CSRNP1

Summary

CSRNP1 (cysteine and serine rich nuclear protein 1, HGNC:14300) is a protein-coding gene on chromosome 3p22.2, encoding Cysteine/serine-rich nuclear protein 1 (Q96S65). Binds to the consensus sequence 5’-AGAGTG-3’ and has transcriptional activator activity.

This gene encodes a protein that localizes to the nucleus and expression of this gene is induced in response to elevated levels of axin. The Wnt signalling pathway, which is negatively regulated by axin, is important in axis formation in early development and impaired regulation of this signalling pathway is often involved in tumors. A decreased level of expression of this gene in tumors compared to the level of expression in their corresponding normal tissues suggests that this gene product has a tumor suppressor function. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 64651 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 107 total
• MANE Select transcript: NM_033027

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14300
Approved symbol	CSRNP1
Name	cysteine and serine rich nuclear protein 1
Location	3p22.2
Locus type	gene with protein product
Status	Approved
Aliases	URAX1, DKFZp566F164, FAM130B, TAIP-3
Ensembl gene	ENSG00000144655
Ensembl biotype	protein_coding
OMIM	606458
Entrez	64651

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 18 protein_coding

ENST00000273153, ENST00000514182, ENST00000909282, ENST00000909283, ENST00000909284, ENST00000909285, ENST00000909286, ENST00000909287, ENST00000909288, ENST00000909289, ENST00000909290, ENST00000938863, ENST00000938864, ENST00000938865, ENST00000958140, ENST00000958141, ENST00000958142, ENST00000958143

RefSeq mRNA: 3 — MANE Select: NM_033027 NM_001320559, NM_001320560, NM_033027

CCDS: CCDS2682

Canonical transcript exons

ENST00000273153 — 5 exons

Exon	Start	End
ENSE00000966315	39146478	39146722
ENSE00000966316	39144997	39145256
ENSE00000966317	39144137	39144451
ENSE00001029997	39141855	39144044
ENSE00001825461	39153438	39153591

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 98.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.3141 / max 2025.9550, expressed in 1765 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41735	13.9081	1565
41734	13.6570	1590
41738	0.2346	112
41739	0.2086	102
41725	0.1677	82
41737	0.1381	72

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of stomach	UBERON:0001199	98.46	gold quality
vena cava	UBERON:0004087	97.33	gold quality
saphenous vein	UBERON:0007318	96.92	gold quality
gall bladder	UBERON:0002110	96.49	gold quality
left uterine tube	UBERON:0001303	96.15	gold quality
right lung	UBERON:0002167	96.12	gold quality
trachea	UBERON:0003126	95.62	gold quality
upper lobe of left lung	UBERON:0008952	95.32	gold quality
epithelial cell of pancreas	CL:0000083	94.49	silver quality
bone marrow cell	CL:0002092	94.22	gold quality
upper lobe of lung	UBERON:0008948	94.13	gold quality
smooth muscle tissue	UBERON:0001135	93.95	gold quality
tibial artery	UBERON:0007610	93.68	gold quality
popliteal artery	UBERON:0002250	93.67	gold quality
pericardium	UBERON:0002407	93.46	gold quality
omental fat pad	UBERON:0010414	93.38	gold quality
peritoneum	UBERON:0002358	93.34	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.03	gold quality
kidney epithelium	UBERON:0004819	92.75	silver quality
aorta	UBERON:0000947	92.68	gold quality
hindlimb stylopod muscle	UBERON:0004252	92.57	gold quality
nipple	UBERON:0002030	92.41	gold quality
parotid gland	UBERON:0001831	92.04	gold quality
skin of abdomen	UBERON:0001416	91.90	gold quality
adipose tissue of abdominal region	UBERON:0007808	91.86	gold quality
monocyte	CL:0000576	91.81	gold quality
ascending aorta	UBERON:0001496	91.78	gold quality
leukocyte	CL:0000738	91.42	gold quality
thoracic aorta	UBERON:0001515	91.38	gold quality
skin of leg	UBERON:0001511	91.15	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	49.47
E-CURD-122	yes	27.87
E-ANND-3	yes	12.82
E-MTAB-7606	no	555.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

83 targeting CSRNP1, 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-4283	100.00	66.42	2097
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6505-5P	99.73	69.25	1595

Literature-anchored findings (GeneRIF, showing 3)

• Three candidate tumor-suppressor genes, SEMA3B, AXUD1 and GNAT1 may be involved in oral squamous cell carcinoma. (PMID:23292452)
• cFos bound to the AP-1 cis element within the proximal MMP1 promoter only when the gene was transcriptionally silent as previously observed for MMP13. cFos contributes to MMP1 expression. Silencing of ATF3 (a prime MMP13 modulator) did not affect MMP1 expression whilst silencing CSRNP1 resulted in substantial repression of MMP1 but not MMP13. (PMID:30440036)
• Silencing of cysteine and serine rich nuclear protein 1 inhibits apoptosis, senescence and collagen degradation in human-derived vaginal fibroblasts in response to oxidative stress or DNA damage. (PMID:38908423)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	csrnp1a	ENSDARG00000031426
danio_rerio	csrnp1b	ENSDARG00000038429
mus_musculus	Csrnp1	ENSMUSG00000032515
rattus_norvegicus	Csrnp1	ENSRNOG00000033433
drosophila_melanogaster	Axud1	FBGN0261647
caenorhabditis_elegans	C41D11.3	WBGENE00016562

Paralogs (2): CSRNP2 (ENSG00000110925), CSRNP3 (ENSG00000178662)

Protein

Protein identifiers

Cysteine/serine-rich nuclear protein 1 — Q96S65 (reviewed: Q96S65)

Alternative names: Axin-1 up-regulated gene 1 protein, Protein URAX1, TGF-beta-induced apoptosis protein 3

All UniProt accessions (1): Q96S65

UniProt curated annotations — full annotation on UniProt →

Function. Binds to the consensus sequence 5’-AGAGTG-3’ and has transcriptional activator activity. May have a tumor-suppressor function. May play a role in apoptosis.

Subcellular location. Nucleus.

Tissue specificity. Ubiquitous. Most abundantly expressed in lung, placenta, skeletal muscle, pancreas and leukocyte. Frequently down-regulated in lung, kidney, liver and colon cancers compared with their corresponding normal tissues.

Similarity. Belongs to the AXUD1 family.

RefSeq proteins (3): NP_001307488, NP_001307489, NP_149016* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR023260	Cys/Ser-rich_nuc_prot	Family
IPR031972	CSRNP_N	Domain

Pfam: PF16019

UniProt features (6 total): region of interest 2, compositionally biased region 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96S65-F1	59.38	0.23

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 309 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, GSE45365_NK_CELL_VS_CD11B_DC_DN, GSE45365_NK_CELL_VS_BCELL_UP, GOBP_PLATELET_DERIVED_GROWTH_FACTOR_RECEPTOR_SIGNALING_PATHWAY, E2F_Q4_01, GOBP_BODY_MORPHOGENESIS, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, XU_GH1_AUTOCRINE_TARGETS_UP, PEREZ_TP63_TARGETS, TGACCTY_ERR1_Q2, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, FOSTER_TOLERANT_MACROPHAGE_UP, SCHMAHL_PDGF_SIGNALING, NF1_Q6_01

GO Biological Process (9): regulation of transcription by RNA polymerase II (GO:0006357), apoptotic process (GO:0006915), post-embryonic development (GO:0009791), positive regulation of transcription by RNA polymerase II (GO:0045944), platelet-derived growth factor receptor signaling pathway (GO:0048008), skeletal system morphogenesis (GO:0048705), roof of mouth development (GO:0060021), face morphogenesis (GO:0060325), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA-binding transcription factor activity (GO:0003700), sequence-specific DNA binding (GO:0043565), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
multicellular organism development	1
multicellular organismal process	1
positive regulation of DNA-templated transcription	1
cell surface receptor protein tyrosine kinase signaling pathway	1
skeletal system development	1
animal organ morphogenesis	1
anatomical structure development	1
anatomical structure morphogenesis	1
head morphogenesis	1
face development	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
DNA binding	1
nucleic acid binding	1
binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

752 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSRNP1	MSX1	P28360	844
CSRNP1	PAX7	P23759	690
CSRNP1	AXIN1	O15169	668
CSRNP1	CTNNB1	P35222	477
CSRNP1	SH2D3C	Q8N5H7	406
CSRNP1	GADD45B	O75293	378
CSRNP1	ARL14EPL	P0DKL9	368
CSRNP1	ZNF185	O15231	367
CSRNP1	UBFD1	O14562	351
CSRNP1	SLC22A14	Q9Y267	351
CSRNP1	FOSB	P53539	333
CSRNP1	ATF3	P18847	332
CSRNP1	FOXD3	Q9UJU5	327
CSRNP1	CUTC	Q9NTM9	326
CSRNP1	SPRY3	O43610	325

IntAct

40 interactions, top by confidence:

A	B	Type	Score
PPP1CA	CSRNP1	psi-mi:“MI:0915”(physical association)	0.870
CSRNP1	PPP1CA	psi-mi:“MI:0915”(physical association)	0.870
PPP1CC	CSRNP1	psi-mi:“MI:0915”(physical association)	0.740
CSRNP1	PPP1CC	psi-mi:“MI:0915”(physical association)	0.740
PPP1CA	CCDC85C	psi-mi:“MI:0914”(association)	0.670
MCRS1	CSRNP1	psi-mi:“MI:0915”(physical association)	0.670
CSRNP1	PPP1CB	psi-mi:“MI:0915”(physical association)	0.670
AQP1	CSRNP1	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	CSRNP1	psi-mi:“MI:0915”(physical association)	0.560
ZNF417	CSRNP1	psi-mi:“MI:0915”(physical association)	0.560
CSRNP1	ZNF587	psi-mi:“MI:0915”(physical association)	0.560
CSRNP1	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
CSRNP1	AQP1	psi-mi:“MI:0915”(physical association)	0.560
CSRNP1	ZNF417	psi-mi:“MI:0915”(physical association)	0.560
CSRNP1	PRPF18	psi-mi:“MI:0915”(physical association)	0.560
CSRNP1	PPP1CC	psi-mi:“MI:0915”(physical association)	0.370
CSRNP1	TAF5L	psi-mi:“MI:0914”(association)	0.350
PPP1CC	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MCRS1	CSRNP1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (34): CSRNP1 (Two-hybrid), CSRNP1 (Two-hybrid), CSRNP1 (Two-hybrid), ZNF587 (Two-hybrid), ZNF417 (Two-hybrid), TCEANC (Two-hybrid), CSRNP1 (Affinity Capture-MS), CSRNP1 (Synthetic Lethality), CSRNP1 (Affinity Capture-MS), PRPF18 (Two-hybrid), PPP1CA (Two-hybrid), TCEANC (Two-hybrid), MCRS1 (Two-hybrid), PPP1CB (Two-hybrid), CSRNP1 (Affinity Capture-MS)

ESM2 similar proteins: A2A7Y5, A2ALU4, A7MB40, A7YWL5, B0BN13, E9PV82, F1QGH6, F1QN48, H2M146, O94983, Q13796, Q14153, Q1L899, Q29RM2, Q2T9L4, Q3U2K0, Q5JXC2, Q5M9G5, Q5PQ25, Q5R638, Q5R815, Q5SW24, Q5SX79, Q5ZKN5, Q673G8, Q68DK7, Q6AYH0, Q6NSI3, Q6PB51, Q6PBC9, Q6PDM1, Q7TN08, Q7TNF9, Q80Y50, Q8BG26, Q8BGR5, Q8BP99, Q8BXQ8, Q8CD60, Q8IWD4

Diamond homologs: P59054, P59055, Q5R638, Q8BGQ2, Q8WYN3, Q96S65, Q9H175

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	95
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

919 predictions. Top by Δscore:

Variant	Effect	Δscore
3:39144041:CCAT:C	acceptor_gain	1.0000
3:39144042:CAT:C	acceptor_gain	1.0000
3:39144042:CATC:C	acceptor_gain	1.0000
3:39144043:ATC:A	acceptor_loss	1.0000
3:39144044:TCTG:T	acceptor_loss	1.0000
3:39144045:C:CA	acceptor_loss	1.0000
3:39144045:C:CC	acceptor_gain	1.0000
3:39144046:T:A	acceptor_loss	1.0000
3:39144153:G:A	donor_gain	1.0000
3:39144991:CTCTA:C	donor_loss	1.0000
3:39144992:TCTAC:T	donor_loss	1.0000
3:39144993:CTAC:C	donor_loss	1.0000
3:39144994:TAC:T	donor_loss	1.0000
3:39144996:C:CT	donor_loss	1.0000
3:39144999:T:A	donor_gain	1.0000
3:39145252:CAGGG:C	acceptor_gain	1.0000
3:39145253:AGGG:A	acceptor_gain	1.0000
3:39145254:GGG:G	acceptor_gain	1.0000
3:39145254:GGGC:G	acceptor_loss	1.0000
3:39145255:GGC:G	acceptor_loss	1.0000
3:39145257:C:CC	acceptor_gain	1.0000
3:39146719:CAGC:C	acceptor_gain	1.0000
3:39144043:AT:A	acceptor_gain	0.9900
3:39144131:CCACA:C	donor_loss	0.9900
3:39144132:CACA:C	donor_loss	0.9900
3:39144133:ACAC:A	donor_loss	0.9900
3:39144134:CACCT:C	donor_loss	0.9900
3:39144136:C:CG	donor_loss	0.9900
3:39144138:TGGC:T	donor_gain	0.9900
3:39144149:G:A	donor_gain	0.9900

AlphaMissense

3869 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:39143973:A:C	F284L	0.999
3:39143973:A:T	F284L	0.999
3:39143975:A:G	F284L	0.999
3:39144141:C:G	C259S	0.998
3:39144142:A:G	C259R	0.998
3:39144142:A:T	C259S	0.998
3:39144027:G:C	F266L	0.997
3:39144027:G:T	F266L	0.997
3:39144029:A:G	F266L	0.997
3:39144161:G:C	C252W	0.997
3:39144167:G:C	C250W	0.997
3:39144169:A:G	C250R	0.997
3:39144162:C:G	C252S	0.996
3:39144162:C:T	C252Y	0.996
3:39144163:A:G	C252R	0.996
3:39144163:A:T	C252S	0.996
3:39144168:C:T	C250Y	0.996
3:39143974:A:G	F284S	0.995
3:39144140:G:C	C259W	0.995
3:39144168:C:G	C250S	0.995
3:39144169:A:T	C250S	0.995
3:39144183:C:G	C245S	0.995
3:39144183:C:T	C245Y	0.995
3:39144184:A:G	C245R	0.995
3:39144184:A:T	C245S	0.995
3:39145162:G:C	F100L	0.995
3:39145162:G:T	F100L	0.995
3:39145164:A:G	F100L	0.995
3:39144168:C:A	C250F	0.994
3:39144162:C:A	C252F	0.993

dbSNP variants (sampled 300 via entrez): RS1000184066 (3:39153445 C>A,G,T), RS1000198980 (3:39150353 G>A), RS1000632803 (3:39150045 C>A), RS1000639366 (3:39153187 G>A), RS1000880784 (3:39142365 T>C,G), RS1000973718 (3:39142140 T>C), RS1001019223 (3:39145938 A>G), RS1001306994 (3:39143442 A>G), RS1001697783 (3:39143109 G>A,C), RS1001857005 (3:39148540 T>C), RS1002146338 (3:39155461 A>G), RS1002336754 (3:39142804 G>C,T), RS1002410408 (3:39155086 G>T), RS1002475546 (3:39146246 C>T), RS1002714325 (3:39146022 C>T)

Disease associations

OMIM: gene MIM:606458 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST002367_11	Social communication problems	9.000000e-09
GCST002701_3	Verbal declarative memory	2.000000e-06
GCST002701_39	Verbal declarative memory	3.000000e-06
GCST003075_110	Cognitive decline rate in late mild cognitive impairment	3.000000e-07
GCST003075_6	Cognitive decline rate in late mild cognitive impairment	5.000000e-08
GCST003468_25	Chronic lymphocytic leukemia	2.000000e-07
GCST003518_42	Daytime sleep phenotypes	8.000000e-06
GCST011378_3	Brain-derived neurotrophic factor levels	6.000000e-11
GCST90002400_356	Plateletcrit	3.000000e-13
GCST90002402_305	Platelet count	2.000000e-12

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0005427	social communication impairment
EFO:0004874	memory performance
EFO:0006806	paragraph delayed recall measurement
EFO:0007710	cognitive decline measurement
EFO:0007828	daytime rest measurement
EFO:0011018	brain-derived neurotrophic factor measurement
EFO:0007985	platelet crit
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects cotreatment, decreases expression, increases abundance, increases oxidation, affects expression (+1 more)	3
Benzo(a)pyrene	affects methylation, increases expression	3
Ozone	affects cotreatment, decreases expression, increases oxidation, increases abundance, affects expression	3
Tobacco Smoke Pollution	decreases methylation, increases expression, affects expression	3
Particulate Matter	increases abundance, increases expression, affects expression, increases reaction	3
sodium arsenite	decreases expression, increases expression	2
methacrylaldehyde	affects cotreatment, decreases expression, increases oxidation, increases abundance	2
Acetaminophen	increases expression	2
Acrolein	increases abundance, affects cotreatment, decreases expression, increases oxidation	2
Cisplatin	affects cotreatment, decreases expression, increases expression	2
Valproic Acid	decreases methylation, increases expression	2
Cyclosporine	increases expression	2
Asbestos, Crocidolite	affects expression, increases expression	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	increases expression	1
TAK-243	increases sumoylation	1
urushiol	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases oxidation, increases abundance	1
bisphenol A	decreases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
beta-lapachone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	increases expression	1
ferrous chloride	increases expression	1
propionic acid	increases expression	1
cupric chloride	increases expression	1
pentanal	increases expression	1
diethyl malate	increases expression	1

Clinical trials (associated diseases)

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