HNRNPA1L2

Summary

HNRNPA1L2 (heterogeneous nuclear ribonucleoprotein A1 like 2, HGNC:27067) is a protein-coding gene on chromosome 13q14.3, encoding Heterogeneous nuclear ribonucleoprotein A1-like 2 (Q32P51). Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection. It is a selective cancer dependency (DepMap: 15.6% of cell lines).

Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in cytoplasm and nucleus. Predicted to be part of catalytic step 2 spliceosome.

Source: NCBI Gene 144983 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 62 total
• Cancer dependency (DepMap): dependent in 15.6% of screened cell lines
• MANE Select transcript: NM_001389320

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27067
Approved symbol	HNRNPA1L2
Name	heterogeneous nuclear ribonucleoprotein A1 like 2
Location	13q14.3
Locus type	gene with protein product
Status	Approved
Aliases	LOC144983
Ensembl gene	ENSG00000139675
Ensembl biotype	protein_coding
Entrez	144983

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000357495

RefSeq mRNA: 3 — MANE Select: NM_001389320 NM_001011724, NM_001011725, NM_001389320

CCDS: CCDS31980

Canonical transcript exons

ENST00000357495 — 1 exons

Exon	Start	End
ENSE00001408724	52642431	52643773

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 86.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.5378 / max 217.9673, expressed in 1779 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
135233	12.1646	1767
135235	1.8204	1015
135230	0.3518	161
135229	0.2010	85

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	86.36	gold quality
cortical plate	UBERON:0005343	86.17	gold quality
granulocyte	CL:0000094	85.18	gold quality
cerebellar hemisphere	UBERON:0002245	84.91	gold quality
cerebellar cortex	UBERON:0002129	84.89	gold quality
cerebellum	UBERON:0002037	84.88	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.11	gold quality
ventricular zone	UBERON:0003053	83.68	gold quality
right ovary	UBERON:0002118	82.97	gold quality
left ovary	UBERON:0002119	82.94	gold quality
hypothalamus	UBERON:0001898	82.90	gold quality
ovary	UBERON:0000992	82.82	gold quality
body of uterus	UBERON:0009853	82.20	gold quality
adenohypophysis	UBERON:0002196	82.15	gold quality
pituitary gland	UBERON:0000007	82.14	gold quality
substantia nigra	UBERON:0002038	81.99	gold quality
spleen	UBERON:0002106	81.50	gold quality
brain	UBERON:0000955	81.32	gold quality
anterior cingulate cortex	UBERON:0009835	81.31	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	81.30	gold quality
descending thoracic aorta	UBERON:0002345	81.18	gold quality
putamen	UBERON:0001874	81.12	gold quality
Ammon’s horn	UBERON:0001954	81.11	gold quality
stromal cell of endometrium	CL:0002255	80.98	gold quality
prostate gland	UBERON:0002367	80.97	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	80.97	gold quality
right uterine tube	UBERON:0001302	80.86	gold quality
nucleus accumbens	UBERON:0001882	80.72	gold quality
thyroid gland	UBERON:0002046	80.72	gold quality
myometrium	UBERON:0001296	80.69	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	19.35

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting HNRNPA1L2, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-4722-3P	99.35	65.22	1099
HSA-MIR-421	98.90	67.04	1883
HSA-MIR-496	98.66	69.80	931
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-649	97.96	67.21	704
HSA-MIR-7111-3P	97.80	66.75	1467
HSA-MIR-339-5P	96.73	66.01	820
HSA-MIR-6741-5P	93.86	63.06	437

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• H3.3-G34W in giant cell tumor of bone functionally aligns with the exon choice repressor hnRNPA1L2. (PMID:38811797)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio	hnrnpa1b	ENSDARG00000036675

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), RBMX (ENSG00000147274), A1CF (ENSG00000148584), TIAL1 (ENSG00000151923), RBM46 (ENSG00000151962), HNRNPDL (ENSG00000152795), MSI2 (ENSG00000153944), RBM47 (ENSG00000163694), RBMY1F (ENSG00000169800), HNRNPA3 (ENSG00000170144), 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 A1-like 2 — Q32P51 (reviewed: Q32P51)

Alternative names: hnRNP core protein A1-like 2

All UniProt accessions (1): Q32P51

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection.

Subcellular location. Nucleus. Cytoplasm.

RefSeq proteins (3): NP_001011724, NP_001011725, NP_001376249* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR021662	HnRNPA1/A2_C	Domain
IPR034845	hnRNPA1_RRM1	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076, PF11627

UniProt features (26 total): modified residue 12, region of interest 6, compositionally biased region 3, domain 2, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q32P51-F1	72.25	0.45

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 (12): 6, 22, 194, 194, 206, 206, 218, 218, 225, 225, 284, 298

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 67 (showing top): PAL_PRMT5_TARGETS_UP, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOBP_RNA_SPLICING, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, SANSOM_APC_TARGETS_UP, YAMAZAKI_TCEB3_TARGETS_DN, GOBP_RNA_LOCALIZATION, chr13q14, MARSON_BOUND_BY_FOXP3_STIMULATED, GOCC_CATALYTIC_STEP_2_SPLICEOSOME, GOCC_SPLICEOSOMAL_COMPLEX

GO Biological Process (4): mRNA splicing, via spliceosome (GO:0000398), mRNA transport (GO:0051028), mRNA processing (GO:0006397), RNA splicing (GO:0008380)

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

GO Cellular Component (5): cytoplasm (GO:0005737), catalytic step 2 spliceosome (GO:0071013), nucleus (GO:0005634), spliceosomal complex (GO:0005681), ribonucleoprotein complex (GO:1990904)

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
RNA transport	1
mRNA metabolic process	1
mRNA binding	1
nucleic acid binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
Prp19 complex	1
spliceosomal complex	1
U5 snRNP	1
catalytic complex	1
intracellular membrane-bounded organelle	1
nuclear protein-containing complex	1
ribonucleoprotein complex	1
protein-containing complex	1

Protein interactions and networks

STRING

2020 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HNRNPA1L2	LRRC74B	Q6ZQY2	471
HNRNPA1L2	HNRNPLL	Q8WVV9	425
HNRNPA1L2	STEEP1	Q9H5V9	416
HNRNPA1L2	FUNDC2	Q9BWH2	393
HNRNPA1L2	UBQLN2	Q9UHD9	387
HNRNPA1L2	PLD5	Q8N7P1	382
HNRNPA1L2	PRSS21	Q9Y6M0	377
HNRNPA1L2	FMO5	P49326	374
HNRNPA1L2	COG5	Q9UP83	374
HNRNPA1L2	RAB28	P51157	372
HNRNPA1L2	PNPLA8	Q9NP80	371
HNRNPA1L2	RAB30	Q15771	371
HNRNPA1L2	SUGT1	Q9Y2Z0	367
HNRNPA1L2	NAP1L1	P55209	362
HNRNPA1L2	TTBK2	Q6IQ55	360

IntAct

102 interactions, top by confidence:

A	B	Type	Score
EGFR	HSP90AA1	psi-mi:“MI:0914”(association)	0.820
HNRNPA1	PTCD1	psi-mi:“MI:0914”(association)	0.530
SSX4	CDR2	psi-mi:“MI:0914”(association)	0.530
HNRNPA1	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.500
ESR1		psi-mi:“MI:0914”(association)	0.460
NOLC1	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
HNRNPA3	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
HNRNPA2B1	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
KTN1	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
PNO1	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
HNRNPA1L2	HNRNPA0	psi-mi:“MI:0915”(physical association)	0.400
DOCK6	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
CYP2C9	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
HNRNPDL	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
XPNPEP3	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
HNRNPA1L2	HNRNPD	psi-mi:“MI:0915”(physical association)	0.400
ERCC6L2	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
IQCG	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
CEP95	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
TTN	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
MATR3	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
NKRF	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
STARD9	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
SMARCA4	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
MGAT4C	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
CFDP1	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
DYNC2H1	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
RPS25	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
HNRNPC	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400
EXOC3	HNRNPA1L2	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (185): HNRNPA1L2 (Affinity Capture-MS), FDPS (Co-fractionation), HNRNPF (Co-fractionation), HNRNPH1 (Co-fractionation), HNRNPH2 (Co-fractionation), HNRNPH3 (Co-fractionation), TOX4 (Affinity Capture-MS), KIF14 (Affinity Capture-MS), TRIB1 (Affinity Capture-MS), PAICS (Affinity Capture-MS), SIRT1 (Affinity Capture-MS), UQCRQ (Affinity Capture-MS), STX18 (Affinity Capture-MS), MIA3 (Affinity Capture-MS), HNRNPA1L2 (Affinity Capture-MS)

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

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 114 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
Processing of Capped Intron-Containing Pre-mRNA	9	10.6×	9e-05
mRNA Polyadenylation	8	10.0×	3e-04
mRNA Splicing - Major Pathway	9	7.0×	9e-04
Dengue Virus-Host Interactions	9	5.9×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	49
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

14 predictions. Top by Δscore:

Variant	Effect	Δscore
13:52642444:T:TA	acceptor_gain	0.9800
13:52642438:T:TA	acceptor_gain	0.9700
13:52642445:G:A	acceptor_gain	0.9200
13:52642489:C:A	acceptor_gain	0.8200
13:52642500:A:G	acceptor_gain	0.8200
13:52642494:T:G	acceptor_gain	0.6300
13:52642442:C:CA	acceptor_gain	0.4200
13:52642499:AAGT:A	acceptor_gain	0.3700
13:52642500:AGT:A	acceptor_gain	0.3100
13:52642486:TGCCG:T	acceptor_gain	0.2300
13:52642499:A:AG	acceptor_gain	0.2200
13:52642499:A:AC	acceptor_gain	0.2100
13:52642548:G:C	acceptor_gain	0.2100
13:52642498:TAAG:T	acceptor_gain	0.2000

AlphaMissense

2126 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:52642661:T:C	F57L	1.000
13:52642663:T:A	F57L	1.000
13:52642663:T:G	F57L	1.000
13:52642541:T:C	F17L	0.999
13:52642543:C:A	F17L	0.999
13:52642543:C:G	F17L	0.999
13:52642667:T:C	F59L	0.999
13:52642669:T:A	F59L	0.999
13:52642669:T:G	F59L	0.999
13:52642934:T:C	F148L	0.999
13:52642936:T:A	F148L	0.999
13:52642936:T:G	F148L	0.999
13:52642814:T:C	F108L	0.998
13:52642816:T:A	F108L	0.998
13:52642816:T:G	F108L	0.998
13:52642940:T:C	F150L	0.998
13:52642942:T:A	F150L	0.998
13:52642942:T:G	F150L	0.998
13:52642665:G:A	G58E	0.996
13:52642662:T:C	F57S	0.995
13:52642668:T:C	F59S	0.995
13:52642671:T:A	V60D	0.995
13:52642548:G:A	G19E	0.994
13:52642657:G:C	R55S	0.994
13:52642657:G:T	R55S	0.994
13:52642537:G:C	K15N	0.993
13:52642537:G:T	K15N	0.993
13:52642542:T:C	F17S	0.993
13:52642664:G:T	G58W	0.993
13:52642668:T:G	F59C	0.993

dbSNP variants (sampled 300 via entrez): RS1000165340 (13:52630925 T>A), RS1000218296 (13:52630563 G>A,T), RS1000275863 (13:52616274 A>C,G), RS1000426176 (13:52636868 A>G), RS1000626250 (13:52616008 A>G), RS1000627091 (13:52618165 T>C), RS1000679598 (13:52617865 C>T), RS1000775915 (13:52637223 G>A), RS1000881591 (13:52642740 T>G), RS1001189423 (13:52624592 G>A,T), RS1001275409 (13:52629129 G>T), RS1001372504 (13:52635727 G>T), RS1001514103 (13:52640377 C>T), RS1001686439 (13:52616516 C>G), RS1001736085 (13:52623291 T>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	3
sodium arsenite	decreases expression	2
Cadmium Chloride	decreases expression, increases expression	2
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression, affects localization, increases expression	1
butyraldehyde	increases expression	1
diallyl trisulfide	increases expression	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
epigallocatechin gallate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Cadmium	increases expression	1
Doxorubicin	decreases expression	1
Furaldehyde	affects cotreatment, affects localization, decreases expression, increases expression	1
Polycyclic Aromatic Hydrocarbons	affects expression	1
Sodium Chloride	decreases expression, increases expression, affects cotreatment, affects localization	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Copper Sulfate	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2YY	Abcam HEK293T HNRNPA1L2 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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