CSRNP2

Summary

CSRNP2 (cysteine and serine rich nuclear protein 2, HGNC:16006) is a protein-coding gene on chromosome 12q13.12, encoding Cysteine/serine-rich nuclear protein 2 (Q9H175). Binds to the consensus sequence 5’-AGAGTG-3’ and has transcriptional activator activity.

The protein encoded by this gene belongs to the CSRNP family of nuclear proteins that share conserved regions, including cysteine- and serine- rich regions, a basic domain, a transcriptional activation domain, and bind the sequence ‘AGAGTG’, thus have the hallmark of transcription factors. Studies in mice suggest that these genes may have redundant functions. Alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 81566 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 81 total
• MANE Select transcript: NM_030809

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16006
Approved symbol	CSRNP2
Name	cysteine and serine rich nuclear protein 2
Location	12q13.12
Locus type	gene with protein product
Status	Approved
Aliases	C12ORF2, TAIP-12, PPP1R72
Ensembl gene	ENSG00000110925
Ensembl biotype	protein_coding
OMIM	620404
Entrez	81566

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 16 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000228515, ENST00000546935, ENST00000548206, ENST00000548981, ENST00000550461, ENST00000550533, ENST00000552680, ENST00000552899, ENST00000863897, ENST00000863898, ENST00000863899, ENST00000863900, ENST00000863901, ENST00000863902, ENST00000927000, ENST00000927001, ENST00000927002, ENST00000927003, ENST00000956406

RefSeq mRNA: 1 — MANE Select: NM_030809 NM_030809

CCDS: CCDS8807

Canonical transcript exons

ENST00000228515 — 5 exons

Exon	Start	End
ENSE00000743673	51067673	51067969
ENSE00001156228	51061205	51064669
ENSE00001156235	51076411	51076647
ENSE00002383976	51083339	51083596
ENSE00003618134	51073823	51074082

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 96.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.0029 / max 388.2914, expressed in 1798 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
130931	11.8846	1798
206699	0.1183	33

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	96.67	gold quality
ganglionic eminence	UBERON:0004023	93.47	gold quality
sural nerve	UBERON:0015488	92.91	gold quality
endothelial cell	CL:0000115	89.12	gold quality
cerebellar cortex	UBERON:0002129	88.79	gold quality
cerebellar hemisphere	UBERON:0002245	88.74	gold quality
right hemisphere of cerebellum	UBERON:0014890	88.45	gold quality
middle temporal gyrus	UBERON:0002771	88.40	gold quality
cerebellum	UBERON:0002037	88.17	gold quality
right testis	UBERON:0004534	87.92	gold quality
left testis	UBERON:0004533	87.75	gold quality
cerebellar vermis	UBERON:0004720	87.75	gold quality
stromal cell of endometrium	CL:0002255	87.59	gold quality
prefrontal cortex	UBERON:0000451	87.47	gold quality
ventricular zone	UBERON:0003053	87.29	gold quality
testis	UBERON:0000473	87.08	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.07	gold quality
right frontal lobe	UBERON:0002810	87.05	gold quality
secondary oocyte	CL:0000655	87.04	gold quality
Brodmann (1909) area 9	UBERON:0013540	86.76	gold quality
primary visual cortex	UBERON:0002436	86.66	gold quality
adenohypophysis	UBERON:0002196	86.52	gold quality
neocortex	UBERON:0001950	86.35	gold quality
Brodmann (1909) area 23	UBERON:0013554	86.35	gold quality
frontal cortex	UBERON:0001870	86.23	gold quality
pituitary gland	UBERON:0000007	86.03	gold quality
cerebral cortex	UBERON:0000956	85.89	gold quality
cingulate cortex	UBERON:0003027	85.74	gold quality
embryo	UBERON:0000922	85.73	gold quality
gastrocnemius	UBERON:0001388	85.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

138 targeting CSRNP2, 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-6867-5P	100.00	82.21	3464
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-7152-3P	99.97	67.47	849
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-4302	99.89	67.94	1187

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	csrnp2	ENSDARG00000075972
mus_musculus	Csrnp2	ENSMUSG00000044636
rattus_norvegicus	Csrnp2	ENSRNOG00000019653
drosophila_melanogaster	Axud1	FBGN0261647
caenorhabditis_elegans	C41D11.3	WBGENE00016562

Paralogs (2): CSRNP1 (ENSG00000144655), CSRNP3 (ENSG00000178662)

Protein

Protein identifiers

Cysteine/serine-rich nuclear protein 2 — Q9H175 (reviewed: Q9H175)

Alternative names: Protein FAM130A1, TGF-beta-induced apoptosis protein 12

All UniProt accessions (5): Q9H175, F8VTU0, F8VVN1, F8VZY2, F8W1G8

UniProt curated annotations — full annotation on UniProt →

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

Subcellular location. Nucleus.

Similarity. Belongs to the AXUD1 family.

RefSeq proteins (1): NP_110436* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF16019

UniProt features (9 total): region of interest 3, compositionally biased region 3, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H175-F1	64.02	0.26

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 (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 203 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, TGGTGCT_MIR29A_MIR29B_MIR29C, BROWNE_HCMV_INFECTION_4HR_UP, MYAATNNNNNNNGGC_UNKNOWN, GCM_GSPT1, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, TGACCTY_ERR1_Q2, AP2_Q3, SP1_Q2_01, GCM_BCL2L1, CATTTCA_MIR203, IRF1_Q6, WANG_CISPLATIN_RESPONSE_AND_XPC_DN, BENPORATH_NOS_TARGETS, P300_01

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), apoptotic process (GO:0006915), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (7): 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), phosphatase binding (GO:0019902), 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
positive regulation of DNA-templated transcription	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
enzyme binding	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

546 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSRNP2	ZBTB39	O15060	543
CSRNP2	FAM199X	Q6PEV8	447
CSRNP2	NAV3	Q8IVL0	435
CSRNP2	C2orf15	Q8WU43	434
CSRNP2	ESYT1	Q9BSJ8	432
CSRNP2	GPR84	Q9NQS5	420
CSRNP2	ANKRD52	Q8NB46	402
CSRNP2	ZNF786	Q8N393	370
CSRNP2	TARBP2	Q15633	368
CSRNP2	HAGHL	Q6PII5	355
CSRNP2	NCKAP5L	Q9HCH0	355
CSRNP2	UTP14C	Q5TAP6	350
CSRNP2	PPP1R37	O75864	348
CSRNP2	BRD10	Q5HYC2	348
CSRNP2	DRC2	Q8IXS2	348
CSRNP2	OSER1	Q9NX31	348

IntAct

29 interactions, top by confidence:

A	B	Type	Score
CSRNP2	PPP1CA	psi-mi:“MI:0915”(physical association)	0.920
PPP1CA	CSRNP2	psi-mi:“MI:0915”(physical association)	0.920
PPP1CA	CSRNP2	psi-mi:“MI:0407”(direct interaction)	0.920
CSRNP2	PPP1CC	psi-mi:“MI:0915”(physical association)	0.830
PPP1CC	CSRNP2	psi-mi:“MI:0915”(physical association)	0.830
CSRNP2	PPP1CB	psi-mi:“MI:0915”(physical association)	0.740
PPP1CB	CSRNP2	psi-mi:“MI:0915”(physical association)	0.740
PPP1CC	CCDC85C	psi-mi:“MI:0914”(association)	0.740
PPP1CA	CCDC85C	psi-mi:“MI:0914”(association)	0.670
PPP1CC	CCDC85C	psi-mi:“MI:0914”(association)	0.350
PPP1CC	CSRNP2	psi-mi:“MI:0915”(physical association)	0.000
PPP1CA	CSRNP2	psi-mi:“MI:0915”(physical association)	0.000
PPP1CB	CSRNP2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (17): CSRNP2 (Two-hybrid), CSRNP2 (Two-hybrid), CSRNP2 (Two-hybrid), CSRNP2 (Affinity Capture-MS), CSRNP2 (Affinity Capture-MS), CSRNP2 (Affinity Capture-MS), CSRNP2 (Affinity Capture-MS), PPP1CC (Two-hybrid), PPP1CA (Two-hybrid), PPP1CC (Two-hybrid), PPP1CB (Two-hybrid), CSRNP2 (Affinity Capture-RNA), CSRNP2 (Affinity Capture-MS), CSRNP2 (Affinity Capture-MS), DAXX (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1A4L6, F1QDF8, O35914, O75113, O95238, P01105, P10157, P13474, P14921, P15036, P15037, P15062, P15375, P18755, P18756, P19102, P19335, P27577, P40649, P41156, P78545, Q28EW4, Q28F43, Q32NH9, Q3MHT3, Q3UM89, Q3UPW2, Q3YFL6, Q4G112, Q4V7E1, Q5M7N6, Q5SW75, Q66IG8, Q6IE24, Q6NRK3, Q6PUR7, Q708W1, Q708W2, Q76I76, Q7M6U3

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1570 predictions. Top by Δscore:

Variant	Effect	Δscore
12:51067668:CTGA:C	donor_loss	1.0000
12:51067669:TGAC:T	donor_loss	1.0000
12:51067670:GAC:G	donor_loss	1.0000
12:51067671:A:AT	donor_loss	1.0000
12:51067672:CCTGG:C	donor_gain	1.0000
12:51067749:T:TA	donor_gain	1.0000
12:51067750:C:A	donor_gain	1.0000
12:51067965:GTCAG:G	acceptor_gain	1.0000
12:51067967:CAG:C	acceptor_gain	1.0000
12:51067968:AG:A	acceptor_gain	1.0000
12:51067969:GC:G	acceptor_loss	1.0000
12:51067970:C:CA	acceptor_loss	1.0000
12:51067970:C:CC	acceptor_gain	1.0000
12:51067971:T:C	acceptor_loss	1.0000
12:51067974:C:CT	acceptor_gain	1.0000
12:51074078:TGTGG:T	acceptor_gain	1.0000
12:51074079:GTGG:G	acceptor_gain	1.0000
12:51074080:TGG:T	acceptor_gain	1.0000
12:51074083:C:CC	acceptor_gain	1.0000
12:51076405:A:AC	donor_gain	1.0000
12:51076406:C:CC	donor_gain	1.0000
12:51064668:ACC:A	acceptor_loss	0.9900
12:51064671:T:A	acceptor_loss	0.9900
12:51065385:A:C	acceptor_gain	0.9900
12:51065391:C:CT	acceptor_gain	0.9900
12:51065392:A:T	acceptor_gain	0.9900
12:51067671:A:AC	donor_gain	0.9900
12:51067672:C:CC	donor_gain	0.9900
12:51067966:TCAG:T	acceptor_gain	0.9900
12:51067967:CAGC:C	acceptor_gain	0.9900

AlphaMissense

3545 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:51064551:A:G	L276P	1.000
12:51064556:C:A	M274I	1.000
12:51064556:C:G	M274I	1.000
12:51064556:C:T	M274I	1.000
12:51064563:G:A	T272I	1.000
12:51064569:A:G	L270P	1.000
12:51064573:A:C	Y269D	1.000
12:51064574:A:C	H268Q	1.000
12:51064574:A:T	H268Q	1.000
12:51064575:T:C	H268R	1.000
12:51064576:G:C	H268D	1.000
12:51064576:G:T	H268N	1.000
12:51064578:G:A	T267I	1.000
12:51064581:C:G	R266P	1.000
12:51064584:A:G	V265A	1.000
12:51064584:A:T	V265D	1.000
12:51064595:A:C	N261K	1.000
12:51064595:A:T	N261K	1.000
12:51064598:A:C	F260L	1.000
12:51064598:A:T	F260L	1.000
12:51064599:A:C	F260C	1.000
12:51064599:A:G	F260S	1.000
12:51064600:A:C	F260V	1.000
12:51064600:A:G	F260L	1.000
12:51064600:A:T	F260I	1.000
12:51064609:G:T	R257S	1.000
12:51064611:C:T	G256E	1.000
12:51064619:G:C	N253K	1.000
12:51064619:G:T	N253K	1.000
12:51064625:A:C	C251W	1.000

dbSNP variants (sampled 300 via entrez): RS1000908649 (12:51080680 C>G), RS1000949262 (12:51073950 A>G), RS1001114766 (12:51072647 A>T), RS1001167206 (12:51072955 C>T), RS1001299864 (12:51082759 G>A), RS1001322862 (12:51066501 C>A), RS1001358586 (12:51081323 A>T), RS1001391367 (12:51068404 G>A), RS1001399082 (12:51075114 A>G), RS1001538716 (12:51062336 T>A,C), RS1001548570 (12:51061160 C>T), RS1001729031 (12:51081846 C>A), RS1001888788 (12:51063651 G>A,T), RS1002007998 (12:51068762 T>C), RS1002144189 (12:51062264 AAC>A)

Disease associations

OMIM: gene MIM:620404 | 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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	4
(+)-JQ1 compound	increases expression	4
Acetaminophen	increases expression	3
Benzo(a)pyrene	decreases methylation, increases expression, increases methylation	2
Cyclosporine	increases expression	2
aristolochic acid I	increases expression	1
trichostatin A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	increases expression	1
ICG 001	increases expression	1
perfluorobutanesulfonic acid	decreases expression	1
licochalcone B	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases expression, increases abundance	1
Arsenic	increases abundance, increases expression, affects cotreatment	1
Benzene	increases expression	1
Calcitriol	decreases expression	1
Coumestrol	decreases expression, affects cotreatment	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	decreases expression	1
Drugs, Chinese Herbal	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SJ95	HAP1 CSRNP2 (-) 1	Cancer cell line	Male
CVCL_SJ96	HAP1 CSRNP2 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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