INCENP

inner centromere protein, the group of Chromosomal passenger complex

Basic information

Region (hg38): 11:62123998-62155474

Links

ENSG00000149503 ∙ NCBI:3619 ∙ OMIM:604411 ∙ HGNC:6058 ∙ Uniprot:Q9NQS7 ∙ 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 INCENP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INCENP 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				4	9	13
missense			90	4	8	102
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		4	5
non coding					47	47
Total	0	0	90	8	64

Variants in INCENP

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

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

Position	Type	Phenotype	Significance	ClinVar
11-62127971-TA-T			Benign (May 12, 2021)
11-62127972-AG-A			Benign (May 24, 2021)
11-62128004-G-A			Benign (May 12, 2021)
11-62128069-A-G			Benign (May 12, 2021)
11-62128172-C-T		not specified	Uncertain significance (Dec 16, 2023)
11-62128177-C-T		not specified	Uncertain significance (Nov 22, 2023)
11-62128198-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-62128246-A-G		not specified	Uncertain significance (Apr 13, 2022)
11-62128269-A-G			Benign (May 04, 2021)
11-62128282-G-T		not specified	Uncertain significance (Jul 25, 2023)
11-62128289-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-62128743-G-A			Benign (May 12, 2021)
11-62128787-C-T		not specified	Uncertain significance (Nov 15, 2023)
11-62128805-C-T		not specified	Uncertain significance (Dec 28, 2022)
11-62128823-G-A		not specified	Uncertain significance (Apr 26, 2023)
11-62129117-T-G			Benign (May 12, 2021)
11-62129601-C-T			Benign (May 16, 2021)
11-62129725-C-T			Benign (May 12, 2021)
11-62129782-G-T		not specified	Uncertain significance (Apr 13, 2022)
11-62129801-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-62129802-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-62129814-T-C		not specified	Uncertain significance (Jan 10, 2022)
11-62129820-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-62129823-G-A		not specified	Uncertain significance (Mar 21, 2023)
11-62129826-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INCENP	protein_coding	protein_coding	ENST00000394818	18	29191

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.886	0.114	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.766	545	598	0.912	0.0000437	5931
Missense in Polyphen		29	52.112	0.55649		561
Synonymous	0.0863	233	235	0.993	0.0000153	1826
Loss of Function	5.11	9	46.7	0.193	0.00000244	530

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000561	0.000500
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.0000556	0.0000544
South Asian	0.0000657	0.0000653
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the chromosomal passenger complex (CPC), a complex that acts as a key regulator of mitosis. The CPC complex has essential functions at the centromere in ensuring correct chromosome alignment and segregation and is required for chromatin-induced microtubule stabilization and spindle assembly. Acts as a scaffold regulating CPC localization and activity. The C-terminus associates with AURKB or AURKC, the N-terminus associated with BIRC5/survivin and CDCA8/borealin tethers the CPC to the inner centromere, and the microtubule binding activity within the central SAH domain directs AURKB/C toward substrates near microtubules (PubMed:15316025, PubMed:12925766, PubMed:27332895). The flexibility of the SAH domain is proposed to allow AURKB/C to follow substrates on dynamic microtubules while ensuring CPC docking to static chromatin (By similarity). Activates AURKB and AURKC (PubMed:27332895). Required for localization of CBX5 to mitotic centromeres (PubMed:21346195). Controls the kinetochore localization of BUB1 (PubMed:16760428). {ECO:0000250|UniProtKB:P53352, ECO:0000269|PubMed:12925766, ECO:0000269|PubMed:15316025, ECO:0000269|PubMed:16760428, ECO:0000269|PubMed:21346195, ECO:0000269|PubMed:27332895}.
• Pathway: Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;Regulation of nuclear beta catenin signaling and target gene transcription;Aurora C signaling;Aurora B signaling;PLK1 signaling events (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.413
• rvis_EVS: 0.83
• rvis_percentile_EVS: 88.13

Haploinsufficiency Scores

• pHI: 0.166
• hipred: Y
• hipred_score: 0.677
• ghis: 0.502

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.849

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Incenp
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype

Gene ontology

• Biological process: mitotic sister chromatid segregation;mitotic cytokinesis;chromosome segregation;regulation of mitotic cytokinesis
• Cellular component: chromosome, centromeric region;kinetochore;condensed chromosome kinetochore;lateral element;central element;nucleus;nucleoplasm;pericentric heterochromatin;spindle;cytosol;microtubule;chromocenter;nuclear body;midbody;protein-containing complex
• Molecular function: protein binding