SNRPF

Summary

SNRPF (small nuclear ribonucleoprotein polypeptide F, HGNC:11162) is a protein-coding gene on chromosome 12q23.1, encoding Small nuclear ribonucleoprotein F (P62306). Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

Enables RNA binding activity. Involved in spliceosomal snRNP assembly. Located in cytosol and nucleus. Part of several cellular components, including methylosome; nucleus; and pICln-Sm protein complex. Biomarker of nasopharynx carcinoma.

Source: NCBI Gene 6636 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 6 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_003095

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11162
Approved symbol	SNRPF
Name	small nuclear ribonucleoprotein polypeptide F
Location	12q23.1
Locus type	gene with protein product
Status	Approved
Aliases	Sm-F
Ensembl gene	ENSG00000139343
Ensembl biotype	protein_coding
OMIM	603541
Entrez	6636

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 2 retained_intron

ENST00000266735, ENST00000549580, ENST00000551316, ENST00000552085, ENST00000553192, ENST00000929920, ENST00000929921, ENST00000929922

RefSeq mRNA: 2 — MANE Select: NM_003095 NM_001394209, NM_003095

CCDS: CCDS9055

Canonical transcript exons

ENST00000266735 — 4 exons

Exon	Start	End
ENSE00000937646	95865324	95865388
ENSE00001365408	95858952	95859076
ENSE00001365662	95861168	95861293
ENSE00002371573	95866005	95866140

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 97.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 176.2320 / max 3220.7102, expressed in 1822 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
127443	176.2320	1822

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endometrium epithelium	UBERON:0004811	97.24	gold quality
oocyte	CL:0000023	96.61	gold quality
embryo	UBERON:0000922	96.46	gold quality
ganglionic eminence	UBERON:0004023	96.46	gold quality
colonic epithelium	UBERON:0000397	96.32	gold quality
ventricular zone	UBERON:0003053	95.65	gold quality
pharyngeal mucosa	UBERON:0000355	95.42	gold quality
cortical plate	UBERON:0005343	94.70	gold quality
bone marrow	UBERON:0002371	94.31	gold quality
mucosa of transverse colon	UBERON:0004991	93.91	gold quality
oral cavity	UBERON:0000167	93.88	gold quality
pericardium	UBERON:0002407	93.27	gold quality
thymus	UBERON:0002370	93.25	gold quality
body of tongue	UBERON:0011876	93.11	gold quality
mucosa of sigmoid colon	UBERON:0004993	92.87	gold quality
periodontal ligament	UBERON:0008266	92.70	gold quality
esophagus mucosa	UBERON:0002469	92.60	gold quality
colonic mucosa	UBERON:0000317	92.53	gold quality
superior surface of tongue	UBERON:0007371	92.47	gold quality
trabecular bone tissue	UBERON:0002483	92.46	gold quality
bone marrow cell	CL:0002092	92.29	gold quality
lower esophagus mucosa	UBERON:0035834	92.28	gold quality
adenohypophysis	UBERON:0002196	92.25	gold quality
caecum	UBERON:0001153	92.19	gold quality
nipple	UBERON:0002030	92.12	gold quality
vermiform appendix	UBERON:0001154	92.02	gold quality
mammalian vulva	UBERON:0000997	91.95	gold quality
tonsil	UBERON:0002372	91.94	gold quality
endometrium	UBERON:0001295	91.66	gold quality
tongue	UBERON:0001723	91.59	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	64.14
E-CURD-122	yes	17.81
E-GEOD-125970	yes	16.51
E-MTAB-10042	yes	13.39
E-MTAB-9388	no	13.06
E-MTAB-8271	no	9.53
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting SNRPF, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-4427	99.34	70.33	1854
HSA-MIR-5693	99.24	66.67	1106
HSA-MIR-4744	99.01	69.91	1581
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-605-5P	98.79	68.24	1161
HSA-MIR-501-5P	98.77	68.88	1328
HSA-MIR-224-5P	98.33	70.12	1256
HSA-MIR-4457	98.09	67.12	1274

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 100.0% of screened cell lines, common-essential.

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	snrpf	ENSDARG00000105037
mus_musculus	Snrpf	ENSMUSG00000020018
rattus_norvegicus	Snrpf	ENSRNOG00000005556
drosophila_melanogaster	SmF	FBGN0000426
caenorhabditis_elegans		WBGENE00004918

Paralogs (1): LSM6 (ENSG00000164167)

Protein

Protein identifiers

Small nuclear ribonucleoprotein F — P62306 (reviewed: P62306)

Alternative names: Sm protein F

All UniProt accessions (3): P62306, A0A0B4J254, F8W0W6

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes. As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs. As part of the U7 snRNP it is involved in histone 3’-end processing.

Subunit / interactions. Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Most spliceosomal snRNPs contain a common set of Sm proteins, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. Component of the U1 snRNP. The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. Component of the U7 snRNP complex, or U7 Sm protein core complex, that is composed of the U7 snRNA and at least LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF and SNRPG; the complex does not contain SNRPD1 and SNRPD2. Component of the minor spliceosome, which splices U12-type introns. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP. Interacts with GEMIN2 (via N-terminus); the interaction is direct. Interacts with SNRPD2; the interaction is direct. Interacts with SNRPE; the interaction is direct.

Subcellular location. Cytoplasm. Cytosol. Nucleus.

Similarity. Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily.

RefSeq proteins (2): NP_001381138, NP_003086* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR016487	Lsm6/sSmF	Family
IPR034100	Sm_F	Family
IPR047575	Sm	Domain

Pfam: PF01423

UniProt features (12 total): strand 5, helix 2, initiator methionine 1, chain 1, domain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

84 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
4F7U	X-RAY DIFFRACTION	1.9
5XJL	X-RAY DIFFRACTION	2.5
7EVO	ELECTRON MICROSCOPY	2.5
5XJU	X-RAY DIFFRACTION	2.58
8H6L	ELECTRON MICROSCOPY	2.6
8H6K	ELECTRON MICROSCOPY	2.7
8HK1	ELECTRON MICROSCOPY	2.7
8C6J	ELECTRON MICROSCOPY	2.8
9NH5	ELECTRON MICROSCOPY	2.82
9NH6	ELECTRON MICROSCOPY	2.82
6ID1	ELECTRON MICROSCOPY	2.86
7DVQ	ELECTRON MICROSCOPY	2.89
6ID0	ELECTRON MICROSCOPY	2.9
5XJT	X-RAY DIFFRACTION	2.92
6QW6	ELECTRON MICROSCOPY	2.92
6ICZ	ELECTRON MICROSCOPY	3
7VPX	ELECTRON MICROSCOPY	3
8I0R	ELECTRON MICROSCOPY	3
8I0T	ELECTRON MICROSCOPY	3
8I0V	ELECTRON MICROSCOPY	3
9GCL	ELECTRON MICROSCOPY	3
4V98	X-RAY DIFFRACTION	3.1
7QTT	ELECTRON MICROSCOPY	3.1
8Q91	ELECTRON MICROSCOPY	3.1
5XJR	X-RAY DIFFRACTION	3.12
9N96	ELECTRON MICROSCOPY	3.18
6V4X	ELECTRON MICROSCOPY	3.2
8H6E	ELECTRON MICROSCOPY	3.2
8Q7Q	ELECTRON MICROSCOPY	3.2
8RC0	ELECTRON MICROSCOPY	3.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P62306-F1	90.24	0.78

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

23 pathways

ID	Pathway
R-HSA-111367	SLBP independent Processing of Histone Pre-mRNAs
R-HSA-191859	snRNP Assembly
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-72165	mRNA Splicing - Minor Pathway
R-HSA-73856	RNA Polymerase II Transcription Termination
R-HSA-77588	SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs
R-HSA-9754678	SARS-CoV-2 modulates host translation machinery
R-HSA-9770562	mRNA Polyadenylation
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-9943411	CHD1 and CHD2 subfamily
R-HSA-1643685	Disease
R-HSA-194441	Metabolism of non-coding RNA
R-HSA-5663205	Infectious disease
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)
R-HSA-75067	Processing of Capped Intronless Pre-mRNA
R-HSA-8953854	Metabolism of RNA
R-HSA-9679506	SARS-CoV Infections
R-HSA-9694516	SARS-CoV-2 Infection
R-HSA-9705683	SARS-CoV-2-host interactions
R-HSA-9824446	Viral Infection Pathways

MSigDB gene sets: 266 (showing top): BORCZUK_MALIGNANT_MESOTHELIOMA_UP, BASSO_B_LYMPHOCYTE_NETWORK, GCM_NPM1, MATTIOLI_MGUS_VS_PCL, GOBP_NEGATIVE_REGULATION_OF_RNA_SPLICING, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOBP_RNA_METHYLATION, PUJANA_CHEK2_PCC_NETWORK, MODULE_388, WEI_MYCN_TARGETS_WITH_E_BOX, MUELLER_PLURINET, GCM_PSME1, GOBP_SPLICEOSOMAL_TRI_SNRNP_COMPLEX_ASSEMBLY, GOBP_RNA_MODIFICATION

GO Biological Process (7): spliceosomal snRNP assembly (GO:0000387), mRNA splicing, via spliceosome (GO:0000398), RNA splicing (GO:0008380), 7-methylguanosine cap hypermethylation (GO:0036261), U2-type prespliceosome assembly (GO:1903241), mRNA processing (GO:0006397), protein-RNA complex assembly (GO:0022618)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (22): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U5 snRNP (GO:0005682), U7 snRNP (GO:0005683), U2-type spliceosomal complex (GO:0005684), U1 snRNP (GO:0005685), U2 snRNP (GO:0005686), U4 snRNP (GO:0005687), U12-type spliceosomal complex (GO:0005689), cytosol (GO:0005829), small nuclear ribonucleoprotein complex (GO:0030532), methylosome (GO:0034709), pICln-Sm protein complex (GO:0034715), SMN-Sm protein complex (GO:0034719), U4/U6 x U5 tri-snRNP complex (GO:0046540), U2-type precatalytic spliceosome (GO:0071005), U2-type catalytic step 2 spliceosome (GO:0071007), catalytic step 2 spliceosome (GO:0071013), cytoplasm (GO:0005737), Sm-like protein family complex (GO:0120114), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-13 pathways:

Category	Pathways
Metabolism of RNA	3
Processing of Capped Intronless Pre-mRNA	2
mRNA Splicing	2
Metabolism of non-coding RNA	1
RNA Polymerase II Transcription	1
SARS-CoV-2-host interactions	1
mRNA 3’-end processing	1
Dengue Virus Infection	1
CHD chromatin remodelers	1
Disease	1
Processing of Capped Intron-Containing Pre-mRNA	1
Gene expression (Transcription)	1
Viral Infection Pathways	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
spliceosomal snRNP complex	4
cytoplasm	4
cellular anatomical structure	3
spliceosomal complex	3
Sm-like protein family complex	3
RNA processing	2
nuclear protein-containing complex	2
ribonucleoprotein complex	2
U5 snRNP	2
U2-type spliceosomal complex	2
U2 snRNP	2
mRNA splicing, via spliceosome	1
protein-RNA complex assembly	1
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
RNA methylation	1
RNA capping	1
spliceosomal complex assembly	1
mRNA metabolic process	1
ribonucleoprotein complex biogenesis	1
protein-containing complex assembly	1
protein-RNA complex organization	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
small nuclear ribonucleoprotein complex	1
methyltransferase complex	1
SMN complex	1
U4/U6 snRNP	1
spliceosomal tri-snRNP complex	1
U1 snRNP	1
U4/U6 x U5 tri-snRNP complex	1
precatalytic spliceosome	1
U6 snRNP	1
catalytic step 2 spliceosome	1
Prp19 complex	1
catalytic complex	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

3421 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNRPF	SNRPE	P08578	995
SNRPF	SNRPG	P62308	995
SNRPF	SNRPD2	P43330	982
SNRPF	SNRPB	P14678	960
SNRPF	SNRPC	P09234	777
SNRPF	LSM3	P62310	715
SNRPF	SNRPD1	P13641	655
SNRPF	SNRPN	P14648	646
SNRPF	EFTUD2	Q15029	638
SNRPF	SNRNP200	O75643	604
SNRPF	SNRNP70	P08621	597
SNRPF	LSM7	Q9UK45	589
SNRPF	CRNKL1	Q9BZJ0	588
SNRPF	SF3B3	Q15393	585
SNRPF	SNW1	Q13573	581

IntAct

239 interactions, top by confidence:

A	B	Type	Score
SMN1	GEMIN2	psi-mi:“MI:0914”(association)	0.960
SNRPE	SNRPF	psi-mi:“MI:0915”(physical association)	0.940
IFIT1	IFIT3	psi-mi:“MI:0914”(association)	0.920
GEMIN2	SNRPF	psi-mi:“MI:0915”(physical association)	0.910
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
SNRPF	SNRPD2	psi-mi:“MI:0915”(physical association)	0.890
SNRPF	LSM5	psi-mi:“MI:0915”(physical association)	0.880
LSM5	SNRPF	psi-mi:“MI:0915”(physical association)	0.880
SNRPF	COIL	psi-mi:“MI:0915”(physical association)	0.830
COIL	SNRPF	psi-mi:“MI:0915”(physical association)	0.830
SNRPB	SNRNP70	psi-mi:“MI:0915”(physical association)	0.830
CLNS1A	PRMT5	psi-mi:“MI:0914”(association)	0.830
GEMIN6	SNRPF	psi-mi:“MI:0407”(direct interaction)	0.810
IFIT2	IFIT3	psi-mi:“MI:0914”(association)	0.780
CLNS1A	SNRPE	psi-mi:“MI:0914”(association)	0.770
CLNS1A	SNRPE	psi-mi:“MI:0915”(physical association)	0.770
GEMIN2	SNRPE	psi-mi:“MI:0914”(association)	0.770

BioGRID (674): COIL (Two-hybrid), HOMER3 (Two-hybrid), IKZF1 (Two-hybrid), LSM5 (Two-hybrid), LNX1 (Two-hybrid), SNRPF (Affinity Capture-MS), SNRPF (Affinity Capture-MS), SNRPF (Affinity Capture-MS), SNRPF (Affinity Capture-MS), SNRPF (Two-hybrid), SNRPD1 (Co-fractionation), SNRPE (Co-fractionation), SNRPF (Co-fractionation), SNRPF (Co-fractionation), SNRPF (Co-fractionation)

ESM2 similar proteins: A5GFZ5, A8MWD9, C9WPN6, O35900, O60762, O70152, P02362, P50894, P62084, P62306, P62307, P62308, P62309, P62310, P62311, P62314, P62315, P62318, P62320, P62321, P62323, P62487, P62488, P62489, P82931, Q16576, Q1JQ93, Q24572, Q2TBV5, Q2VIR3, Q32PE9, Q3SWX8, Q3T0Z8, Q3ZBL0, Q3ZC10, Q4R304, Q4R5F6, Q5E9B8, Q5ZMS3, Q60973

Diamond homologs: A1CE19, A1DM27, A4RQ29, A5DRQ6, A6R363, A6S5C9, A6ZYX7, A7F5M4, A7TK72, A7UXE4, A8NHT8, B0DWN3, C6A1T2, O22823, O26745, O59734, P0CR24, P0CR25, P34659, P54999, P62306, P62307, P62312, P62313, P62321, Q06406, Q0UWI9, Q0W8R9, Q1DRN0, Q1H595, Q24297, Q2HAN0, Q3T0Z8, Q465S1, Q4PG71, Q4WNI0, Q54TF6, Q54XP2, Q552U1, Q6BR90

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
SNRPF	“form complex”	“U4/U6.U5 snRNP complex”	binding
SNRPF	“form complex”	“U2 snRNP complex”	binding
SNRPF	“form complex”	“U1 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 134 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
Metabolism of non-coding RNA	7	40.4×	8e-09
mRNA Splicing	28	27.9×	2e-31
mRNA Splicing - Minor Pathway	11	22.4×	7e-11
Processing of Capped Intron-Containing Pre-mRNA	29	21.7×	3e-29
mRNA Splicing - Major Pathway	39	19.4×	6e-38
snRNP Assembly	10	19.2×	4e-09
mRNA Polyadenylation	24	19.2×	1e-22
CHD1 and CHD2 subfamily	17	16.8×	7e-15

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	14	68.3×	6e-21
spliceosomal snRNP assembly	14	63.6×	2e-20
spliceosomal complex assembly	10	47.0×	7e-13
spliceosomal tri-snRNP complex assembly	5	43.9×	6e-06
RNA splicing, via transesterification reactions	8	39.0×	2e-09
regulation of mRNA splicing, via spliceosome	5	34.6×	2e-05
mRNA splicing, via spliceosome	36	25.8×	2e-38
RNA splicing	20	13.8×	3e-15

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

2315 predictions. Top by Δscore:

Variant	Effect	Δscore
12:95859075:TGG:T	donor_loss	1.0000
12:95859076:GGTA:G	donor_loss	1.0000
12:95859077:G:C	donor_loss	1.0000
12:95859077:G:GG	donor_gain	1.0000
12:95861166:A:AG	acceptor_gain	1.0000
12:95861166:AG:A	acceptor_loss	1.0000
12:95861167:G:GA	acceptor_loss	1.0000
12:95861167:G:GG	acceptor_gain	1.0000
12:95861167:GA:G	acceptor_gain	1.0000
12:95861167:GAGT:G	acceptor_gain	1.0000
12:95865318:T:A	acceptor_gain	1.0000
12:95865322:A:G	acceptor_gain	1.0000
12:95867185:CCCAA:C	acceptor_gain	1.0000
12:95867186:CCAA:C	acceptor_gain	1.0000
12:95867186:CCAAC:C	acceptor_gain	1.0000
12:95867187:CAA:C	acceptor_gain	1.0000
12:95867187:CAAC:C	acceptor_gain	1.0000
12:95867188:AA:A	acceptor_gain	1.0000
12:95867188:AACTG:A	acceptor_loss	1.0000
12:95867189:ACTGA:A	acceptor_loss	1.0000
12:95867190:C:CC	acceptor_gain	1.0000
12:95867190:CTGAA:C	acceptor_loss	1.0000
12:95869475:CAAA:C	donor_loss	1.0000
12:95869476:AAACC:A	donor_loss	1.0000
12:95869477:AACC:A	donor_loss	1.0000
12:95869478:A:T	donor_loss	1.0000
12:95869571:AACC:A	acceptor_loss	1.0000
12:95869574:C:CC	acceptor_gain	1.0000
12:95869574:CTGT:C	acceptor_loss	1.0000
12:95869575:T:A	acceptor_loss	1.0000

AlphaMissense

562 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:95861237:T:A	W25R	1.000
12:95861237:T:C	W25R	1.000
12:95861249:T:C	Y29H	1.000
12:95861255:G:C	G31R	1.000
12:95861255:G:T	G31C	1.000
12:95861256:G:T	G31V	1.000
12:95861262:T:C	L33P	1.000
12:95861267:T:C	S35P	1.000
12:95861273:G:C	D37H	1.000
12:95861274:A:T	D37V	1.000
12:95865325:T:A	L44H	1.000
12:95865325:T:C	L44P	1.000
12:95865388:G:C	R65T	1.000
12:95865388:G:T	R65M	1.000
12:95866014:T:A	N68K	1.000
12:95866014:T:G	N68K	1.000
12:95861196:T:A	L11H	0.999
12:95861196:T:C	L11P	0.999
12:95861205:T:C	L14P	0.999
12:95861211:G:T	G16V	0.999
12:95861220:T:A	V19E	0.999
12:95861226:T:A	V21E	0.999
12:95861232:T:A	L23H	0.999
12:95861232:T:C	L23P	0.999
12:95861234:A:G	K24E	0.999
12:95861235:A:T	K24M	0.999
12:95861236:G:C	K24N	0.999
12:95861236:G:T	K24N	0.999
12:95861239:G:C	W25C	0.999
12:95861239:G:T	W25C	0.999

dbSNP variants (sampled 300 via entrez): RS1000265940 (12:95858421 T>C), RS1000296302 (12:95865151 A>G), RS1000324323 (12:95864815 A>C,T), RS1000396755 (12:95861247 A>C), RS1000569604 (12:95859902 A>G), RS1000637566 (12:95858751 T>C,G), RS1001143592 (12:95862616 C>G), RS1001206146 (12:95857710 A>G), RS1001242670 (12:95857419 C>T), RS1001258530 (12:95857952 G>A), RS1001675955 (12:95857140 G>A), RS1002430977 (12:95863528 A>G), RS1002766886 (12:95863862 T>C), RS1002924121 (12:95859051 T>G), RS1004609904 (12:95857712 A>T)

Disease associations

OMIM: gene MIM:603541 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST007430_123	Peak expiratory flow	2.000000e-12
GCST007431_117	Lung function (FEV1/FVC)	1.000000e-46
GCST007692_69	Chronic obstructive pulmonary disease	3.000000e-09
GCST010002_220	Refractive error	1.000000e-19
GCST011816_7	Vitamin C levels	2.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0009718	peak expiratory flow
EFO:0004713	FEV/FVC ratio
EFO:0600003	vitamin C measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067167 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	5
bisphenol A	affects expression, decreases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
Cadmium	increases abundance, increases expression, decreases expression	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment	2
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
arsenite	affects binding, increases reaction	1
cobaltous chloride	decreases expression	1
ochratoxin A	affects cotreatment, decreases expression	1
yessotoxin	decreases expression	1
S 1 (combination)	increases response to substance	1
CD 437	decreases expression	1
chloropicrin	increases expression	1
corosolic acid	increases expression	1
K 7174	decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	decreases expression	1
3-(4’-hydroxy-3’-adamantylbiphenyl-4-yl)acrylic acid	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
PP242	decreases expression	1
bisphenol AF	increases expression	1
Irinotecan	increases response to substance	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	increases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652981	Binding	Binding affinity to human SNRPF 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.