CENPL

centromere protein L, the group of Constitutive centromere associated network

Basic information

Region (hg38): 1:173799549-173824883

Previous symbols: [ "C1orf155" ]

Links

ENSG00000120334 ∙ NCBI:91687 ∙ OMIM:611503 ∙ HGNC:17879 ∙ Uniprot:Q8N0S6 ∙ 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 CENPL gene.

• Inborn genetic diseases (14 variants)
• Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CENPL 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	16	2	0

Variants in CENPL

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

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

Position	Type	Phenotype	Significance	ClinVar
1-173800465-T-C		not specified	Likely benign (Jul 21, 2022)
1-173800501-G-C		not specified	Uncertain significance (Aug 04, 2023)
1-173803085-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-173803160-T-C		not specified	Uncertain significance (Nov 27, 2023)
1-173803202-A-T		not specified	Uncertain significance (May 03, 2023)
1-173803295-A-C		not specified	Uncertain significance (Oct 03, 2023)
1-173803322-T-C		not specified	Uncertain significance (Mar 16, 2022)
1-173803365-A-C		not specified	Uncertain significance (Dec 20, 2023)
1-173803433-C-T		not specified	Likely benign (Dec 08, 2023)
1-173807307-A-G		not specified	Uncertain significance (Jun 26, 2023)
1-173807364-G-A		not specified	Uncertain significance (May 31, 2023)
1-173807392-T-C		not specified	Uncertain significance (Jun 11, 2021)
1-173807427-T-C		not specified	Uncertain significance (Aug 13, 2021)
1-173807478-T-C		not specified	Uncertain significance (Dec 15, 2023)
1-173807488-G-A		not specified	Uncertain significance (Jan 27, 2022)
1-173811151-G-A		not specified	Uncertain significance (May 26, 2022)
1-173811226-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-173811248-C-T		not specified	Likely benign (Dec 28, 2022)
1-173811250-G-C		not specified	Uncertain significance (Nov 18, 2022)
1-173811283-G-A		not specified	Likely benign (Dec 09, 2023)
1-173824687-C-T		Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome	Uncertain significance (Jan 13, 2018)
1-173824697-G-A		Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome	Uncertain significance (Jan 12, 2018)
1-173824708-G-C		Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome	Uncertain significance (Jan 12, 2018)
1-173824742-G-C		Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CENPL	protein_coding	protein_coding	ENST00000356198	5	25171

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0712	0.926	125735	0	10	125745	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.758	159	188	0.845	0.00000860	2521
Missense in Polyphen		38	59.405	0.63967		824
Synonymous	0.547	64	69.8	0.917	0.00000336	766
Loss of Function	2.66	5	16.7	0.299	8.70e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000537	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
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. {ECO:0000269|PubMed:16716197}.
• 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: 0.0780

Intolerance Scores

• loftool: 0.441
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.430
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cenpl
• Phenotype: skeleton phenotype; limbs/digits/tail 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)

Zebrafish Information Network

• Gene name: cenpl
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved dorsal

Gene ontology

• Biological process: CENP-A containing nucleosome assembly
• Cellular component: chromosome, centromeric region;nucleoplasm;cytosol
• Molecular function: protein binding