CEP85L

centrosomal protein 85 like

Basic information

Region (hg38): 6:118460772-118710075

Previous symbols: [ "C6orf204" ]

Links

ENSG00000111860 ∙ NCBI:387119 ∙ OMIM:618865 ∙ HGNC:21638 ∙ Uniprot:Q5SZL2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• lissencephaly 10 (Strong), mode of inheritance: AD
• lissencephaly 10 (Strong), mode of inheritance: AD
• lissencephaly due to LIS1 mutation (Strong), mode of inheritance: AD
• lissencephaly 10 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lissencephaly 10	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Ophthalmologic	32097630
As with other genetic conditions that can involve seizures, knowledge of the genetic cause may be helpful for medication selection based on what has been beneficial in other patients

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP85L gene.

• Dilated cardiomyopathy 1P (5 variants)
• Posterior Predominant Lissencephaly (2 variants)
• Lissencephaly (1 variants)
• Lissencephaly;Thick corpus callosum (1 variants)
• Cardiomyopathy (1 variants)
• Lissencephaly 10 (1 variants)
• not provided (1 variants)
• Primary dilated cardiomyopathy (1 variants)
• Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP85L 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				5		5
missense		3	46	9	2	60
nonsense		1	1			2
start loss	2					2
frameshift		1	4			5
inframe indel						0
splice donor/acceptor (+/-2bp)	2		1			3
splice region			1			1
non coding	5	2	84	27	15	133
Total	9	7	136	41	17

Variants in CEP85L

This is a list of pathogenic ClinVar variants found in the CEP85L region.

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

Position	Type	Phenotype	Significance	ClinVar
6-118465442-T-C			Uncertain significance (Jun 17, 2019)
6-118465476-T-C		Inborn genetic diseases	Likely benign (Sep 30, 2021)
6-118469191-A-G		Lissencephaly 10	Uncertain significance (Nov 21, 2021)
6-118469237-G-A		Lissencephaly 10	Likely pathogenic (Mar 25, 2024)
6-118470565-A-G		Lissencephaly 10	Uncertain significance (-)
6-118470598-A-G			Uncertain significance (Jun 01, 2023)
6-118479870-C-A			Uncertain significance (Feb 22, 2023)
6-118479908-T-C			Uncertain significance (Mar 01, 2023)
6-118479910-GCTGT-G		Lissencephaly 10	Uncertain significance (Nov 22, 2021)
6-118480474-G-A		CEP85L-related disorder	Likely benign (Apr 23, 2024)
6-118481816-T-C		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
6-118481844-T-C			Likely benign (Jan 01, 2024)
6-118481863-T-G		CEP85L-related disorder	Uncertain significance (Dec 14, 2022)
6-118481910-A-AT			Uncertain significance (Jan 16, 2024)
6-118481924-G-C		Inborn genetic diseases	Uncertain significance (Oct 21, 2021)
6-118483703-T-A		Lissencephaly 10	Uncertain significance (Dec 08, 2022)
6-118483726-C-T		not specified	Uncertain significance (Jun 27, 2024)
6-118483728-T-C			Uncertain significance (Oct 21, 2022)
6-118483807-C-A			Uncertain significance (Apr 06, 2023)
6-118491618-TGACA-T		CEP85L-related disorder	Likely benign (Dec 01, 2022)
6-118491658-C-A			Uncertain significance (Jan 16, 2024)
6-118491702-T-C		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
6-118491728-T-C			Likely benign (Jul 01, 2023)
6-118491817-C-T		CEP85L-related disorder	Likely benign (Oct 25, 2022)
6-118491829-A-C		Inborn genetic diseases	Likely benign (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP85L	protein_coding	protein_coding	ENST00000368488	13	249304

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.54e-9	1.00	125706	1	41	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.401	374	396	0.943	0.0000197	5306
Missense in Polyphen		110	142.48	0.77203		1948
Synonymous	-0.431	147	141	1.05	0.00000680	1437
Loss of Function	3.09	21	42.8	0.491	0.00000210	558

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000354	0.000347
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.0000941	0.0000924
European (Non-Finnish)	0.000240	0.000229
Middle Eastern	0.00	0.00
South Asian	0.000239	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0934

Intolerance Scores

• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.48

Haploinsufficiency Scores

• pHI: 0.278
• hipred: N
• hipred_score: 0.443
• ghis: 0.421

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: Cep85l

Gene ontology

• Cellular component: cytoplasm;centrosome