HNRNPA3

Summary

HNRNPA3 (heterogeneous nuclear ribonucleoprotein A3, HGNC:24941) is a protein-coding gene on chromosome 2q31.2, encoding Heterogeneous nuclear ribonucleoprotein A3 (P51991). Plays a role in cytoplasmic trafficking of RNA.

Enables RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Located in nucleus. Part of catalytic step 2 spliceosome.

Source: NCBI Gene 220988 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 36 total
• Druggable target: yes
• MANE Select transcript: NM_194247

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24941
Approved symbol	HNRNPA3
Name	heterogeneous nuclear ribonucleoprotein A3
Location	2q31.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000170144
Ensembl biotype	protein_coding
OMIM	605372
Entrez	220988

Gene structure

Transcript identifiers

Ensembl transcripts: 107 — 99 protein_coding, 4 retained_intron, 4 nonsense_mediated_decay

ENST00000392524, ENST00000411529, ENST00000432457, ENST00000435711, ENST00000483137, ENST00000676488, ENST00000676629, ENST00000676681, ENST00000676736, ENST00000676762, ENST00000676874, ENST00000677043, ENST00000677337, ENST00000677508, ENST00000677863, ENST00000678111, ENST00000678421, ENST00000679159, ENST00000679328, ENST00000861950, ENST00000861951, ENST00000861952, ENST00000861953, ENST00000861954, ENST00000861955, ENST00000861956, ENST00000861957, ENST00000861958, ENST00000861959, ENST00000861960, ENST00000861961, ENST00000861962, ENST00000861963, ENST00000861964, ENST00000861965, ENST00000861966, ENST00000861967, ENST00000861968, ENST00000861969, ENST00000861970, ENST00000861971, ENST00000861972, ENST00000861973, ENST00000861974, ENST00000861975, ENST00000861976, ENST00000861977, ENST00000861978, ENST00000861979, ENST00000861980, ENST00000861981, ENST00000925136, ENST00000925137, ENST00000925138, ENST00000925139, ENST00000925140, ENST00000925141, ENST00000925142, ENST00000925143, ENST00000925144, ENST00000925145, ENST00000925146, ENST00000925147, ENST00000925148, ENST00000925149, ENST00000925150, ENST00000925151, ENST00000925152, ENST00000925153, ENST00000925154, ENST00000925155, ENST00000925156, ENST00000925157, ENST00000925158, ENST00000925159, ENST00000925160, ENST00000925161, ENST00000925162, ENST00000925163, ENST00000925164, ENST00000925165, ENST00000925166, ENST00000925167, ENST00000925168, ENST00000925169, ENST00000925170, ENST00000925171, ENST00000925172, ENST00000925173, ENST00000925174, ENST00000925175, ENST00000925176, ENST00000925177, ENST00000925178, ENST00000925179, ENST00000925180, ENST00000925181, ENST00000925182, ENST00000925183, ENST00000925184, ENST00000925185, ENST00000947718, ENST00000947719, ENST00000947720, ENST00000947721, ENST00000947722, ENST00000947723

RefSeq mRNA: 7 — MANE Select: NM_194247 NM_001330247, NM_001330248, NM_001330249, NM_001330250, NM_001330251, NM_001395170, NM_194247

CCDS: CCDS2273, CCDS82536, CCDS92902

Canonical transcript exons

ENST00000392524 — 11 exons

Exon	Start	End
ENSE00001125660	177215750	177215896
ENSE00001125664	177215539	177215661
ENSE00001162013	177215978	177216188
ENSE00001304011	177216503	177216592
ENSE00001340569	177216676	177216771
ENSE00001389783	177216860	177216940
ENSE00002235107	177219037	177219159
ENSE00002246445	177217705	177217845
ENSE00002248460	177219247	177219314
ENSE00003978127	177219408	177223959
ENSE00003978128	177212794	177212871

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.55.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6929 / max 13.9922, expressed in 453 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
23887	0.6929	453

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	99.55	gold quality
ventricular zone	UBERON:0003053	99.50	gold quality
right testis	UBERON:0004534	99.36	gold quality
left testis	UBERON:0004533	99.34	gold quality
monocyte	CL:0000576	99.20	gold quality
cortical plate	UBERON:0005343	99.18	gold quality
mononuclear cell	CL:0000842	99.14	gold quality
Brodmann (1909) area 23	UBERON:0013554	99.14	gold quality
right lobe of thyroid gland	UBERON:0001119	99.13	gold quality
left lobe of thyroid gland	UBERON:0001120	99.13	gold quality
left ovary	UBERON:0002119	99.13	gold quality
colonic epithelium	UBERON:0000397	99.11	gold quality
leukocyte	CL:0000738	99.09	gold quality
right ovary	UBERON:0002118	99.06	gold quality
endocervix	UBERON:0000458	99.05	gold quality
thyroid gland	UBERON:0002046	99.05	gold quality
body of uterus	UBERON:0009853	99.05	gold quality
endometrium	UBERON:0001295	99.03	gold quality
stromal cell of endometrium	CL:0002255	99.00	gold quality
ectocervix	UBERON:0012249	99.00	gold quality
mucosa of transverse colon	UBERON:0004991	98.99	gold quality
ovary	UBERON:0000992	98.97	gold quality
left uterine tube	UBERON:0001303	98.94	gold quality
rectum	UBERON:0001052	98.93	gold quality
skin of abdomen	UBERON:0001416	98.89	gold quality
adenohypophysis	UBERON:0002196	98.89	gold quality
esophagus mucosa	UBERON:0002469	98.89	gold quality
metanephros cortex	UBERON:0010533	98.89	gold quality
skin of leg	UBERON:0001511	98.88	gold quality
upper lobe of left lung	UBERON:0008952	98.84	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	44.88
E-HCAD-4	yes	43.08
E-CURD-122	yes	24.81
E-HCAD-5	yes	18.64
E-MTAB-10553	yes	7.82
E-MTAB-6819	no	510.27
E-GEOD-125970	no	3.17
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

155 targeting HNRNPA3, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548AR-5P	99.94	71.28	3515
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

Literature-anchored findings (GeneRIF, showing 10)

• These biochemical properties of hnRNP A3 suggest that hnRNP A3 can participate in telomere regulation in vivo. (PMID:17919748)
• Results suggest that hnRNP A3 is associated with telomere in vivo and acts as a negative regulator of telomere length maintenance. (PMID:20600361)
• characterization of hnRNP A3 in human and mouse cell lines (PMID:22546510)
• The results of this study suggested that mutations in hnRNPA1, A2/B1, and A3 genes are a rare finding in amyotrophic lateral sclerosis. (PMID:23827524)
• Neurons in the hippocampus of C9orf72 patients are frequently devoid of hnRNPA3. Reduced nuclear hnRNPA3 in the hippocampus of patients with extended C9orf72 repeats correlates with increased DPR deposition. (PMID:27461252)
• Study investigated the pattern of hnRNP A1, A2/B1 and A3 immunostaining across a range of clinical, pathological and genetic forms of Frontotemporal Lobar Degeneration and Motor Neurone Disease. Data suggest there might be a derangement of movement of hnRNP A1, and other hnRNP proteins, across all pathological forms of Frontotemporal Lobar Degeneration beyond that involving just TDP-43 or FUS. (PMID:28431575)
• This study showed that HNRNPA3 variants identified in Australian patients with familial amyotrophic lateral sclerosis (FALS) and associated alternate allele frequencies in cases and controls. (PMID:29131108)
• results indicated a specific interaction of A3B with hnRNP A3 (heterogeneous nuclear ribonucleoprotein). This interaction was verified by co-immunoprecipitation and was found to be RNA-dependent. Furthermore, A3B and hnRNP A3 colocalized as evident from immunofluorescence analysis. (PMID:29693745)
• Heterogeneous nuclear ribonucleoprotein A3 controls mitotic progression of neural progenitors via interaction with cohesin. (PMID:32321712)
• Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration. (PMID:33469008)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	hnrnpa0l	ENSDARG00000036161
danio_rerio	hnrnpa0b	ENSDARG00000036162
danio_rerio	hnrnpa0a	ENSDARG00000089302
rattus_norvegicus	Hnrnpa3	ENSRNOG00000027006
rattus_norvegicus		ENSRNOG00000055020

Paralogs (36): DAZAP1 (ENSG00000071626), CIRBP (ENSG00000099622), RBM23 (ENSG00000100461), RBM3 (ENSG00000102317), NCL (ENSG00000115053), TIA1 (ENSG00000116001), HNRNPA2B1 (ENSG00000122566), RBM19 (ENSG00000122965), RBM39 (ENSG00000131051), MSI1 (ENSG00000135097), HNRNPA1 (ENSG00000135486), HNRNPD (ENSG00000138668), HNRNPA1L2 (ENSG00000139675), RBMX (ENSG00000147274), A1CF (ENSG00000148584), TIAL1 (ENSG00000151923), RBM46 (ENSG00000151962), HNRNPDL (ENSG00000152795), MSI2 (ENSG00000153944), RBM47 (ENSG00000163694), RBMY1F (ENSG00000169800), RBMXL2 (ENSG00000170748), RBM4B (ENSG00000173914), RBM4 (ENSG00000173933), RBMXL3 (ENSG00000175718), HNRNPA0 (ENSG00000177733), TRNAU1AP (ENSG00000180098), HNRNPAB (ENSG00000197451), RBMXL1 (ENSG00000213516), HNRNPA1L3 (ENSG00000224578), RBMY1J (ENSG00000226941), RBMY1A1 (ENSG00000234414), RBMY1E (ENSG00000242389), RBMY1B (ENSG00000242875), RBMY1D (ENSG00000244395), DND1 (ENSG00000256453)

Protein

Protein identifiers

Heterogeneous nuclear ribonucleoprotein A3 — P51991 (reviewed: P51991)

All UniProt accessions (9): P51991, A0A384NL63, A0A7I2V2R3, A0A7I2V402, A0A7I2V4G0, A0A7I2V4J6, A0A7I2V5D8, B4DDB6, H7C1J8

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in cytoplasmic trafficking of RNA. Binds to the cis-acting response element, A2RE. May be involved in pre-mRNA splicing.

Subunit / interactions. Identified in the spliceosome C complex.

Subcellular location. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
P51991-1	1	yes
P51991-2	2

RefSeq proteins (7): NP_001317176, NP_001317177, NP_001317178, NP_001317179, NP_001317180, NP_001382099, NP_919223* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034516	hnRNPA1/3_RRM2	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076

UniProt features (48 total): modified residue 31, cross-link 6, compositionally biased region 4, region of interest 3, domain 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P51991-F1	69.10	0.42

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 (37): 1, 14, 43, 52, 52, 76, 112, 116, 124, 134, 214, 214, 216, 216, 226, 226, 239, 239, 246, 246 …

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

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

MSigDB gene sets: 211 (showing top): FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP, HORIUCHI_WTAP_TARGETS_DN, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10, CMYB_01, GGCNKCCATNK_UNKNOWN, PUJANA_CHEK2_PCC_NETWORK, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, REACTOME_MRNA_3_END_PROCESSING, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, USF_01, GOBP_RNA_SPLICING, TGACATY_UNKNOWN, REACTOME_MRNA_SPLICING, SCHLOSSER_SERUM_RESPONSE_DN, LYF1_01

GO Biological Process (3): mRNA splicing, via spliceosome (GO:0000398), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

GO Molecular Function (4): RNA binding (GO:0003723), mRNA 3’-UTR binding (GO:0003730), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), catalytic step 2 spliceosome (GO:0071013), ribonucleoprotein complex (GO:1990904), spliceosomal complex (GO:0005681)

Reactome top-level categories

Rollup of top-5 pathways:

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
binding	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
mRNA metabolic process	1
nucleic acid binding	1
mRNA binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
Prp19 complex	1
spliceosomal complex	1
U5 snRNP	1
catalytic complex	1
protein-containing complex	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1

Protein interactions and networks

STRING

3031 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HNRNPA3	HNRNPC	P07910	856
HNRNPA3	HNRNPH1	P31943	783
HNRNPA3	PTBP1	P26599	768
HNRNPA3	C9orf72	Q96LT7	750
HNRNPA3	HNRNPH2	P55795	746
HNRNPA3	PURA	Q00577	740
HNRNPA3	TARDBP	Q13148	726
HNRNPA3	HNRNPA2B1	P22626	717
HNRNPA3	FMR1	Q06787	709
HNRNPA3	HNRNPL	P14866	702
HNRNPA3	ADARB2	Q9NS39	696
HNRNPA3	PCBP1	Q15365	691
HNRNPA3	DHX9	Q08211	684
HNRNPA3	HNRNPU	Q00839	680
HNRNPA3	HNRNPR	O43390	660

IntAct

265 interactions, top by confidence:

A	B	Type	Score
HNRNPC	KPNA3	psi-mi:“MI:0914”(association)	0.850
RBM45	HNRNPA1	psi-mi:“MI:0914”(association)	0.740
N	HNRNPR	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
USE1	NBAS	psi-mi:“MI:0914”(association)	0.640
IGF2BP1	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
NCBP1	KPNA3	psi-mi:“MI:0914”(association)	0.640
HNRNPA2B1	HNRNPA3	psi-mi:“MI:0915”(physical association)	0.560
HNRNPA1	HNRNPA3	psi-mi:“MI:0915”(physical association)	0.560
HNRNPH2	PLOD2	psi-mi:“MI:0914”(association)	0.530
TUBB3	POTEF	psi-mi:“MI:0914”(association)	0.530
N	HNRNPDL	psi-mi:“MI:0914”(association)	0.530
SYNGAP1	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
RBM45	HNRNPA3	psi-mi:“MI:0403”(colocalization)	0.510
CPSF6	DDX39A	psi-mi:“MI:0914”(association)	0.480
ESR1		psi-mi:“MI:0914”(association)	0.460
RBM45	HNRNPDL	psi-mi:“MI:0914”(association)	0.460
FUS	DDX3X	psi-mi:“MI:0914”(association)	0.430
LTK	PIK3R2	psi-mi:“MI:0914”(association)	0.420
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
HNRNPA3	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
STARD9	HNRNPA3	psi-mi:“MI:0915”(physical association)	0.400
FERMT2	HNRNPA3	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (666): HNRNPA3 (Affinity Capture-MS), HNRNPA3 (Affinity Capture-MS), HNRNPA3 (Affinity Capture-MS), HNRNPA3 (Affinity Capture-MS), HNRNPA3 (Affinity Capture-MS), HNRNPA3 (Affinity Capture-MS), HNRNPA3 (Affinity Capture-MS), HNRNPA3 (Affinity Capture-MS), HNRNPA3 (Affinity Capture-MS), ATP1B1 (Co-fractionation), CHMP2A (Co-fractionation), CYB5B (Co-fractionation), DDX17 (Co-fractionation), FDPS (Co-fractionation), HNRNPA3 (Co-fractionation)

ESM2 similar proteins: A0A0A0LLY1, A0A2R8Y4L2, A5A6H4, O89086, O93235, P04256, P09651, P09867, P10979, P17130, P21522, P27484, P49310, P49311, P49312, P51968, P51989, P51991, P51992, P60824, P60825, P60826, P98179, Q03250, Q03251, Q03878, Q05966, Q13151, Q14011, Q28521, Q28IQ9, Q2HJ60, Q32P51, Q38896, Q41188, Q43472, Q5RF83, Q61B10, Q6URK4, Q8BG05

Diamond homologs: A0A0A0LLY1, A0A0D1C8Z4, A0A2R8Y4L2, A5A6H4, A5A6M3, A7VJC2, D4AE41, O22703, O75526, O88569, O89086, O93235, P04256, P09651, P09867, P10979, P17130, P19682, P19683, P19684, P22626, P28644, P38159, P39697, P41891, P49310, P49311, P49312, P49313, P49314, P51968, P51989, P51990, P51991, P51992, P60824, P60825, P60826, P84586, P98179

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
HNRNPA3	“down-regulates quantity”	C9orf72
UBQLN2	“up-regulates quantity by stabilization”	HNRNPA3	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 218 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	5	19.9×	2e-04
RHOBTB2 GTPase cycle	5	15.0×	8e-04
RHOBTB1 GTPase cycle	5	15.0×	8e-04
mRNA Polyadenylation	23	12.7×	9e-17
Processing of Capped Intron-Containing Pre-mRNA	22	11.4×	4e-15
Selective autophagy	6	10.5×	9e-04
mRNA Splicing - Major Pathway	29	10.0×	3e-18
RNA Polymerase II Transcription Termination	7	9.7×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
alternative mRNA splicing, via spliceosome	6	21.4×	5e-05
spliceosomal snRNP assembly	5	15.4×	1e-03
regulation of alternative mRNA splicing, via spliceosome	11	14.2×	2e-07
mRNA splicing, via spliceosome	28	13.6×	9e-21
mRNA export from nucleus	8	12.5×	5e-05
mRNA stabilization	6	11.6×	1e-03
autophagosome maturation	6	11.2×	1e-03
positive regulation of interferon-beta production	5	10.4×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1331 predictions. Top by Δscore:

Variant	Effect	Δscore
2:177212869:G:GT	donor_gain	1.0000
2:177215533:TCTCA:T	acceptor_loss	1.0000
2:177215536:CAGG:C	acceptor_loss	1.0000
2:177215537:A:AG	acceptor_gain	1.0000
2:177215537:AG:A	acceptor_gain	1.0000
2:177215538:G:GG	acceptor_gain	1.0000
2:177215538:GG:G	acceptor_gain	1.0000
2:177215538:GGGCC:G	acceptor_gain	1.0000
2:177215657:GTGTG:G	donor_gain	1.0000
2:177215659:GTG:G	donor_gain	1.0000
2:177215660:TGGTA:T	donor_loss	1.0000
2:177215661:GGTAA:G	donor_loss	1.0000
2:177215662:G:A	donor_loss	1.0000
2:177215662:G:GG	donor_gain	1.0000
2:177215663:TAAGT:T	donor_loss	1.0000
2:177215744:TTGTA:T	acceptor_loss	1.0000
2:177215745:TGTA:T	acceptor_loss	1.0000
2:177215746:GTAG:G	acceptor_loss	1.0000
2:177215747:TA:T	acceptor_loss	1.0000
2:177215748:A:C	acceptor_loss	1.0000
2:177215749:G:GA	acceptor_loss	1.0000
2:177215894:G:GT	donor_gain	1.0000
2:177215894:GAG:G	donor_gain	1.0000
2:177215970:A:AG	acceptor_gain	1.0000
2:177215971:T:G	acceptor_gain	1.0000
2:177215973:T:TA	acceptor_gain	1.0000
2:177215975:TA:T	acceptor_loss	1.0000
2:177215976:A:AG	acceptor_gain	1.0000
2:177215976:AG:A	acceptor_gain	1.0000
2:177215977:G:A	acceptor_gain	1.0000

AlphaMissense

2455 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:177215570:G:C	R35T	1.000
2:177215570:G:T	R35I	1.000
2:177215571:A:C	R35S	1.000
2:177215571:A:T	R35S	1.000
2:177215572:A:C	K36Q	1.000
2:177215572:A:G	K36E	1.000
2:177215573:A:T	K36I	1.000
2:177215574:A:C	K36N	1.000
2:177215574:A:T	K36N	1.000
2:177215576:T:A	L37Q	1.000
2:177215576:T:C	L37P	1.000
2:177215578:T:A	F38I	1.000
2:177215578:T:C	F38L	1.000
2:177215578:T:G	F38V	1.000
2:177215579:T:C	F38S	1.000
2:177215579:T:G	F38C	1.000
2:177215580:T:A	F38L	1.000
2:177215580:T:G	F38L	1.000
2:177215581:A:T	I39F	1.000
2:177215582:T:A	I39N	1.000
2:177215582:T:G	I39S	1.000
2:177215584:G:A	G40S	1.000
2:177215584:G:C	G40R	1.000
2:177215584:G:T	G40C	1.000
2:177215585:G:A	G40D	1.000
2:177215585:G:T	G40V	1.000
2:177215587:G:C	G41R	1.000
2:177215587:G:T	G41C	1.000
2:177215588:G:A	G41D	1.000
2:177215588:G:T	G41V	1.000

dbSNP variants (sampled 300 via entrez): RS1000317932 (2:177223994 T>C), RS1000328376 (2:177215204 G>A), RS1000350105 (2:177213493 T>A), RS1000515874 (2:177223222 G>A,C), RS1000616694 (2:177218433 A>T), RS1001152069 (2:177217495 T>G), RS1001236041 (2:177213277 G>A,C), RS1001366569 (2:177216307 A>G,T), RS1001603857 (2:177213162 G>A), RS1001828779 (2:177223637 C>A,G), RS1001894015 (2:177222658 G>A,C), RS1001958798 (2:177223460 T>C), RS1002254146 (2:177212394 G>A), RS1002493984 (2:177222809 A>G), RS1003322689 (2:177212585 G>A)

Disease associations

OMIM: gene MIM:605372 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST003983_42	Male-pattern baldness	4.000000e-08
GCST003989_13	Chin dimples	2.000000e-19
GCST010002_405	Refractive error	1.000000e-70

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066874 (SINGLE PROTEIN)

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

ChEMBL bioactivities

4 potent at pChembl≥5 of 4 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.76	Kd	174.2	nM	CHEMBL3752910
6.76	ED50	174.2	nM	CHEMBL3752910
5.97	Kd	1070	nM	CHEMBL5653589
5.97	ED50	1070	nM	CHEMBL5653589

PubChem BioAssay actives

2 with measured affinity, of 4 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-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148526: Binding affinity to human HNRNPA3 incubated for 45 mins by Kinobead based pull down assay	kd	0.1742	uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148526: Binding affinity to human HNRNPA3 incubated for 45 mins by Kinobead based pull down assay	kd	1.0699	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects binding, increases reaction, decreases expression	5
bisphenol A	decreases expression, affects expression	4
Ethanol	decreases expression, affects cotreatment, increases abundance, increases expression	2
Benzo(a)pyrene	decreases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
Valproic Acid	affects expression, decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
Particulate Matter	increases expression, affects cotreatment, decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
dicrotophos	decreases expression	1
2,4,6-tribromophenol	decreases expression	1
nobiletin	decreases expression, decreases reaction	1
sodium arsenate	decreases expression, decreases reaction	1
pyrogallol 1,3-dimethyl ether	affects localization, increases expression, affects cotreatment, decreases expression	1
testosterone undecanoate	decreases expression	1
decabromobiphenyl ether	decreases expression	1
trichostatin A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
tetrabromobisphenol A	decreases expression	1
butylidenephthalide	decreases expression	1
isobutyl alcohol	affects cotreatment, increases abundance, increases expression	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
nutlin 3	affects cotreatment, increases secretion	1
bisphenol B	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	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
CHEMBL5651568	Binding	Binding affinity to human HNRNPA3 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

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2Z0	Abcam HEK293T HNRNPA3 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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