SNRPA1

Summary

SNRPA1 (small nuclear ribonucleoprotein polypeptide A’, HGNC:11152) is a protein-coding gene on chromosome 15q26.3, encoding U2 small nuclear ribonucleoprotein A’ (P09661). Involved in pre-mRNA splicing as component of the spliceosome. It is a common-essential gene (DepMap: required in 100.0% of cancer cell lines).

Enables RNA binding activity. Involved in mRNA splicing, via spliceosome and spermatogenesis. Located in nuclear speck. Part of U2-type catalytic step 2 spliceosome and U2-type precatalytic spliceosome. Implicated in connective tissue disease.

Source: NCBI Gene 6627 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 38 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• Cancer dependency (DepMap): dependent in 100.0% of screened cell lines (common-essential)
• MANE Select transcript: NM_003090

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11152
Approved symbol	SNRPA1
Name	small nuclear ribonucleoprotein polypeptide A'
Location	15q26.3
Locus type	gene with protein product
Status	Approved
Aliases	Lea1, U2A'
Ensembl gene	ENSG00000131876
Ensembl biotype	protein_coding
OMIM	603521
Entrez	6627

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 8 protein_coding, 6 retained_intron, 5 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000254193, ENST00000394082, ENST00000540017, ENST00000558020, ENST00000558036, ENST00000558059, ENST00000559309, ENST00000559686, ENST00000560307, ENST00000560383, ENST00000560433, ENST00000560496, ENST00000560856, ENST00000560987, ENST00000561187, ENST00000916942, ENST00000916943, ENST00000916944, ENST00000916945, ENST00000949749

RefSeq mRNA: 1 — MANE Select: NM_003090 NM_003090

CCDS: CCDS10391

Canonical transcript exons

ENST00000254193 — 9 exons

Exon	Start	End
ENSE00001618359	101281510	101281782
ENSE00002560508	101295097	101295248
ENSE00003458255	101286908	101287010
ENSE00003546798	101284967	101285060
ENSE00003562637	101286214	101286293
ENSE00003582908	101291962	101292040
ENSE00003608227	101293025	101293172
ENSE00003610959	101287656	101287702
ENSE00003614409	101285726	101285801

Expression profiles

Bgee: expression breadth ubiquitous, 141 present calls, max score 96.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 33.4205 / max 236.6490, expressed in 1813 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
151820	32.6183	1813
151821	0.7581	454
151819	0.0354	6
207678	0.0088	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	96.41	gold quality
skin of leg	UBERON:0001511	96.38	gold quality
zone of skin	UBERON:0000014	96.32	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.32	gold quality
skin of abdomen	UBERON:0001416	96.31	gold quality
lymph node	UBERON:0000029	96.26	gold quality
right testis	UBERON:0004534	96.19	gold quality
tonsil	UBERON:0002372	96.08	gold quality
testis	UBERON:0000473	96.04	gold quality
bone marrow	UBERON:0002371	95.99	gold quality
spleen	UBERON:0002106	95.90	gold quality
monocyte	CL:0000576	95.82	gold quality
mucosa of transverse colon	UBERON:0004991	95.78	gold quality
vermiform appendix	UBERON:0001154	95.60	gold quality
leukocyte	CL:0000738	95.51	gold quality
thoracic mammary gland	UBERON:0005200	95.50	gold quality
mammary gland	UBERON:0001911	95.49	gold quality
small intestine Peyer’s patch	UBERON:0003454	95.49	gold quality
tibial nerve	UBERON:0001323	95.41	gold quality
right lung	UBERON:0002167	95.39	gold quality
left ovary	UBERON:0002119	95.27	gold quality
rectum	UBERON:0001052	95.23	gold quality
small intestine	UBERON:0002108	95.21	gold quality
ectocervix	UBERON:0012249	95.20	gold quality
minor salivary gland	UBERON:0001830	95.19	gold quality
vagina	UBERON:0000996	95.18	gold quality
left uterine tube	UBERON:0001303	95.15	gold quality
right ovary	UBERON:0002118	95.13	gold quality
right uterine tube	UBERON:0001302	95.07	gold quality
cerebellar cortex	UBERON:0002129	95.07	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-13	yes	20.15
E-HCAD-4	yes	19.23
E-ANND-3	yes	7.78
E-MTAB-6911	no	402.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting SNRPA1, 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-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-4760-5P	99.80	69.88	1619
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-8061	99.63	69.44	1411
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-4696	99.48	67.48	1040
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-3674	97.01	68.86	1171
HSA-MIR-4436B-5P	96.71	68.37	1346
HSA-MIR-4512	95.26	63.08	371
HSA-MIR-3174	94.63	63.64	577

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 8)

• PMID:10811961 pertains mostly to salmon, but has some reference to human. (PMID:10811961)
• Data suggest that protein-protein interactions localize U2A’ (SNRPA1) to the U2 snRNP (U2 small nuclear ribonucleoprotein) and exclude it from the U1 snRNP, rather than to enhance U2 snRNA (U2 small nuclear RNA; RNU2-1) binding of U2B’’ (SNRPB2). (PMID:24866816)
• Data suggest that SNRPA1, SNRPD1, and PNN are key players in the regulation of pluripotency-specific spliceosome assembly and the acquisition and maintenance of pluripotency. (PMID:28595116)
• These novel findings identified new roles played by SNRPA1 in the progression of colorectal cancer. (PMID:31203132)
• Identification of RNA-binding protein SNRPA1 for prognosis in prostate cancer. (PMID:33460399)
• A prometastatic splicing program regulated by SNRPA1 interactions with structured RNA elements. (PMID:33986153)
• Splicing factor SNRPA associated with microvascular invasion promotes hepatocellular carcinoma metastasis through activating NOTCH1/Snail pathway and is mediated by circSEC62/miR-625-5p axis. (PMID:36715182)
• High SNRPA1 expression leads to poor prognosis in patients with lung adenocarcinoma. (PMID:37277111)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	snrpa1	ENSDARG00000024651
mus_musculus	Snrpa1	ENSMUSG00000030512
rattus_norvegicus	Snrpa1	ENSRNOG00000011932
drosophila_melanogaster	U2A	FBGN0033210
caenorhabditis_elegans		WBGENE00003390

Paralogs (2): LRMDA (ENSG00000148655), LRRC72 (ENSG00000205858)

Protein

Protein identifiers

U2 small nuclear ribonucleoprotein A’ — P09661 (reviewed: P09661)

All UniProt accessions (4): P09661, H0YKK0, H0YLR3, H0YMA0

UniProt curated annotations — full annotation on UniProt →

Function. Involved in pre-mRNA splicing as component of the spliceosome. Associated with sn-RNP U2, where it contributes to the binding of stem loop IV of U2 snRNA.

Subunit / interactions. Identified in the spliceosome B complex. Identified in the spliceosome C complex. Found in a pre-mRNA splicing complex with SFRS4, SFRS5, SNRNP70, SNRPA1, SRRM1 and SRRM2. Found in a pre-mRNA exonic splicing enhancer (ESE) complex with SNRNP70, SNRPA1, SRRM1 and TRA2B. Contributes to the binding of stem loop IV of U2 snRNA with SNRPB2.

Subcellular location. Nucleus.

Similarity. Belongs to the U2 small nuclear ribonucleoprotein A family.

RefSeq proteins (1): NP_003081* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR003603	U2A’_phosphoprotein32A_C	Domain
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR044640	RU2A	Family

Pfam: PF14580

UniProt features (40 total): helix 8, mutagenesis site 7, strand 7, modified residue 5, repeat 4, cross-link 2, region of interest 2, initiator methionine 1, chain 1, sequence conflict 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

50 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
1A9N	X-RAY DIFFRACTION	2.38
7EVO	ELECTRON MICROSCOPY	2.5
8H6L	ELECTRON MICROSCOPY	2.6
8H6K	ELECTRON MICROSCOPY	2.7
8HK1	ELECTRON MICROSCOPY	2.7
8C6J	ELECTRON MICROSCOPY	2.8
6ID1	ELECTRON MICROSCOPY	2.86
6ID0	ELECTRON MICROSCOPY	2.9
6ICZ	ELECTRON MICROSCOPY	3
7VPX	ELECTRON MICROSCOPY	3
8I0R	ELECTRON MICROSCOPY	3
8I0T	ELECTRON MICROSCOPY	3
8I0V	ELECTRON MICROSCOPY	3
8H6E	ELECTRON MICROSCOPY	3.2
8H6J	ELECTRON MICROSCOPY	3.25
6QX9	ELECTRON MICROSCOPY	3.28
6QDV	ELECTRON MICROSCOPY	3.3
8I0U	ELECTRON MICROSCOPY	3.3
9FMD	ELECTRON MICROSCOPY	3.3
8I0P	ELECTRON MICROSCOPY	3.4
8I0W	ELECTRON MICROSCOPY	3.4
5XJC	ELECTRON MICROSCOPY	3.6
7W59	ELECTRON MICROSCOPY	3.6
7W5A	ELECTRON MICROSCOPY	3.6
6AHD	ELECTRON MICROSCOPY	3.8
5YZG	ELECTRON MICROSCOPY	4.1
8QZS	ELECTRON MICROSCOPY	4.1
8I0S	ELECTRON MICROSCOPY	4.2
7W5B	ELECTRON MICROSCOPY	4.3
8R09	ELECTRON MICROSCOPY	4.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P09661-F1	88.28	0.70

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 (7): 172, 178, 197, 236, 255, 172, 221

Mutagenesis-validated functional residues (7):

Position	Phenotype
15	results in defective spliceosome assembly.
27	no change in spliceosome assembly.
68	no change in spliceosome assembly.
72	no change in spliceosome assembly.
73	no change in spliceosome assembly.
92	results in defective spliceosome assembly.
148	results in defective spliceosome assembly.

Function

Pathways and Gene Ontology

Reactome pathways

13 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-8950505	Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation
R-HSA-9770562	mRNA Polyadenylation
R-HSA-9918481	Dengue Virus-Host Interactions
R-HSA-9943411	CHD1 and CHD2 subfamily
R-HSA-1280215	Cytokine Signaling in Immune system
R-HSA-168256	Immune System
R-HSA-447115	Interleukin-12 family signaling
R-HSA-449147	Signaling by Interleukins
R-HSA-72172	mRNA Splicing
R-HSA-72203	Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854	Metabolism of RNA
R-HSA-9020591	Interleukin-12 signaling

MSigDB gene sets: 253 (showing top): TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, CROONQUIST_NRAS_SIGNALING_DN, GCM_NPM1, MORF_UBE2N, GOBP_MALE_GAMETE_GENERATION, MODULE_16, PATIL_LIVER_CANCER, PUJANA_CHEK2_PCC_NETWORK, CHANG_IMMORTALIZED_BY_HPV31_DN, MODULE_388, BROWNE_HCMV_INFECTION_24HR_UP, MORF_SKP1A, GCM_PSME1, ONKEN_UVEAL_MELANOMA_UP

GO Biological Process (5): mRNA splicing, via spliceosome (GO:0000398), spermatogenesis (GO:0007283), RNA splicing (GO:0008380), U2-type prespliceosome assembly (GO:1903241), mRNA processing (GO:0006397)

GO Molecular Function (3): RNA binding (GO:0003723), U2 snRNA binding (GO:0030620), protein binding (GO:0005515)

GO Cellular Component (12): nucleus (GO:0005634), nucleoplasm (GO:0005654), spliceosomal complex (GO:0005681), U2-type spliceosomal complex (GO:0005684), U2 snRNP (GO:0005686), nuclear body (GO:0016604), nuclear speck (GO:0016607), small nuclear ribonucleoprotein complex (GO:0030532), U2-type precatalytic spliceosome (GO:0071005), U2-type catalytic step 2 spliceosome (GO:0071007), catalytic step 2 spliceosome (GO:0071013), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-11 pathways:

Category	Pathways
mRNA Splicing	1
Interleukin-12 signaling	1
mRNA 3’-end processing	1
Dengue Virus Infection	1
CHD chromatin remodelers	1
Immune System	1
Signaling by Interleukins	1
Cytokine Signaling in Immune system	1
Processing of Capped Intron-Containing Pre-mRNA	1
Metabolism of RNA	1
Interleukin-12 family signaling	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
nuclear protein-containing complex	2
ribonucleoprotein complex	2
spliceosomal complex	2
U2-type spliceosomal complex	2
U2 snRNP	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
developmental process involved in reproduction	1
male gamete generation	1
spliceosomal complex assembly	1
mRNA metabolic process	1
nucleic acid binding	1
snRNA binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
spliceosomal snRNP complex	1
nucleoplasm	1
intracellular membraneless organelle	1
nuclear ribonucleoprotein granule	1
Sm-like protein family 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
U5 snRNP	1
catalytic complex	1
protein-containing complex	1

Protein interactions and networks

STRING

3102 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNRPA1	SNRPB2	P08579	997
SNRPA1	SNRPA	P09012	871
SNRPA1	SF3A3	Q12874	853
SNRPA1	SF3B3	Q15393	847
SNRPA1	SNRPC	P09234	819
SNRPA1	SF3A2	Q15428	791
SNRPA1	SF3B1	O75533	790
SNRPA1	SF3A1	Q15459	783
SNRPA1	SNRPD3	P43331	782
SNRPA1	SF3B4	Q15427	762
SNRPA1	XAB2	Q9HCS7	746
SNRPA1	U2AF2	P26368	739
SNRPA1	SF3B2	Q13435	730
SNRPA1	SNRNP70	P08621	694
SNRPA1	EFTUD2	Q15029	666

IntAct

190 interactions, top by confidence:

A	B	Type	Score
IFIT1	IFIT3	psi-mi:“MI:0914”(association)	0.920
SNRPB2	SNRPA1	psi-mi:“MI:0915”(physical association)	0.910
SNRPA1	SNRPB2	psi-mi:“MI:0915”(physical association)	0.910
SNRPA1	SNRPA	psi-mi:“MI:0915”(physical association)	0.830
SNRPA	SNRPA1	psi-mi:“MI:0915”(physical association)	0.830
IFIT2	IFIT3	psi-mi:“MI:0914”(association)	0.780
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
SNRPA1	SF3A2	psi-mi:“MI:0915”(physical association)	0.740
SNRPF	SNRPA1	psi-mi:“MI:0915”(physical association)	0.740
PHF5A	SF3B1	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SNRPD2	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPA1	XAB2	psi-mi:“MI:0407”(direct interaction)	0.690
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
SNRPA1	HTATSF1	psi-mi:“MI:0914”(association)	0.640
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
SF3B1	SAP18	psi-mi:“MI:0914”(association)	0.640
SNRPA1	U2SURP	psi-mi:“MI:0914”(association)	0.640
SNRPB	SART1	psi-mi:“MI:0914”(association)	0.640
TOP1	HNRNPR	psi-mi:“MI:0914”(association)	0.600

BioGRID (567): SNRPA1 (Affinity Capture-MS), SNRPA1 (Two-hybrid), SNRPA1 (Affinity Capture-RNA), SNRPA1 (Affinity Capture-MS), SNRPA1 (Affinity Capture-MS), SNRPA1 (Affinity Capture-MS), SNRPA1 (Affinity Capture-MS), SNRPA1 (Affinity Capture-MS), SF3B3 (Affinity Capture-MS), SF3B1 (Affinity Capture-MS), TOE1 (Affinity Capture-MS), GEMIN5 (Affinity Capture-MS), SF3B2 (Affinity Capture-MS), HTATSF1 (Affinity Capture-MS), ICE2 (Affinity Capture-MS)

ESM2 similar proteins: A0A096MJZ0, D0MYB4, O35125, O94489, P09661, P0C895, P11745, P22194, P36047, P41391, P43333, P45969, P57784, Q05A62, Q08963, Q15435, Q28G94, Q2KID4, Q32PL1, Q3T0W4, Q3UM45, Q4LDG9, Q4P5F9, Q4R8Y8, Q4V8D9, Q4WV66, Q54Q39, Q5BGW9, Q5FVQ9, Q5HZV9, Q5RFS7, Q5U378, Q5U508, Q641R9, Q6BT60, Q6C417, Q6DHB1, Q6DIQ3, Q6GPJ5, Q7S9P4

Diamond homologs: A6H759, A6NJI9, P09661, P57784, Q4R8Y8, B6CZ40, B6CZ45, B6CZ54, B6CZ61, O35125, O43822, P34390, Q16RY9, Q28CU0, Q32KP2, Q4V8C9, Q53EV4, Q5EAD8, Q7PK92, Q8IYG6, Q8K375, Q96E66, Q9DAK8, A0A1L8G016, B3DH20, Q09JZ4, Q28FY0, Q6AYH9, Q8CDN9, P43333, Q6NRC9, Q6ZRR7, Q9BLB6, Q3SZC6, Q4P5F9, Q4WV66, Q5A449, Q5BGW9, Q6A1I3, Q6BT60

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SNRPA1	“form complex”	“U2 snRNP complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 177 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	9	43.9×	7e-12
mRNA Splicing	35	29.6×	6e-41
Processing of Capped Intron-Containing Pre-mRNA	38	24.0×	6e-41
mRNA Splicing - Minor Pathway	13	22.4×	7e-13
mRNA Polyadenylation	33	22.3×	4e-34
mRNA Splicing - Major Pathway	46	19.3×	4e-45
snRNP Assembly	11	17.9×	1e-09
CHD1 and CHD2 subfamily	21	17.6×	7e-19

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	16	64.0×	8e-24
spliceosomal snRNP assembly	11	41.0×	3e-13
mRNA cis splicing, via spliceosome	6	38.1×	7e-07
spliceosomal complex assembly	9	34.7×	5e-10
regulation of mRNA splicing, via spliceosome	5	28.4×	6e-05
RNA splicing, via transesterification reactions	7	28.0×	5e-07
NLS-bearing protein import into nucleus	5	25.7×	9e-05
mRNA splicing, via spliceosome	40	23.5×	4e-41

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1545 predictions. Top by Δscore:

Variant	Effect	Δscore
15:101286212:A:AC	donor_gain	1.0000
15:101286213:C:CC	donor_gain	1.0000
15:101286903:CT:C	donor_loss	1.0000
15:101286904:TT:T	donor_loss	1.0000
15:101286905:T:TG	donor_loss	1.0000
15:101286906:A:AC	donor_gain	1.0000
15:101286906:AC:A	donor_loss	1.0000
15:101286907:C:CC	donor_gain	1.0000
15:101287009:TA:T	acceptor_gain	1.0000
15:101287011:C:CC	acceptor_gain	1.0000
15:101293021:GT:G	donor_loss	1.0000
15:101293022:TA:T	donor_loss	1.0000
15:101293023:A:AC	donor_gain	1.0000
15:101293024:C:CA	donor_loss	1.0000
15:101293024:C:CC	donor_gain	1.0000
15:101293169:TACC:T	acceptor_gain	1.0000
15:101293170:ACCC:A	acceptor_loss	1.0000
15:101293171:CC:C	acceptor_gain	1.0000
15:101293171:CCCTA:C	acceptor_gain	1.0000
15:101293172:CC:C	acceptor_gain	1.0000
15:101293173:C:CC	acceptor_gain	1.0000
15:101293173:CTAT:C	acceptor_loss	1.0000
15:101293174:T:A	acceptor_loss	1.0000
15:101293180:A:AC	acceptor_gain	1.0000
15:101293180:A:C	acceptor_gain	1.0000
15:101295092:CTCA:C	donor_loss	1.0000
15:101295093:TCACC:T	donor_loss	1.0000
15:101295094:CACC:C	donor_loss	1.0000
15:101295095:A:AC	donor_gain	1.0000
15:101295095:AC:A	donor_gain	1.0000

AlphaMissense

1652 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:101285005:A:G	L224P	1.000
15:101285017:A:G	L220P	1.000
15:101285044:G:T	A211D	1.000
15:101285045:C:G	A211P	1.000
15:101285053:A:T	I208K	1.000
15:101285057:C:G	A207P	1.000
15:101285730:A:C	I204S	1.000
15:101285730:A:T	I204N	1.000
15:101286268:A:G	F162S	1.000
15:101286280:G:T	A158E	1.000
15:101286281:C:G	A158P	1.000
15:101286289:C:G	R155P	1.000
15:101286290:G:T	R155S	1.000
15:101286918:A:T	V150E	1.000
15:101286926:G:C	F147L	1.000
15:101286926:G:T	F147L	1.000
15:101286928:A:G	F147L	1.000
15:101286930:T:A	D146V	1.000
15:101286931:C:G	D146H	1.000
15:101286933:A:G	L145P	1.000
15:101286971:T:A	R132S	1.000
15:101286971:T:G	R132S	1.000
15:101286972:C:A	R132I	1.000
15:101286972:C:G	R132T	1.000
15:101286998:A:C	N123K	1.000
15:101286998:A:T	N123K	1.000
15:101287010:A:C	S119R	1.000
15:101287010:A:T	S119R	1.000
15:101287657:T:G	S119R	1.000
15:101287659:A:G	L118P	1.000

dbSNP variants (sampled 300 via entrez): RS1000008826 (15:101295209 A>G,T), RS1000410584 (15:101287814 ACT>A), RS1000597095 (15:101283702 T>C), RS1000672047 (15:101282514 T>C,G), RS1000687369 (15:101294307 T>C,G), RS1000914421 (15:101289688 T>G), RS1000915673 (15:101295385 T>C,G), RS1001011237 (15:101284182 T>C), RS1001513851 (15:101290024 G>A,T), RS1001919743 (15:101284795 C>G,T), RS1002236005 (15:101294914 T>G), RS1002265370 (15:101284454 C>G,T), RS1002284347 (15:101284102 C>A), RS1002311868 (15:101295403 T>G), RS1002337256 (15:101289115 T>G)

Disease associations

OMIM: gene MIM:603521 | 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
GCST002183_3	Relative hand skill in reading disability	9.000000e-09
GCST004748_29	Lung cancer	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009902	handedness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066166 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL1232461	MOLIBRESIB	2	1,538

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

ChEMBL bioactivities

3 potent at pChembl≥5 of 3 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.96	Kd	108.3	nM	CHEMBL5653589
6.96	ED50	108.3	nM	CHEMBL5653589
6.05	IC50	890	nM	MOLIBRESIB

PubChem BioAssay actives

2 with measured affinity, of 8 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149455: Binding affinity to human SNRPA1 incubated for 45 mins by Kinobead based pull down assay	kd	0.1084	uM
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2178713: Inhibition of SNRPA1 (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	ic50	0.8900	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression	3
trichostatin A	affects cotreatment, increases expression	3
sodium arsenite	decreases expression, increases abundance, increases expression	2
2,2’,4,4’-tetrabromodiphenyl ether	increases expression, decreases expression	2
Air Pollutants	increases expression, decreases expression, increases abundance	2
Smoke	decreases expression, increases abundance, increases expression	2
Valproic Acid	decreases expression, decreases methylation	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	increases phosphorylation	1
dicrotophos	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression	1
decabromobiphenyl ether	decreases expression	1
beta-lapachone	increases expression, decreases expression	1
arsenite	affects binding, increases reaction	1
perfluorooctanoic acid	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
pentabromodiphenyl ether	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
bromovanin	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
NSC 689534	increases expression, affects binding, decreases expression	1
bisphenol AF	increases expression	1
Irinotecan	decreases expression, affects cotreatment, affects response to substance	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants, Occupational	affects expression	1
Ethanol	affects cotreatment, increases expression	1
Arsenic	increases abundance, increases 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
CHEMBL5652497	Binding	Binding affinity to human SNRPA1 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.