CENPQ

centromere protein Q, the group of Constitutive centromere associated network

Basic information

Region (hg38): 6:49463370-49493107

Previous symbols: [ "C6orf139" ]

Links

ENSG00000031691 ∙ NCBI:55166 ∙ OMIM:611506 ∙ HGNC:21347 ∙ Uniprot:Q7L2Z9 ∙ 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 CENPQ gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPQ 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						0
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in CENPQ

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

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

Position	Type	Phenotype	Significance	ClinVar
6-49470210-G-A		not specified	Uncertain significance (Feb 28, 2024)
6-49470217-A-G		not specified	Uncertain significance (Mar 07, 2025)
6-49470241-A-T		not specified	Uncertain significance (Dec 15, 2023)
6-49471005-A-G		not specified	Uncertain significance (Feb 15, 2023)
6-49472097-G-C		not specified	Uncertain significance (May 14, 2024)
6-49472794-A-G		not specified	Uncertain significance (May 21, 2024)
6-49472854-A-G		not specified	Uncertain significance (Feb 17, 2024)
6-49480970-A-G		not specified	Uncertain significance (Aug 04, 2024)
6-49488377-C-G		not specified	Uncertain significance (Jun 03, 2022)
6-49488415-A-G		not specified	Uncertain significance (Nov 01, 2022)
6-49488459-G-C		not specified	Uncertain significance (May 14, 2024)
6-49488608-T-C		not specified	Uncertain significance (Sep 27, 2024)
6-49488611-A-G		not specified	Uncertain significance (Jun 03, 2022)
6-49488626-G-A		not specified	Uncertain significance (Sep 27, 2021)
6-49488656-A-C		not specified	Uncertain significance (Jan 22, 2025)
6-49492156-G-A		not specified	Likely benign (Apr 25, 2022)
6-49492191-C-G		not specified	Uncertain significance (Dec 21, 2023)
6-49492193-T-G		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPQ	protein_coding	protein_coding	ENST00000335783	8	29730

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.05e-7	0.336	125680	0	9	125689	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.268	112	120	0.931	0.00000531	1756
Missense in Polyphen		22	25.031	0.87892		417
Synonymous	-0.701	49	43.1	1.14	0.00000221	460
Loss of Function	0.587	12	14.4	0.833	7.07e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000149	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the CENPA-CAD (nucleosome distal) complex, a complex recruited to centromeres which is involved in assembly of kinetochore proteins, mitotic progression and chromosome segregation. May be involved in incorporation of newly synthesized CENPA into centromeres via its interaction with the CENPA-NAC complex (PubMed:16622420). Plays an important role in chromosome congression and in the recruitment of CENP-O complex (which comprises CENPO, CENPP, CENPQ and CENPU), CENPE and PLK1 to the kinetochores (PubMed:25395579). {ECO:0000269|PubMed:16622420, ECO:0000269|PubMed:25395579}.
• 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;Nucleosome assembly;RHO GTPase Effectors;Signaling by Rho GTPases;Chromosome Maintenance;Deposition of new CENPA-containing nucleosomes at the centromere;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.817
• rvis_EVS: 0.7
• rvis_percentile_EVS: 85.42

Haploinsufficiency Scores

• pHI: 0.187
• hipred: N
• hipred_score: 0.351
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpq

Gene ontology

• Biological process: CENP-A containing nucleosome assembly;metaphase plate congression;positive regulation of protein localization to kinetochore
• Cellular component: chromosome, centromeric region;nucleoplasm;cytosol;actin cytoskeleton