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
• GTEx eGene: eQTL in 31 tissues, sQTL in 3 (q < 0.05)
• Constraint (gnomAD): pLI 1.00 (loss-of-function intolerant), LOEUF 0.47 (moderately constrained)
• MANE Select transcript: NM_030809
• Notable: 81 clinical variants but no curated precision-oncology (CIViC) evidence yet

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: 21 — 18 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

MANE Select: ENST00000228515

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1, TSL 3: 2, TSL 4: 2, TSL 5: 2

ENST00000228515, ENST00000546935, ENST00000548206, ENST00000548981, ENST00000550461, ENST00000550533, ENST00000552680, ENST00000552899, ENST00000863897, ENST00000863898, ENST00000863899, ENST00000863900, ENST00000863901, ENST00000863902, ENST00000927000, ENST00000927001, ENST00000927002, ENST00000927003, ENST00000956406, ENST00000984343, ENST00001140228

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.

Highest expression (Bgee): cortical plate, ganglionic eminence, sural nerve, endothelial cell, cerebellar cortex.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CSRNP2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 31 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 34 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Brain Cerebellum	eqtl	1.4e-25	+0.67	12:51045882:G:C
Brain Cerebellar Hemisphere	eqtl	1.2e-12	+0.42	12:51074528:G:A
Thyroid	eqtl	2.1e-12	+0.25	12:51096625:G:A
Skin Not Sun Exposed Suprapubic	eqtl	9.1e-12	-0.33	12:51112120:C:T
Nerve Tibial	eqtl	3.1e-10	-0.23	12:51092911:A:G
Heart Atrial Appendage	eqtl	3.6e-10	-0.34	12:51090362:T:C
Esophagus Muscularis	eqtl	4.8e-08	+0.28	12:51123927:C:T
Muscle Skeletal	eqtl	5.5e-08	+0.24	12:51038331:A:G
Artery Tibial	eqtl	1.9e-07	-0.17	12:51094099:T:C
Colon Sigmoid	eqtl	5.3e-07	-0.22	12:51090362:T:C
Heart Left Ventricle	eqtl	1.4e-06	+0.35	12:51078780:A:T
Skin Sun Exposed Lower leg	eqtl	2.6e-06	-0.18	12:51072645:C:CGAAGAA
Lung	eqtl	5.8e-06	+0.24	12:50941362:G:A
Adipose Subcutaneous	eqtl	8.6e-06	-0.19	12:51092911:A:G
Artery Aorta	eqtl	9.4e-05	+0.19	12:50941005:C:T
Esophagus Gastroesophageal Junction	eqtl	1.3e-04	+0.24	12:51115704:G:A
Whole Blood	eqtl	2.0e-04	-0.13	12:51085652:A:G
Brain Spinal cord cervical c-1	eqtl	2.4e-04	+0.36	12:51175477:C:G
Esophagus Mucosa	eqtl	3.4e-04	-0.15	12:51118854:CT:C
Testis	eqtl	5.0e-04	+0.18	12:51038331:A:G

FANTOM5 promoters

2 alternative TSS:

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

Top tissues by expression

showing 100 of 287 tissues 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
anterior cingulate cortex	UBERON:0009835	85.64	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.61	gold quality
mucosa of stomach	UBERON:0001199	85.38	gold quality
muscle of leg	UBERON:0001383	85.33	gold quality
adrenal tissue	UBERON:0018303	85.17	gold quality
brain	UBERON:0000955	85.04	gold quality
telencephalon	UBERON:0001893	85.00	gold quality
central nervous system	UBERON:0001017	84.94	gold quality
forebrain	UBERON:0001890	84.94	gold quality
nucleus accumbens	UBERON:0001882	84.84	gold quality
cartilage tissue	UBERON:0002418	84.83	gold quality
caudate nucleus	UBERON:0001873	84.82	gold quality
right coronary artery	UBERON:0001625	84.77	gold quality
colonic epithelium	UBERON:0000397	84.76	gold quality
islet of Langerhans	UBERON:0000006	84.49	gold quality
hypothalamus	UBERON:0001898	84.38	gold quality
lower esophagus muscularis layer	UBERON:0035833	84.33	gold quality
lower esophagus	UBERON:0013473	84.31	gold quality
descending thoracic aorta	UBERON:0002345	84.26	gold quality
superior frontal gyrus	UBERON:0002661	84.26	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.22	gold quality
apex of heart	UBERON:0002098	84.15	gold quality
gall bladder	UBERON:0002110	84.12	gold quality
granulocyte	CL:0000094	84.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.03	gold quality
popliteal artery	UBERON:0002250	84.02	gold quality
tibial artery	UBERON:0007610	84.02	gold quality
thoracic aorta	UBERON:0001515	83.97	gold quality
aorta	UBERON:0000947	83.93	gold quality
ascending aorta	UBERON:0001496	83.88	gold quality
occipital lobe	UBERON:0002021	83.87	gold quality
Ammon’s horn	UBERON:0001954	83.82	gold quality
Brodmann (1909) area 10	UBERON:0013541	83.81	gold quality
Brodmann (1909) area 46	UBERON:0006483	83.74	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	83.69	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	83.46	gold quality
putamen	UBERON:0001874	83.43	gold quality
postcentral gyrus	UBERON:0002581	83.33	gold quality
metanephros cortex	UBERON:0010533	83.29	gold quality
endocervix	UBERON:0000458	83.26	gold quality
left uterine tube	UBERON:0001303	83.20	gold quality
body of uterus	UBERON:0009853	83.20	gold quality
right atrium auricular region	UBERON:0006631	83.17	gold quality
omental fat pad	UBERON:0010414	83.07	gold quality
amygdala	UBERON:0001876	83.02	gold quality
peritoneum	UBERON:0002358	83.02	gold quality
left coronary artery	UBERON:0001626	82.93	gold quality
right ovary	UBERON:0002118	82.93	gold quality
right adrenal gland cortex	UBERON:0035827	82.85	gold quality
muscle layer of sigmoid colon	UBERON:0035805	82.79	gold quality
temporal lobe	UBERON:0001871	82.68	gold quality
left ovary	UBERON:0002119	82.59	gold quality
heart left ventricle	UBERON:0002084	82.57	gold quality
pancreas	UBERON:0001264	82.53	gold quality
adipose tissue of abdominal region	UBERON:0007808	82.47	gold quality
upper lobe of left lung	UBERON:0008952	82.46	gold quality
right adrenal gland	UBERON:0001233	82.45	gold quality
orbitofrontal cortex	UBERON:0004167	82.41	gold quality
adult organism	UBERON:0007023	82.36	gold quality
choroid plexus epithelium	UBERON:0003911	82.24	gold quality
cardiac atrium	UBERON:0002081	82.23	gold quality
ovary	UBERON:0000992	82.22	gold quality
tibial nerve	UBERON:0001323	82.22	gold quality
parietal lobe	UBERON:0001872	82.19	gold quality
entorhinal cortex	UBERON:0002728	82.17	gold quality
upper lobe of lung	UBERON:0008948	82.17	gold quality
coronary artery	UBERON:0001621	82.13	gold quality
cardiac ventricle	UBERON:0002082	82.13	gold quality
subcutaneous adipose tissue	UBERON:0002190	82.02	gold quality
left adrenal gland	UBERON:0001234	81.96	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

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Postcentral gyrus	tissue	46.7
Hippocampus	tissue	40.7	medium
Locus coeruleus	tissue	39.8
Nucleus accumbens	tissue	38.7
Choroid plexus	tissue	37.3
Testis	tissue	24.5	high
Retina	tissue	19.0
Pituitary gland	tissue	16.6
Tongue	tissue	13.8
Smooth muscle	tissue	13.6	medium
Thymus	tissue	12.9
Endometrium 1	tissue	12.8	medium
Ovary	tissue	12.5	medium
Cerebral cortex	tissue	11.9	high
Skeletal muscle	tissue	11.9	high
Occipital cortex	tissue	11.9
Insular cortex	tissue	11.8
Frontal cortex	tissue	11.7
Urinary bladder	tissue	11.5	high
Somatosensory cortex	tissue	11.5
Adipose tissue	tissue	11.2	not detected
Epididymis	tissue	11.2	high
Cerebellum	tissue	11.2	medium
Parathyroid gland	tissue	11.1	medium
Retrosplenial and cingulate cortex	tissue	11.0
Prefrontal cortex	tissue	10.9
Gallbladder	tissue	10.9	high
Retrosplenial cortex	tissue	10.9
Motor cortex	tissue	10.7
Placenta	tissue	10.7	high
Thyroid gland	tissue	10.6	medium
Hippocampal formation	tissue	10.5
Entorhinal cortex	tissue	10.5
Temporal cortex	tissue	10.4
Cervix	tissue	10.2	high
Corpus callosum	tissue	10.1
Heart muscle	tissue	10.0	high
Seminal vesicle	tissue	9.9	high
Amygdala	tissue	9.8
Adrenal gland	tissue	9.8	medium
Olfactory bulb	tissue	9.8
Vagina	tissue	9.1	medium
Putamen	tissue	9.0
Ventral forebrain	tissue	9.0
Basal ganglia	tissue	8.9	high
Prostate	tissue	8.8	medium
Septum	tissue	8.8
Caudate putamen	tissue	8.8
Midbrain	tissue	8.6
Thalamus	tissue	8.5
Spleen	tissue	8.4	low
Hypothalamus	tissue	8.3
Superior colliculi	tissue	8.3
Lung	tissue	8.1	high
Kidney	tissue	8.1	medium
Lymph node	tissue	7.8	not detected
Breast	tissue	7.8	high
Pons	tissue	7.7
Substantia nigra	tissue	7.7
Periaqueductal gray	tissue	7.7

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Temporo-occipital transitional zone (54.6), Olfactory area (50.2), Paraventricular nucleus (50.2), Hippocampus, CA3 (49.3), Ventromedial nucleus (49.2).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CSRNP2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 138 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 0.996, LOEUF 0.466, missense Z 3.22 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000228515 splits into 2 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
12:51,063,749–51,064,543	277 / 323.6	0.86	no
12:51,064,544–51,076,561	206 / 367.8	0.56	no

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)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Pongo abelii	Q5R638	96.1%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
LETMD1	protein-coding	25875
TFCP2	protein-coding	7024
TMT1A	protein-coding	25840
SLC11A2	protein-coding	4891
HIGD1C	protein-coding	613227
TMPRSS12	protein-coding	283471
POU6F1	protein-coding	5463

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): F8VTU0, F8VVN1, F8VZY2, F8W1G8, Q9H175

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

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Predicted intracellular proteins, Transcription factors, Yet undefined DNA-binding domains

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nuclear speckles

Antibody reliability (HPA): IH approved · IF approved

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)

Type	Positions
N-acetylmethionine	1

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

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 (4): DNA-templated transcription (GO:0006351), 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

24 GO namespaces:

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
gene expression	1
RNA biosynthetic process	1
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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 13 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO term	NS	Evidence
nucleus	CC	direct assay
phosphatase binding	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 326 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSRNP2	ZBTB39	O15060	538
CSRNP2	ESYT1	Q9BSJ8	447
CSRNP2	ANKRD52	Q8NB46	439
CSRNP2	NAV3	Q8IVL0	437
CSRNP2	C2orf15	Q8WU43	421
CSRNP2	MRPL30	Q8TCC3	372
CSRNP2	DRC2	Q8IXS2	358
CSRNP2	TARBP2	Q15633	357
CSRNP2	FAM199X	Q6PEV8	356
CSRNP2	ZNF786	Q8N393	345
CSRNP2	KCNH7	Q9NS40	340
CSRNP2	PLEKHO2	Q8TD55	337
CSRNP2	NFYA	P23511	327
CSRNP2	HAGHL	Q6PII5	323
CSRNP2	IL20RA	Q9UHF4	318

IntAct

Human interaction partners of CSRNP2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

3 partners by confidence:

Partner	Interaction type	MIscore	Records
PPP1CA	physical association	0.920	9
PPP1CC	physical association	0.830	7
PPP1CB	physical association	0.740	7

BioGRID (17 interactions; top human partners by supporting records): PPP1CA (Two-hybrid; 6 records), PPP1CC (Two-hybrid; 6 records), PPP1CB (Two-hybrid; 2 records), DAXX (Cross-Linking-MS (XL-MS)), HNRNPH1 (Affinity Capture-RNA)

Disease & clinical

Genetic variants

Variant evidence for CSRNP2: 81 ClinVar records (0 pathogenic / likely pathogenic).

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

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 30 predictions of 900):

Position(s)	Effect	Δscore	Sites
12:51067671–51067672	donor_loss	1.0000	5
12:51067750	donor_gain	1.0000
12:51067970–51067971	acceptor_loss	1.0000	6
12:51064670–51064671	acceptor_loss	0.9900	6
12:51065385	acceptor_gain	0.9900
12:51065392	acceptor_gain	0.9900
12:51067968	acceptor_gain	0.9900
12:51067974–51067975	acceptor_gain	0.9900	2
12:51074083–51074084	acceptor_loss	0.9900	6
12:51076547	acceptor_gain	0.9900

AlphaMissense

1,421 missense substitutions predicted likely pathogenic (of 3,545 scored), across 283 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M95	9	0.998	1.000
M274	9	0.976	1.000
H268	8	1.000	1.000
D238	8	0.999	1.000
F68	8	0.998	1.000
F76	8	0.998	1.000
F242	8	0.998	1.000
H99	8	0.997	1.000
F260	8	0.997	1.000
H271	8	0.997	0.999
N253	8	0.996	1.000
F82	8	0.995	1.000
H118	8	0.988	0.999
F174	8	0.987	1.000
N320	8	0.987	0.996
H125	8	0.984	0.999
S91	8	0.977	1.000
F173	8	0.971	0.999
D170	8	0.966	0.994
S87	8	0.960	0.999

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Disease associations

OMIM: gene MIM:620404 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

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	increases expression, increases methylation, decreases 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	affects cotreatment, increases abundance, increases expression	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 expression, affects cotreatment, increases abundance	1
Benzene	increases expression	1
Calcitriol	decreases expression	1
Coumestrol	affects cotreatment, decreases expression	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)

Via MONDO — disease-level, not drug-specific.