGZ0, Q8IWX8, Q8K1P7

Diamond homologs: A5PJN8, Q15428, Q54B65, Q62203, Q6AXT8, Q9P7L8

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
SF3A2	“form complex”	SF3a	binding
SF3A2	“form complex”	“U2 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 153 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
mRNA Splicing - Minor Pathway	23	42.9×	5e-31
Metabolism of non-coding RNA	8	42.3×	2e-10
mRNA Polyadenylation	52	38.1×	4e-70
mRNA Splicing	41	37.5×	4e-54
Transport of Mature Transcript to Cytoplasm	10	31.7×	1e-11
Processing of Capped Intron-Containing Pre-mRNA	45	30.8×	6e-55
mRNA Splicing - Major Pathway	65	29.6×	4e-81
RNA Polymerase II Transcription Termination	16	29.3×	4e-18

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	21	93.0×	6e-37
RNA splicing, via transesterification reactions	13	57.5×	2e-18
negative regulation of mRNA splicing, via spliceosome	9	48.9×	6e-12
spliceosomal snRNP assembly	11	45.3×	4e-14
mRNA cis splicing, via spliceosome	6	42.2×	3e-07
spliceosomal complex assembly	9	38.4×	8e-11
mRNA splicing, via spliceosome	53	34.4×	3e-66
regulation of alternative mRNA splicing, via spliceosome	13	22.5×	2e-12

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1447 predictions. Top by Δscore:

Variant	Effect	Δscore
19:2243370:T:TA	acceptor_gain	1.0000
19:2243371:G:A	acceptor_gain	1.0000
19:2243379:CAGGT:C	acceptor_loss	1.0000
19:2243380:A:AG	acceptor_gain	1.0000
19:2243380:A:C	acceptor_loss	1.0000
19:2243381:G:GG	acceptor_gain	1.0000
19:2243381:GGT:G	acceptor_gain	1.0000
19:2243381:GGTGT:G	acceptor_gain	1.0000
19:2244542:A:AG	acceptor_gain	1.0000
19:2244542:A:G	acceptor_loss	1.0000
19:2244542:AG:A	acceptor_gain	1.0000
19:2244543:G:GA	acceptor_gain	1.0000
19:2244543:GG:G	acceptor_gain	1.0000
19:2244543:GGA:G	acceptor_gain	1.0000
19:2244543:GGAC:G	acceptor_gain	1.0000
19:2244543:GGACC:G	acceptor_gain	1.0000
19:2244776:ACCT:A	donor_gain	1.0000
19:2244777:CCT:C	donor_gain	1.0000
19:2244778:CT:C	donor_gain	1.0000
19:2244778:CTG:C	donor_loss	1.0000
19:2244779:TG:T	donor_loss	1.0000
19:2244780:G:C	donor_loss	1.0000
19:2244780:G:GG	donor_gain	1.0000
19:2244781:TGAG:T	donor_loss	1.0000
19:2245442:GCAG:G	acceptor_loss	1.0000
19:2245443:CA:C	acceptor_loss	1.0000
19:2245444:A:AC	acceptor_loss	1.0000
19:2245444:A:AG	acceptor_gain	1.0000
19:2245444:AG:A	acceptor_gain	1.0000
19:2245444:AGG:A	acceptor_gain	1.0000

AlphaMissense

2989 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:2243441:G:A	G8E	1.000
19:2243446:A:G	K10E	1.000
19:2243452:G:A	G12R	1.000
19:2243452:G:C	G12R	1.000
19:2243452:G:T	G12W	1.000
19:2243453:G:A	G12E	1.000
19:2243458:G:A	G14R	1.000
19:2243458:G:C	G14R	1.000
19:2243459:G:A	G14E	1.000
19:2243462:G:A	G15D	1.000
19:2243468:C:A	A17D	1.000
19:2243489:G:C	R24P	1.000
19:2243494:C:A	R26S	1.000
19:2243494:C:G	R26G	1.000
19:2243494:C:T	R26C	1.000
19:2243495:G:C	R26P	1.000
19:2243497:A:T	R27W	1.000
19:2243498:G:C	R27T	1.000
19:2243498:G:T	R27M	1.000
19:2243499:G:C	R27S	1.000
19:2243499:G:T	R27S	1.000
19:2243500:G:A	E28K	1.000
19:2243503:C:A	R29S	1.000
19:2243503:C:T	R29C	1.000
19:2243504:G:C	R29P	1.000
19:2243506:C:T	L30F	1.000
19:2243507:T:A	L30H	1.000
19:2243507:T:C	L30P	1.000
19:2243509:C:T	R31W	1.000
19:2243510:G:C	R31P	1.000

dbSNP variants (sampled 300 via entrez): RS1000550001 (19:2241422 G>A,T), RS1000622553 (19:2238022 G>C), RS1000720009 (19:2237005 G>C), RS1000948863 (19:2247231 G>A), RS1000979992 (19:2237137 G>A), RS1001228977 (19:2241583 G>A), RS1001282756 (19:2242206 C>T), RS1001289804 (19:2236120 C>G), RS1001514788 (19:2240473 C>A,T), RS1001614100 (19:2245328 C>T), RS1001944209 (19:2240271 G>A), RS1001957098 (19:2240316 C>G), RS1002287157 (19:2237002 C>A,G), RS1002359408 (19:2236739 C>A,G,T), RS1002710351 (19:2235525 A>G)

Disease associations

OMIM: gene MIM:600796 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002475_3	Myocardial infarction	4.000000e-09
GCST003274_10	Pulse pressure	3.000000e-15
GCST010796_4772	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-08
GCST010988_12	Adult body size	1.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005763	pulse pressure measurement
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066159 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	3
bisphenol F	increases expression	2
bisphenol A	decreases expression, increases expression	2
sodium arsenite	decreases expression, increases expression	2
cobaltous chloride	increases expression	2
Cyclosporine	increases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	increases expression	1
FR900359	decreases phosphorylation	1
dicrotophos	increases expression	1
propylparaben	increases expression	1
deoxynivalenol	increases expression	1
lead acetate	increases expression	1
sodium arsenate	increases abundance, increases expression	1
decabromobiphenyl ether	increases expression	1
methylparaben	increases expression	1
tetrabromobisphenol A	increases expression	1
ochratoxin A	decreases expression	1
cupric chloride	increases expression	1
phenanthrene	decreases expression	1
perfluorodecanoic acid	decreases expression	1
hinokiflavone	increases sumoylation	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
hexabrominated diphenyl ether 153	increases expression	1
(+)-JQ1 compound	decreases expression	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652425	Binding	Binding affinity to human SF3A2 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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