CEP57L1

centrosomal protein 57 like 1

Basic information

Region (hg38): 6:109095110-109174418

Previous symbols: [ "C6orf182" ]

Links

ENSG00000183137 ∙ NCBI:285753 ∙ ∙ HGNC:21561 ∙ Uniprot:Q8IYX8 ∙ 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 CEP57L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP57L1 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					1	1
missense			25	2	1	28
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	3	2

Variants in CEP57L1

This is a list of pathogenic ClinVar variants found in the CEP57L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-109145237-A-G		not specified	Uncertain significance (Aug 26, 2022)
6-109145239-G-A		not specified	Uncertain significance (Aug 05, 2023)
6-109145249-G-T			Benign (Sep 11, 2018)
6-109145250-T-C		not specified	Uncertain significance (Apr 23, 2024)
6-109145255-A-G		not specified	Uncertain significance (Dec 27, 2022)
6-109145277-G-A		not specified	Uncertain significance (Sep 30, 2021)
6-109146758-C-G		not specified	Uncertain significance (Jan 16, 2024)
6-109146761-T-G		not specified	Uncertain significance (Oct 12, 2022)
6-109146763-A-G		not specified	Uncertain significance (Apr 30, 2024)
6-109146794-T-A		not specified	Uncertain significance (Jun 26, 2023)
6-109146799-C-T		not specified	Uncertain significance (Feb 23, 2023)
6-109146800-G-A		not specified	Likely benign (Jan 04, 2022)
6-109150126-A-G		not specified	Uncertain significance (Apr 06, 2024)
6-109150170-G-A			Benign (Sep 11, 2018)
6-109153833-G-A		not specified	Uncertain significance (Aug 21, 2023)
6-109155294-A-G		not specified	Uncertain significance (Oct 24, 2023)
6-109155302-T-C		not specified	Uncertain significance (May 03, 2023)
6-109155850-C-A		not specified	Uncertain significance (Oct 04, 2022)
6-109159086-CT-C			Likely benign (Jun 01, 2018)
6-109159090-T-A		not specified	Uncertain significance (Aug 08, 2022)
6-109159274-G-T		not specified	Uncertain significance (Dec 21, 2022)
6-109159282-G-A		not specified	Uncertain significance (Dec 08, 2023)
6-109159314-G-T		not specified	Uncertain significance (Oct 26, 2021)
6-109159342-C-T		not specified	Uncertain significance (Oct 14, 2023)
6-109159375-C-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP57L1	protein_coding	protein_coding	ENST00000407272	10	68823

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.81e-8	0.915	125638	2	87	125727	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00624	226	226	1.00	0.0000107	3070
Missense in Polyphen		81	74.851	1.0821		1154
Synonymous	0.684	64	71.4	0.897	0.00000336	777
Loss of Function	1.79	16	25.8	0.619	0.00000137	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00119	0.00119
Ashkenazi Jewish	0.000992	0.000993
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000435	0.000435
South Asian	0.00111	0.000915
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Centrosomal protein which may be required for microtubule attachment to centrosomes. {ECO:0000250}.

Recessive Scores

• pRec: 0.0864

Intolerance Scores

• rvis_EVS: 0.97
• rvis_percentile_EVS: 90.34

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.123
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cep57l1

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;cytoplasm;centrosome;microtubule
• Molecular function: molecular_function;protein binding;microtubule binding;identical protein binding;gamma-tubulin binding