HNRNPCL1

Summary

HNRNPCL1 (heterogeneous nuclear ribonucleoprotein C like 1, HGNC:29295) is a protein-coding gene on chromosome 1p36.21, encoding Heterogeneous nuclear ribonucleoprotein C-like 1 (O60812). 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 343069 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 56 total
• MANE Select transcript: NM_001013631

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29295
Approved symbol	HNRNPCL1
Name	heterogeneous nuclear ribonucleoprotein C like 1
Location	1p36.21
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000179172
Ensembl biotype	protein_coding
Entrez	343069

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000317869

RefSeq mRNA: 1 — MANE Select: NM_001013631 NM_001013631

CCDS: CCDS30591

Canonical transcript exons

ENST00000317869 — 2 exons

Exon	Start	End
ENSE00001469682	12848681	12848720
ENSE00001665050	12847377	12848470

Expression profiles

Bgee: expression breadth broad, 31 present calls, max score 82.47.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
diaphragm	UBERON:0001103	82.47	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	78.07	silver quality
heart right ventricle	UBERON:0002080	76.60	silver quality
blood vessel layer	UBERON:0004797	72.27	gold quality
superficial temporal artery	UBERON:0001614	70.18	gold quality
choroid plexus epithelium	UBERON:0003911	68.92	silver quality
germinal epithelium of ovary	UBERON:0001304	68.65	gold quality
triceps brachii	UBERON:0001509	68.48	gold quality
amniotic fluid	UBERON:0000173	68.01	gold quality
nasal cavity epithelium	UBERON:0005384	67.80	gold quality
jejunal mucosa	UBERON:0000399	66.90	silver quality
gluteal muscle	UBERON:0002000	66.05	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	65.78	silver quality
secondary oocyte	CL:0000655	65.46	silver quality
epithelium of nasopharynx	UBERON:0001951	65.19	gold quality
mucosa of paranasal sinus	UBERON:0005030	64.60	gold quality
olfactory bulb	UBERON:0002264	64.16	gold quality
type B pancreatic cell	CL:0000169	63.87	gold quality
jejunum	UBERON:0002115	62.20	silver quality
cranial nerve II	UBERON:0000941	61.24	gold quality
palpebral conjunctiva	UBERON:0001812	59.78	silver quality
seminal vesicle	UBERON:0000998	59.53	silver quality
upper arm skin	UBERON:0004263	58.31	gold quality
cartilage tissue	UBERON:0002418	57.50	silver quality
colonic mucosa	UBERON:0000317	57.06	silver quality
mucosa of sigmoid colon	UBERON:0004993	56.89	silver quality
trachea	UBERON:0003126	55.26	gold quality
urethra	UBERON:0000057	55.13	silver quality
vena cava	UBERON:0004087	55.11	silver quality
esophagus squamous epithelium	UBERON:0006920	55.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.43

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), HNRNPCL4 (ENSG00000179412), RALYL (ENSG00000184672), HNRNPCL2 (ENSG00000275774), HNRNPCL3 (ENSG00000277058)

Protein

Protein identifiers

Heterogeneous nuclear ribonucleoprotein C-like 1 — O60812 (reviewed: O60812)

Alternative names: hnRNP core protein C-like 1

All UniProt accessions (1): O60812

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_001013653* (*=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 (12 total): compositionally biased region 4, sequence variant 3, 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-O60812-F1	70.93	0.32

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 3 (showing top): ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, 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

1777 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HNRNPCL1	SLC35F2	Q8IXU6	583
HNRNPCL1	CHRFAM7A	Q494W8	570
HNRNPCL1	DOP1B	Q9Y3R5	475
HNRNPCL1	IMMP2L	Q96T52	446
HNRNPCL1	OR2T2	Q6IF00	435
HNRNPCL1	RALYL	Q86SE5	432
HNRNPCL1	PABPN1L	A6NDY0	419
HNRNPCL1	PRAMEF18	Q5VWM3	400
HNRNPCL1	CSMD1	Q96PZ7	400
HNRNPCL1	OR4M2	Q8NGB6	399
HNRNPCL1	PRAMEF11	O60813	392
HNRNPCL1	PRAMEF7	Q5VXH5	380
HNRNPCL1	ZNF816	Q0VGE8	369
HNRNPCL1	OR52N5	Q8NH56	355
HNRNPCL1	FUBP3	Q96I24	354

IntAct

138 interactions, top by confidence:

A	B	Type	Score
PPIE	AQR	psi-mi:“MI:0914”(association)	0.810
YBX1	HNRNPR	psi-mi:“MI:0914”(association)	0.770
NS	PIK3R2	psi-mi:“MI:0914”(association)	0.750
BUB1	NDC80	psi-mi:“MI:0914”(association)	0.670
HNRNPCL1	HNRNPC	psi-mi:“MI:0915”(physical association)	0.670
HNRNPCL2	HNRNPCL1	psi-mi:“MI:0915”(physical association)	0.670
HNRNPCL1	HNRNPC	psi-mi:“MI:0914”(association)	0.670
SNRPA1	U2SURP	psi-mi:“MI:0914”(association)	0.640
HNRNPCL1	HNRNPCL1	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL1	RALYL	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL1	RAD54L2	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL1	PIAS2	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL1	UBE2I	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL1	RNF4	psi-mi:“MI:0915”(physical association)	0.560
C20orf202	HNRNPCL1	psi-mi:“MI:0915”(physical association)	0.560
HNRNPCL1	RALY	psi-mi:“MI:0915”(physical association)	0.560
NP	KPNA6	psi-mi:“MI:0914”(association)	0.550
ELAVL2	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
ZFC3H1	HNRNPCL1	psi-mi:“MI:0914”(association)	0.530
MRPL13	GTPBP10	psi-mi:“MI:0914”(association)	0.530
EBNA-LP	HAX1	psi-mi:“MI:0914”(association)	0.530
ESR2	FBLL1	psi-mi:“MI:0914”(association)	0.460
FUS	DDX3X	psi-mi:“MI:0914”(association)	0.430
Trim69		psi-mi:“MI:0915”(physical association)	0.400
Tipin	NEMF	psi-mi:“MI:0914”(association)	0.350
Cdc26		psi-mi:“MI:0914”(association)	0.350
CEP135	TBC1D31	psi-mi:“MI:0914”(association)	0.350
HNRNPD	ARHGAP32	psi-mi:“MI:0914”(association)	0.350
JUN		psi-mi:“MI:0914”(association)	0.350

BioGRID (192): HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-MS), HNRNPCL1 (Affinity Capture-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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 132 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
Formation of TC-NER Pre-Incision Complex	6	15.5×	3e-04
Processing of Capped Intron-Containing Pre-mRNA	11	11.0×	2e-06
Dual incision in TC-NER	5	10.6×	8e-03
mRNA Polyadenylation	7	7.5×	5e-03
mRNA Splicing - Major Pathway	11	7.3×	6e-05
Dengue Virus-Host Interactions	12	6.7×	6e-05

GO biological processes:

GO term	Partners	Fold	FDR
mRNA stabilization	5	16.5×	2e-03
intrinsic apoptotic signaling pathway	5	16.1×	2e-03
negative regulation of translation	7	12.4×	6e-04
mRNA splicing, via spliceosome	10	8.2×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	7
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

43 predictions. Top by Δscore:

Variant	Effect	Δscore
1:12848479:A:C	acceptor_gain	0.9900
1:12848481:G:C	acceptor_gain	0.9900
1:12848469:TT:T	acceptor_gain	0.9800
1:12848469:TTCT:T	acceptor_loss	0.9800
1:12848470:TCTG:T	acceptor_loss	0.9800
1:12848471:C:CC	acceptor_gain	0.9800
1:12848471:C:CG	acceptor_loss	0.9800
1:12848472:T:A	acceptor_loss	0.9800
1:12848479:A:AC	acceptor_gain	0.9800
1:12848466:GAATT:G	acceptor_gain	0.9600
1:12848476:A:AC	acceptor_gain	0.9600
1:12848467:AATT:A	acceptor_gain	0.9300
1:12848468:ATT:A	acceptor_gain	0.9200
1:12848481:G:GC	acceptor_gain	0.9200
1:12848476:A:C	acceptor_gain	0.8400
1:12848473:G:C	acceptor_loss	0.7600
1:12848311:T:TG	acceptor_gain	0.7000
1:12848505:T:C	acceptor_gain	0.6900
1:12848312:C:G	acceptor_gain	0.6500
1:12848320:C:CT	acceptor_gain	0.6100
1:12848321:A:T	acceptor_gain	0.5600
1:12848505:T:TC	acceptor_gain	0.5400
1:12848313:A:T	acceptor_gain	0.4700
1:12848312:C:CT	acceptor_gain	0.4300
1:12848501:A:C	acceptor_gain	0.3500
1:12848468:A:C	acceptor_gain	0.3400
1:12848320:C:T	acceptor_gain	0.3300
1:12848492:C:CT	acceptor_gain	0.2700
1:12848674:GACTT:G	donor_loss	0.2700
1:12848675:ACTT:A	donor_loss	0.2700

AlphaMissense

1951 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:12848128:G:C	F54L	0.999
1:12848128:G:T	F54L	0.999
1:12848130:A:G	F54L	0.999
1:12848134:A:C	F52L	0.999
1:12848134:A:T	F52L	0.999
1:12848136:A:G	F52L	0.999
1:12848233:G:C	F19L	0.999
1:12848233:G:T	F19L	0.999
1:12848235:A:G	F19L	0.999
1:12848168:C:A	G41V	0.997
1:12848179:A:C	F37L	0.997
1:12848179:A:T	F37L	0.997
1:12848180:A:G	F37S	0.997
1:12848181:A:G	F37L	0.997
1:12848234:A:G	F19S	0.997
1:12848129:A:G	F54S	0.996
1:12848228:C:T	G21E	0.996
1:12848129:A:C	F54C	0.995
1:12848222:A:G	L23P	0.995
1:12848222:A:T	L23H	0.995
1:12848093:G:T	A66D	0.994
1:12848132:G:T	A53D	0.994
1:12848234:A:C	F19C	0.994
1:12848126:A:T	V55D	0.993
1:12848135:A:G	F52S	0.993
1:12848235:A:T	F19I	0.992
1:12847730:A:G	L187S	0.991
1:12848147:A:T	V48D	0.991
1:12848235:A:C	F19V	0.991
1:12848228:C:A	G21V	0.990

dbSNP variants (sampled 300 via entrez): RS1000874707 (1:12850102 G>C,T), RS1003081800 (1:12849990 C>A,T), RS1003112871 (1:12850232 G>C), RS1003869889 (1:12850143 T>A,C), RS1005436298 (1:12847039 A>G,T), RS1005523247 (1:12850398 G>A,T), RS1006868795 (1:12849475 G>A), RS1007707760 (1:12849124 G>A,C), RS1010377888 (1:12850250 G>A), RS1010410389 (1:12850662 T>C), RS1010742098 (1:12849056 G>A), RS1010843736 (1:12849568 T>G), RS1011128152 (1:12848784 G>A,C), RS1013227948 (1:12846974 T>A,G), RS1013307143 (1:12848391 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): Mayer-Rokitansky-Kuster-Hauser syndrome (MONDO:0017771)

Orphanet (2): Mayer-Rokitansky-Küster-Hauser syndrome type 1 (Orphanet:247775), Mayer-Rokitansky-Küster-Hauser syndrome (Orphanet:3109)

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

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
bisphenol A	affects cotreatment, increases expression	1
tetrahydropalmatine	decreases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
CGP 52608	affects binding, increases reaction	1
corosolic acid	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Panobinostat	affects cotreatment, affects expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Cisplatin	affects cotreatment, affects expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Ozone	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Urethane	decreases expression	1
1-Methyl-3-isobutylxanthine	increases expression, affects cotreatment	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03277430	PHASE3	UNKNOWN	Uterus Transplantation From Live Donors and From Deceased Donors - Clinical Study
NCT01911884	Not specified	COMPLETED	Assessment of Quality of Global and Sexual Life and Impact of Surgical and Non Surgical Vaginal Aplasia in Patients With a Rokitansky Syndrome
NCT02967822	Not specified	RECRUITING	Molecular Genetic Study of Mayer-Rokitansky-Kuster-Hauser Syndrome
NCT03252795	Not specified	RECRUITING	Uterus Transplantation From a Multi-organ Donor
NCT03307356	Not specified	ACTIVE_NOT_RECRUITING	The University of Pennsylvania Uterus Transplant for Uterine Factor Infertility Trial
NCT03689842	Not specified	RECRUITING	Feasibility Study of Uterine Transplantation From Living Donors in Terms of Efficacy and Safety in Patients With Mayer-Rokitansky-Küster-Hauser Syndrome (MRKH)
NCT04314869	Not specified	UNKNOWN	Uterus Transplantation Procedure From a Live Donor
NCT04923217	Not specified	COMPLETED	Quality of Life and Sexual Function in Vaginal Aplasia Patients After Davydov Procedure
NCT05263076	Not specified	RECRUITING	Uterine Transplant for Women With Absolute Uterine Factor Infertility (AUFI)
NCT05415540	Not specified	COMPLETED	Evolution of the Quality of Life and Experience of Young Women With Utero-vaginal Aplasia (MRKHPSY)
NCT05925361	Not specified	UNKNOWN	Peritoneum Vaginoplasty; Implementation According to IDEAL Framework
NCT06508151	Not specified	NOT_YET_RECRUITING	Neovaginoplasty Using Photoinduced-imine-crosslink Hydrogel in MRKH Patients
NCT07186764	Not specified	RECRUITING	Evaluation of the Quality of Life and Gynecological Follow-up of Patients Treated for Mayer-Rokitansky-Küster-Hauser (MRKH) Syndrome
NCT07321782	Not specified	NOT_YET_RECRUITING	Clinical and Imaging Features in MRKH Syndrome