HNRNPCL3

Summary

HNRNPCL3 (heterogeneous nuclear ribonucleoprotein C like 3, HGNC:51235) is a protein-coding gene on chromosome 1p36.21, encoding Heterogeneous nuclear ribonucleoprotein C-like 3 (B7ZW38).

Predicted to enable RNA binding activity. Predicted to be active in nucleus.

Source: NCBI Gene 649330 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001382358

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51235
Approved symbol	HNRNPCL3
Name	heterogeneous nuclear ribonucleoprotein C like 3
Location	1p36.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000277058
Ensembl biotype	protein_coding
Entrez	649330

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000617807, ENST00000681473

RefSeq mRNA: 1 — MANE Select: NM_001382358 NM_001382358

CCDS: CCDS72705

Canonical transcript exons

ENST00000617044 — 0 exons

Expression profiles

Bgee: expression breadth tissue_specific, 4 present calls, max score 45.74.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	45.74	silver quality
cortical plate	UBERON:0005343	41.25	gold quality
hindlimb stylopod muscle	UBERON:0004252	39.91	silver quality
sural nerve	UBERON:0015488	39.39	gold quality
bone marrow cell	CL:0002092	38.00	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
mucosa of transverse colon	UBERON:0004991	35.72	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	34.82	gold quality
bone marrow	UBERON:0002371	32.68	gold quality
right uterine tube	UBERON:0001302	32.31	gold quality
muscle tissue	UBERON:0002385	32.12	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
liver	UBERON:0002107	29.42	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
placenta	UBERON:0001987	28.66	silver quality
leukocyte	CL:0000738	28.56	gold quality
duodenum	UBERON:0002114	28.14	gold quality
monocyte	CL:0000576	28.10	gold quality
blood	UBERON:0000178	27.58	silver quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
urinary bladder	UBERON:0001255	26.78	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
gastrocnemius	UBERON:0001388	25.43	gold quality
right adrenal gland cortex	UBERON:0035827	24.89	gold quality
calcaneal tendon	UBERON:0003701	24.81	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-36552	yes	1870.63
E-ANND-3	no	0.16

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), HNRNPCL2 (ENSG00000275774)

Protein

Protein identifiers

Heterogeneous nuclear ribonucleoprotein C-like 3 — B7ZW38 (reviewed: B7ZW38)

All UniProt accessions (1): B7ZW38

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

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

RefSeq proteins (1): NP_001369287* (*=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 4, region of interest 2, chain 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-B7ZW38-F1	70.54	0.33

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 4 (showing top): chr1p36, MANNO_MIDBRAIN_NEUROTYPES_HRGL3, MANNO_MIDBRAIN_NEUROTYPES_HGABA, KANNAN_BLOOD_2012_2013_TIV_AGE_65PLS_REVACCINATED_IN_6_9_MO_VS_REVACCINATED_IN_12_13_MOS_DN

GO Biological Process (0):

GO Molecular Function (2): RNA binding (GO:0003723), nucleic acid binding (GO:0003676)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1256 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HNRNPCL3	PRAMEF18	Q5VWM3	522
HNRNPCL3	PRAMEF7	Q5VXH5	507
HNRNPCL3	OR52N5	Q8NH56	475
HNRNPCL3	RALYL	Q86SE5	439
HNRNPCL3	FAM131C	Q96AQ9	417
HNRNPCL3	ATP5MC3	P48201	399
HNRNPCL3	ATP5MC1	P05496	392
HNRNPCL3	OR4K1	Q8NGD4	391
HNRNPCL3	PRAMEF1	O95521	370
HNRNPCL3	PRAMEF2	O60811	366
HNRNPCL3	TIGD3	Q6B0B8	366
HNRNPCL3	ATP5ME	P56385	364
HNRNPCL3	OR8U1	Q8NH10	348
HNRNPCL3	SCGB1C1	Q8TD33	339
HNRNPCL3	SCGB1C2	P0DMR2	338

IntAct

3 interactions, top by confidence:

A	B	Type	Score
DYRK2	HNRNPCL2	psi-mi:“MI:2364”(proximity)	0.270
MST1R	SHTN1	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (29): HNRNPCL3 (Affinity Capture-MS), HNRNPCL3 (Affinity Capture-MS), HNRNPCL3 (Affinity Capture-MS), HNRNPCL3 (Affinity Capture-MS), HNRNPCL3 (Affinity Capture-MS), HNRNPCL3 (Affinity Capture-MS), HNRNPCL3 (Affinity Capture-MS), HNRNPCL3 (Affinity Capture-MS), HNRNPCL3 (Proximity Label-MS), HNRNPCL3 (Affinity Capture-MS), HNRNPCL3 (Affinity Capture-MS), HNRNPC (Cross-Linking-MS (XL-MS)), HNRNPCL1 (Cross-Linking-MS (XL-MS)), RALYL (Cross-Linking-MS (XL-MS)), HNRNPCL3 (Cross-Linking-MS (XL-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

0 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

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1156987081 (1:13061374 G>A), RS1157098195 (1:13059144 T>C), RS1157417399 (1:13062154 C>A,T), RS1158702556 (1:13058820 A>G), RS1159218843 (1:13060855 C>T), RS1159632543 (1:13061686 G>A), RS1161426347 (1:13059275 C>G), RS1161833828 (1:13061397 A>C,G), RS1162411667 (1:13061759 C>T), RS1163544956 (1:13058898 G>A), RS1164036819 (1:13060887 T>C), RS1165896881 (1:13061476 G>T), RS1165919202 (1:13061008 C>T), RS1166013106 (1:13058900 G>C,T), RS1166184706 (1:13059288 G>A,C,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

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1

Clinical trials (associated diseases)

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