CIP2A

protein-coding

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

Gene summary

Enables protein homodimerization activity and protein phosphatase inhibitor activity. Involved in broken chromosome clustering. Located in cytosol. Is active in chromosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

KIAA1524

MANE transcript

NM_020890.3

Inheritance

—

ClinVar variants

U:131B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr3:108,549,864-108,589,644

External References & Databases

Ensembl (ENSG00000163507)

Transcript & Mutation Effects

hg38 • Region Span ~39.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CIP2A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 127

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020890.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			126 clinvar	4 clinvar	3 clinvar	133
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	131	5	3	139

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020890.3	RefSeq	NP_065941.2	21	MANE Select
ENST00000295746.13	Ensembl	ENSP00000295746.7	21	MANE Select
ENST00000468953.1	Ensembl	ENSP00000419428.1	2	Standard
ENST00000481530.5	Ensembl	ENSP00000417297.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatogenesis
positive regulation of neural precursor cell proliferation

Molecular Function

protein binding
protein homodimerization activity
cadherin binding

Cellular Component

cytoplasm
cytosol
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295746
Coding exons: 21
Length: 39776
Individuals with no LoFs: 125573
Homozygous LoFs: 0
Heterozygous LoFs: 175
Defined: 125748
p: 0.000696

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.669	401	440	0.910	0.0000214	5893
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0024	0.0023	notable
Latino/Admixed American	0.00020	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0014	0.0014	notable
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00062	0.00058	rare
South Asian	0.0012	0.0012	notable
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): H