CENPX

centromere protein X, the group of Constitutive centromere associated network

Basic information

Region (hg38): 17:82018702-82024107

Previous symbols: [ "STRA13", "MHF2" ]

Links

ENSG00000169689 ∙ NCBI:201254 ∙ OMIM:615128 ∙ HGNC:11422 ∙ Uniprot:A8MT69 ∙ 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 CENPX gene.

Variants pathogenicity by type

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

Variants in CENPX

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

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

Position	Type	Phenotype	Significance	ClinVar
17-82019298-G-C		not specified	Uncertain significance (Aug 12, 2021)
17-82023657-G-A		LRRC45-related disorder	Likely benign (Jul 17, 2024)
17-82023738-G-A		not specified	Uncertain significance (Mar 07, 2024)
17-82023766-C-G		LRRC45-related disorder	Uncertain significance (Jul 17, 2024)
17-82023773-G-A		not specified	Uncertain significance (May 26, 2024)
17-82023786-G-A		not specified	Uncertain significance (May 23, 2023)
17-82023825-C-T		not specified	Uncertain significance (Jun 27, 2022)
17-82023856-C-G		not specified	Uncertain significance (Dec 30, 2024)
17-82023857-G-A		LRRC45-related disorder • not specified	Uncertain significance (Sep 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPX	protein_coding	protein_coding	ENST00000392359	5	5406

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.111	0.787	107623	0	4	107627	0.0000186

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0853	47	48.7	0.966	0.00000320	502
Missense in Polyphen		9	16.013	0.56204		210
Synonymous	-2.16	36	22.9	1.57	0.00000176	158
Loss of Function	1.28	2	5.13	0.390	2.19e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000821	0.0000760
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000644	0.0000601
European (Non-Finnish)	0.0000221	0.0000213
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA-binding component of the Fanconi anemia (FA) core complex. Required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage (PubMed:20347428, PubMed:20347429). In complex with CENPS (MHF heterodimer), crucial cofactor for FANCM in both binding and ATP-dependent remodeling of DNA. Stabilizes FANCM. In complex with CENPS and FANCM (but not other FANC proteins), rapidly recruited to blocked forks and promotes gene conversion at blocked replication forks (PubMed:20347428, PubMed:20347429). In complex with CENPS, CENPT and CENPW (CENP-T-W-S-X heterotetramer), involved in the formation of a functional kinetochore outer plate, which is essential for kinetochore-microtubule attachment and faithful mitotic progression (PubMed:19620631). As a component of MHF and CENP-T-W- S-X complexes, binds DNA and bends it to form a nucleosome-like structure (PubMed:20347428, PubMed:20347429). DNA-binding function is fulfilled in the presence of CENPS, with the following preference for DNA substates: Holliday junction > double-stranded > splay arm > single-stranded. Does not bind DNA on its own (PubMed:20347429). {ECO:0000269|PubMed:19620631, ECO:0000269|PubMed:20347428, ECO:0000269|PubMed:20347429}.
• Pathway: Fanconi anemia pathway - Homo sapiens (human);Fanconi Anemia Pathway;DNA Repair;Nucleosome assembly;Chromosome Maintenance;Deposition of new CENPA-containing nucleosomes at the centromere;Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.0858

Intolerance Scores

• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.79

Haploinsufficiency Scores

• pHI: 0.260
• hipred: Y
• hipred_score: 0.595

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cenpx

Gene ontology

• Biological process: resolution of meiotic recombination intermediates;replication fork processing;positive regulation of protein ubiquitination;CENP-A containing nucleosome assembly;interstrand cross-link repair;cell division;kinetochore assembly
• Cellular component: condensed chromosome kinetochore;nucleoplasm;Fanconi anaemia nuclear complex;FANCM-MHF complex
• Molecular function: DNA binding;double-stranded DNA binding;protein binding