CIP2A

cellular inhibitor of PP2A, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 3:108549864-108589644

Previous symbols: [ "KIAA1524" ]

Links

ENSG00000163507 ∙ NCBI:57650 ∙ OMIM:610643 ∙ HGNC:29302 ∙ Uniprot:Q8TCG1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CIP2A gene.

• not_specified (108 variants)
• not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CIP2A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020890.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			104	4	3	111
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	104	5	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CIP2A	protein_coding	protein_coding	ENST00000295746	21	39776

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-13	0.980	125573	0	175	125748	0.000696

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.669	401	440	0.910	0.0000214	5893
Missense in Polyphen		89	114	0.78069		1570
Synonymous	-1.06	176	159	1.11	0.00000789	1674
Loss of Function	2.44	28	45.9	0.611	0.00000217	645

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00264	0.00248
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00138	0.00136
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000621	0.000580
Middle Eastern	0.00138	0.00136
South Asian	0.00123	0.00118
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Oncoprotein that inhibits PP2A and stabilizes MYC in human malignancies. Promotes anchorage-independent cell growth and tumor formation. {ECO:0000269|PubMed:17632056}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• rvis_EVS: 1.85
• rvis_percentile_EVS: 97.12

Haploinsufficiency Scores

• pHI: 0.147
• hipred: Y
• hipred_score: 0.637
• ghis: 0.509

Essentials

• essential_gene_gene_trap: H

Mouse Genome Informatics

• Gene name: Cip2a
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: spermatogenesis;positive regulation of neural precursor cell proliferation
• Cellular component: cytoplasm;cytosol;plasma membrane;integral component of membrane
• Molecular function: protein binding;protein homodimerization activity;cadherin binding