CIP2A

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

Basic information

Region (hg38): 3:108549863-108589644

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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			40	3	3	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			2			2
Total	0	0	42	4	3

Variants in CIP2A

This is a list of pathogenic ClinVar variants found in the CIP2A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-108551157-T-C		not specified	Uncertain significance (Jul 12, 2022)
3-108551265-C-G		not specified	Uncertain significance (Jun 07, 2024)
3-108551316-A-T		not specified	Uncertain significance (Jun 26, 2023)
3-108552295-A-G		not specified	Uncertain significance (Jun 30, 2022)
3-108552299-T-C		not specified	Uncertain significance (Feb 27, 2023)
3-108552364-T-G		not specified	Uncertain significance (Jan 04, 2024)
3-108553711-C-T		not specified	Uncertain significance (Jul 26, 2022)
3-108554425-T-C			Benign (May 01, 2023)
3-108554433-T-C		not specified	Uncertain significance (Mar 28, 2024)
3-108554461-C-G		not specified	Uncertain significance (Jun 24, 2022)
3-108557280-C-G		not specified	Uncertain significance (Mar 27, 2023)
3-108557284-C-T		not specified	Uncertain significance (Jun 29, 2023)
3-108557326-T-G		not specified	Uncertain significance (Apr 18, 2023)
3-108557396-T-G		not specified	Uncertain significance (Aug 13, 2021)
3-108559786-G-A		not specified	Uncertain significance (Sep 29, 2023)
3-108560704-C-T		not specified	Uncertain significance (Oct 03, 2022)
3-108560735-T-C		not specified	Likely benign (Jul 09, 2021)
3-108560748-A-T		not specified	Uncertain significance (Nov 15, 2021)
3-108560767-C-G		not specified	Uncertain significance (Oct 06, 2022)
3-108560779-C-T		not specified	Uncertain significance (Jun 05, 2023)
3-108560788-T-A		not specified	Uncertain significance (Dec 06, 2021)
3-108563157-C-T		not specified	Uncertain significance (Nov 08, 2022)
3-108566549-A-G		not specified	Uncertain significance (Aug 30, 2021)
3-108568239-G-A		not specified	Uncertain significance (Jun 19, 2024)
3-108568254-T-C		not specified	Uncertain significance (Mar 08, 2024)

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