CENPI

centromere protein I, the group of Constitutive centromere associated network

Basic information

Region (hg38): X:101098187-101166126

Previous symbols: [ "FSHPRH1" ]

Links

ENSG00000102384 ∙ NCBI:2491 ∙ OMIM:300065 ∙ HGNC:3968 ∙ Uniprot:Q92674 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• idiopathic steroid-sensitive nephrotic syndrome (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CENPI gene.

• Inborn genetic diseases (14 variants)
• not provided (6 variants)
• Premature ovarian insufficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPI 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				2		2
missense			13	2	2	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	13	4	2

Variants in CENPI

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

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

Position	Type	Phenotype	Significance	ClinVar
X-101101098-G-A			Benign (May 16, 2018)
X-101101233-G-C		not specified	Uncertain significance (Jul 12, 2023)
X-101102300-G-T		not specified	Uncertain significance (Jul 14, 2023)
X-101102391-T-C		not specified	Uncertain significance (Jan 30, 2024)
X-101109510-C-G		not specified	Uncertain significance (Jul 20, 2021)
X-101109555-C-T			Likely benign (Apr 01, 2022)
X-101109904-G-A		Premature ovarian insufficiency	Likely benign (Jan 01, 2023)
X-101109930-A-C		not specified	Uncertain significance (Jul 13, 2021)
X-101109991-A-C		not specified	Uncertain significance (Jun 23, 2021)
X-101120741-A-G		not specified	Uncertain significance (Aug 01, 2022)
X-101127186-G-A			Benign (Dec 31, 2019)
X-101127529-T-C		not specified	Uncertain significance (Jun 27, 2022)
X-101127618-C-A		not specified	Uncertain significance (Jan 08, 2024)
X-101128724-T-C			Likely benign (Jul 01, 2022)
X-101128842-A-G			Uncertain significance (Apr 01, 2023)
X-101130051-T-G		not specified	Uncertain significance (Feb 02, 2024)
X-101132267-C-A		not specified	Uncertain significance (Oct 26, 2021)
X-101145157-C-A		not specified	Uncertain significance (Feb 22, 2023)
X-101147768-G-A		not specified	Likely benign (Feb 16, 2023)
X-101148025-C-T		not specified	Uncertain significance (Dec 08, 2023)
X-101148058-A-G		not specified	Uncertain significance (Aug 02, 2023)
X-101148082-G-C		not specified	Uncertain significance (Aug 08, 2022)
X-101148109-A-G			Likely benign (-)
X-101148141-G-A		not specified	Uncertain significance (Jun 13, 2023)
X-101162953-A-G		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPI	protein_coding	protein_coding	ENST00000372927	20	65493

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000258	124608	0	6	124614	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	190	256	0.743	0.0000181	4986
Missense in Polyphen		23	41.302	0.55688		878
Synonymous	0.826	82	92.1	0.890	0.00000654	1356
Loss of Function	4.73	1	28.1	0.0356	0.00000177	570

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000736	0.0000531
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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. Required for the localization of CENPF, MAD1L1 and MAD2 (MAD2L1 or MAD2L2) to kinetochores. Involved in the response of gonadal tissues to follicle-stimulating hormone. {ECO:0000269|PubMed:12640463, ECO:0000269|PubMed:16622420}.
• 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: 0.131

Intolerance Scores

• loftool: 0.0337
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.0552
• hipred: N
• hipred_score: 0.326
• ghis: 0.405

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.640

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpi

Gene ontology

• Biological process: sex differentiation;CENP-A containing nucleosome assembly
• Cellular component: kinetochore;nucleoplasm;cytosol;nuclear body
• Molecular function: protein binding