CSNK2A2IP

Summary

CSNK2A2IP (casein kinase 2 subunit alpha’ interacting protein, HGNC:53637) is a protein-coding gene on chromosome 3p11.1, encoding Casein kinase II subunit alpha’-interacting protein (A0A1B0GTH6). May play a role in chromatin regulation of male germ cells.

Predicted to be located in male germ cell nucleus.

Source: NCBI Gene 111064647 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001368165

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53637
Approved symbol	CSNK2A2IP
Name	casein kinase 2 subunit alpha’ interacting protein
Location	3p11.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000283434
Ensembl biotype	protein_coding
Entrez	111064647

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000635844, ENST00000636323, ENST00000636504, ENST00000636795, ENST00000637986, ENST00000638109

RefSeq mRNA: 4 — MANE Select: NM_001368165 NM_001368165, NM_001368166, NM_001368167, NM_001368168

CCDS: CCDS93323

Canonical transcript exons

ENST00000637986 — 2 exons

Exon	Start	End
ENSE00003794061	88465088	88467594
ENSE00003797497	88338456	88338643

Expression profiles

Bgee: expression breadth broad, 56 present calls, max score 88.16.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0246 / max 23.0053, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
37464	0.0246	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.16	gold quality
left testis	UBERON:0004533	85.12	gold quality
testis	UBERON:0000473	84.59	gold quality
right testis	UBERON:0004534	81.44	gold quality
Brodmann (1909) area 9	UBERON:0013540	58.82	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	57.50	gold quality
right frontal lobe	UBERON:0002810	54.41	gold quality
primary visual cortex	UBERON:0002436	53.67	gold quality
cerebellar hemisphere	UBERON:0002245	52.08	gold quality
cerebellar cortex	UBERON:0002129	51.51	gold quality
cerebellum	UBERON:0002037	51.27	gold quality
right hemisphere of cerebellum	UBERON:0014890	50.20	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	49.87	silver quality
anterior cingulate cortex	UBERON:0009835	49.56	gold quality
cerebral cortex	UBERON:0000956	49.36	gold quality
substantia nigra	UBERON:0002038	48.61	gold quality
hypothalamus	UBERON:0001898	47.74	gold quality
colonic epithelium	UBERON:0000397	46.47	gold quality
frontal cortex	UBERON:0001870	46.24	gold quality
brain	UBERON:0000955	45.32	gold quality
amygdala	UBERON:0001876	45.08	gold quality
superior frontal gyrus	UBERON:0002661	44.88	gold quality
temporal lobe	UBERON:0001871	44.86	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	44.13	gold quality
Ammon’s horn	UBERON:0001954	44.04	gold quality
nucleus accumbens	UBERON:0001882	42.77	gold quality
ventricular zone	UBERON:0003053	41.92	gold quality
putamen	UBERON:0001874	41.78	gold quality
prefrontal cortex	UBERON:0000451	40.87	gold quality
sural nerve	UBERON:0015488	39.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.93

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Csnk2a2ip	ENSMUSG00000068167
rattus_norvegicus	Csnka2ip	ENSRNOG00000068003

Protein

Protein identifiers

Casein kinase II subunit alpha’-interacting protein — A0A1B0GTH6 (reviewed: A0A1B0GTH6)

Alternative names: Casein kinase 2 alpha prime interacting protein

All UniProt accessions (1): A0A1B0GTH6

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in chromatin regulation of male germ cells.

Subunit / interactions. Interacts (via C-terminus) with CSNK2A2.

Subcellular location. Nucleus.

Post-translational modifications. Phosphorylated by CK2 (casein kinase II), specifically by complexes containing catalytic subunit CSNK2A2.

RefSeq proteins (4): NP_001355094, NP_001355095, NP_001355096, NP_001355097 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038954	CSNKA2IP	Family

UniProt features (3 total): chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GTH6-F1	44.73	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): GSE12003_4D_VS_8D_CULTURE_BM_PROGENITOR_DN, chr3p11

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

100 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSNK2A2IP	CYLC2	Q14093	547
CSNK2A2IP	RIMS2	Q9UQ26	449
CSNK2A2IP	UTP3	Q9NQZ2	437
CSNK2A2IP	KATNB1	Q9BVA0	405
CSNK2A2IP	DPEP3	Q9H4B8	398
CSNK2A2IP	ZPBP2	Q6X784	389
CSNK2A2IP	CABYR	O75952	379
CSNK2A2IP	TRIM52	Q96A61	378
CSNK2A2IP	SPATA16	Q9BXB7	377
CSNK2A2IP	TEX12	Q9BXU0	370
CSNK2A2IP	TSSK2	Q96PF2	370
CSNK2A2IP	NDRG2	Q9UN36	370
CSNK2A2IP	TBPL1	P62380	310
CSNK2A2IP	SPAG1	Q07617	310
CSNK2A2IP	CROCC	Q5TZA2	300

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTH6, A0A1D5RMD1, A1KXM5, A2AEY4, A6NCI8, A6QQS3, A7KBS4, C4P6S0, O94713, P0C9Z7, P53963, P53976, Q0P670, Q0VAV2, Q10668, Q196W1, Q2KHR3, Q2YDJ5, Q32MG2, Q3V0A6, Q3V3Q4, Q4V8E9, Q5JRM2, Q68FV4, Q6AXV6, Q6AYN3, Q6NS59, Q7TSG5, Q80VJ6, Q80Y39, Q80YD3, Q810T2, Q86XD8, Q8C5U4, Q8CH19, Q8IWI9, Q8K4E0, Q8NDH2, Q8NEV8, Q8NFU7

Diamond homologs: A0A1B0GTH6, Q8CH19

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

4742 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:88466637:T:A	V427D	0.981
3:88466783:T:C	C476R	0.979
3:88466865:T:A	V503D	0.978
3:88467413:T:C	F686L	0.978
3:88467415:T:A	F686L	0.978
3:88467415:T:G	F686L	0.978
3:88467404:T:A	W683R	0.976
3:88467404:T:C	W683R	0.976
3:88466785:C:G	C476W	0.974
3:88466722:A:C	R455S	0.973
3:88466722:A:T	R455S	0.973
3:88466781:T:A	V475D	0.972
3:88466859:T:A	L501H	0.968
3:88466622:T:A	V422D	0.966
3:88466700:T:C	L448P	0.964
3:88466859:T:C	L501P	0.962
3:88466721:G:C	R455T	0.961
3:88466688:T:C	I444T	0.960
3:88466731:G:C	R458S	0.960
3:88466731:G:T	R458S	0.960
3:88466853:C:A	A499E	0.960
3:88466727:T:C	M457T	0.959
3:88467387:T:C	L677S	0.959
3:88467406:G:C	W683C	0.959
3:88467406:G:T	W683C	0.959
3:88467140:T:A	W595R	0.958
3:88467140:T:C	W595R	0.958
3:88466725:G:C	R456S	0.957
3:88466725:G:T	R456S	0.957
3:88467414:T:C	F686S	0.957

dbSNP variants (sampled 300 via entrez): RS1000081669 (3:88371227 G>A), RS1000090434 (3:88412051 A>T), RS1000119705 (3:88357291 A>T), RS1000120158 (3:88411760 A>T), RS1000174117 (3:88357022 G>A), RS1000180002 (3:88434059 C>A,T), RS1000218521 (3:88393060 TG>T,TGG), RS1000315603 (3:88405756 C>T), RS1000360972 (3:88439650 G>A), RS1000380581 (3:88362131 T>A), RS1000477825 (3:88418194 T>C), RS1000492731 (3:88373051 C>T), RS1000570553 (3:88393410 A>G), RS1000657392 (3:88352158 G>A,C), RS1000766656 (3:88400977 TAGA>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)

Clinical trials (associated diseases)

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