HNRNPCL2

Summary

HNRNPCL2 (heterogeneous nuclear ribonucleoprotein C like 2, HGNC:48813) is a protein-coding gene on chromosome 1p36.21, encoding Heterogeneous nuclear ribonucleoprotein C-like 2 (B2RXH8). May play a role in nucleosome assembly by neutralizing basic proteins such as A and B core hnRNPs.

Enables identical protein binding activity. Predicted to be part of ribonucleoprotein complex. Predicted to be active in nucleus.

Source: NCBI Gene 440563 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 59 total
• MANE Select transcript: NM_001136561

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48813
Approved symbol	HNRNPCL2
Name	heterogeneous nuclear ribonucleoprotein C like 2
Location	1p36.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000275774
Ensembl biotype	protein_coding
Entrez	440563

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000621994

RefSeq mRNA: 1 — MANE Select: NM_001136561 NM_001136561

CCDS: CCDS76105

Canonical transcript exons

ENST00000619361 — 0 exons

Expression profiles

Bgee: expression breadth tissue_specific, 1 present calls, max score 81.45.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.45	gold quality
bone marrow cell	CL:0002092	42.78	gold quality
cortical plate	UBERON:0005343	39.83	gold quality
stromal cell of endometrium	CL:0002255	39.74	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
bone marrow	UBERON:0002371	35.12	gold quality
skeletal muscle tissue	UBERON:0001134	34.96	gold quality
muscle tissue	UBERON:0002385	32.22	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
blood	UBERON:0000178	29.55	gold quality
prefrontal cortex	UBERON:0000451	29.38	gold quality
liver	UBERON:0002107	28.80	gold quality
gall bladder	UBERON:0002110	28.74	gold quality
tonsil	UBERON:0002372	28.67	gold quality
muscle of leg	UBERON:0001383	28.27	gold quality
urinary bladder	UBERON:0001255	28.26	gold quality
right uterine tube	UBERON:0001302	28.21	gold quality
duodenum	UBERON:0002114	28.14	gold quality
islet of Langerhans	UBERON:0000006	27.74	gold quality
gastrocnemius	UBERON:0001388	27.64	gold quality
lymph node	UBERON:0000029	27.57	gold quality
pancreas	UBERON:0001264	26.43	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
heart left ventricle	UBERON:0002084	25.58	gold quality
myometrium	UBERON:0001296	25.53	gold quality
calcaneal tendon	UBERON:0003701	25.32	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.19

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Hnrnpc	ENSMUSG00000060373
rattus_norvegicus	LOC100911576	ENSRNOG00000011621

Paralogs (6): HNRNPC (ENSG00000092199), RALY (ENSG00000125970), HNRNPCL1 (ENSG00000179172), HNRNPCL4 (ENSG00000179412), RALYL (ENSG00000184672), HNRNPCL3 (ENSG00000277058)

Protein

Protein identifiers

Heterogeneous nuclear ribonucleoprotein C-like 2 — B2RXH8 (reviewed: B2RXH8)

All UniProt accessions (1): B2RXH8

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in nucleosome assembly by neutralizing basic proteins such as A and B core hnRNPs.

Subcellular location. Nucleus.

Similarity. Belongs to the RRM HNRPC family. RALY subfamily.

RefSeq proteins (1): NP_001130033* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR017347	hnRNP_C	Family
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR051186	RRM_HNRPC/RALY_subfam	Family

Pfam: PF00076

UniProt features (9 total): compositionally biased region 3, region of interest 2, chain 1, domain 1, coiled-coil region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B2RXH8-F1	70.72	0.32

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): GOCC_RIBONUCLEOPROTEIN_COMPLEX, chr1p36

GO Biological Process (0):

GO Molecular Function (4): RNA binding (GO:0003723), identical protein binding (GO:0042802), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), ribonucleoprotein complex (GO:1990904)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
nucleic acid binding	1
protein binding	1
intracellular membrane-bounded organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

1396 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HNRNPCL2	PRAMEF18	Q5VWM3	524
HNRNPCL2	PRAMEF7	Q5VXH5	507
HNRNPCL2	OR52N5	Q8NH56	475
HNRNPCL2	RALYL	Q86SE5	431
HNRNPCL2	ATP5ME	P56385	418
HNRNPCL2	FAM131C	Q96AQ9	417
HNRNPCL2	ATP5MC3	P48201	399
HNRNPCL2	ATP5MC1	P05496	392
HNRNPCL2	OR4K1	Q8NGD4	391
HNRNPCL2	PRAMEF1	O95521	370
HNRNPCL2	PRAMEF2	O60811	367
HNRNPCL2	TIGD3	Q6B0B8	366
HNRNPCL2	OR8U1	Q8NH10	349
HNRNPCL2	SCGB1C1	Q8TD33	348
HNRNPCL2	SCGB1C2	P0DMR2	348

IntAct

58 interactions, top by confidence:

A	B	Type	Score
HNRNPCL2	HNRNPCL1	psi-mi:“MI:0915”(physical association)	0.670
HNRNPCL2	HNRNPC	psi-mi:“MI:0915”(physical association)	0.670
RALY	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.560
TRIP11	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL2	RALY	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL2	RALYL	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL2	PPP1R37	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL2	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL2	RNF4	psi-mi:“MI:0915”(physical association)	0.560
FLT4	ILVBL	psi-mi:“MI:0914”(association)	0.420
SLC22A8	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
HMGN5	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
AKAP9	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
PHIP	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
FANCC	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
FREM2	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
HNRNPCL2	PLCB2	psi-mi:“MI:0915”(physical association)	0.400
HNRNPCL2	RPUSD1	psi-mi:“MI:0915”(physical association)	0.400
GLT8D2	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
ANXA2	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
ROCK2	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
PHACTR4	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
LRP1B	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
ARHGEF11	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
C2orf78	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
ERICH3	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
BROX	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
VDAC2	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
MAST1	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400
FSBP	HNRNPCL2	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (290): HNRNPCL2 (Affinity Capture-MS), HNRNPCL2 (Affinity Capture-MS), HNRNPCL2 (Two-hybrid), HNRNPCL2 (Two-hybrid), HNRNPCL2 (Two-hybrid), HNRNPCL2 (Two-hybrid), HNRNPCL2 (Two-hybrid), HNRNPCL2 (Two-hybrid), HNRNPCL2 (Two-hybrid), HNRNPCL2 (Affinity Capture-MS), MRC1 (Proximity Label-MS), ECT2L (Proximity Label-MS), THUMPD2 (Proximity Label-MS), HNRNPCL2 (Proximity Label-MS), FSBP (Proximity Label-MS)

ESM2 similar proteins: B2RXH8, B7ZW38, C0SUW7, F4JP52, F4JQZ3, F4JTI1, F4KIA8, G3V9R8, O48802, O60812, O77768, P07910, P0DMR1, P19600, P93831, Q08BJ2, Q08DJ0, Q0VFL3, Q0VFL7, Q0WNR6, Q0WUR5, Q10MI4, Q149C2, Q3ED78, Q41583, Q5DU00, Q5RA82, Q5VN06, Q5XIN3, Q64012, Q6K641, Q84PB3, Q84UI6, Q86SE5, Q86XZ4, Q8BTF8, Q8K1N4, Q8RWQ4, Q8S4P4, Q8S4P6

Diamond homologs: B2RXH8, B7ZW38, G3V9R8, O60812, O77768, P07910, P0DMR1, P19600, Q08DJ0, Q0VFL7, Q5RA82, Q64012, Q86SE5, Q8BTF8, Q9UKM9, Q9V3V0, Q9Z204, Q16629, Q3T106, Q8BL97, Q9W4D2, P38996, Q13247, Q29RT0, Q3B7L6, Q9WX39, F4JHI7, O22315, P84103, P84104, Q10145, Q3SZR8, Q74ZS6, Q94901, Q9FYB7, Q9LIS2, Q9XFR5, G3V6S8, Q3TWW8, Q6IQ97

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	52
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

216 predictions. Top by Δscore:

Variant	Effect	Δscore
1:13116592:G:C	acceptor_gain	0.9700
1:13116581:TC:T	acceptor_loss	0.9600
1:13116590:A:C	acceptor_gain	0.9600
1:13116582:C:CC	acceptor_gain	0.9500
1:13116787:ACTT:A	donor_loss	0.9500
1:13116788:CTT:C	donor_loss	0.9500
1:13116577:GAATT:G	acceptor_gain	0.9400
1:13116587:A:AC	acceptor_gain	0.9400
1:13116590:A:AC	acceptor_gain	0.9400
1:13116786:GACTT:G	donor_loss	0.9400
1:13116791:A:AC	donor_gain	0.9400
1:13116792:C:CC	donor_gain	0.9400
1:13116592:G:GC	acceptor_gain	0.9300
1:13116580:TT:T	acceptor_gain	0.9200
1:13116579:ATT:A	acceptor_gain	0.9000
1:13116579:ATTCT:A	acceptor_gain	0.8900
1:13116580:TTCT:T	acceptor_gain	0.8800
1:13116578:AATT:A	acceptor_gain	0.8700
1:13116581:TCTG:T	acceptor_gain	0.8500
1:13116582:C:A	acceptor_gain	0.8400
1:13116583:T:A	acceptor_gain	0.8300
1:13116578:AATTC:A	acceptor_gain	0.8200
1:13115676:C:A	donor_gain	0.7900
1:13116785:TGAC:T	donor_loss	0.7700
1:13116587:A:C	acceptor_gain	0.7300
1:13116784:GTGAC:G	donor_loss	0.7200
1:13115766:T:TA	donor_gain	0.6800
1:13116792:CCAG:C	donor_gain	0.6800
1:13115710:T:A	donor_gain	0.6500
1:13115529:T:TA	donor_gain	0.6300

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1002232719 (1:13117918 T>G), RS1002601034 (1:13118089 T>A), RS1002618846 (1:13116940 T>A), RS1002696828 (1:13118115 G>A), RS1002748315 (1:13117669 A>G), RS1002809859 (1:13118802 C>G), RS1005741521 (1:13118085 C>G), RS1005923055 (1:13117819 A>T), RS1005934239 (1:13117625 A>C), RS1008939634 (1:13115425 A>G), RS1009143648 (1:13115139 G>A), RS1009882580 (1:13117289 C>G,T), RS1010008589 (1:13118465 C>T), RS1010065352 (1:13118123 C>A,G,T), RS1010075198 (1:13117885 G>A,T)

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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation, increases mutagenesis	2
Cadmium	increases abundance, increases expression	1
Urethane	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1

Clinical trials (associated diseases)

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