OCEL1

occludin/ELL domain containing 1

Basic information

Region (hg38): 19:17226213-17229219

Links

ENSG00000099330 ∙ NCBI:79629 ∙ ∙ HGNC:26221 ∙ Uniprot:Q9H607 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Aicardi syndrome (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OCEL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OCEL1 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	3	4
missense			19	5	2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					2	2
splice region						0
non coding						0
Total	0	0	19	6	7

Variants in OCEL1

This is a list of pathogenic ClinVar variants found in the OCEL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17226257-C-A			Benign (Dec 31, 2019)
19-17226258-C-G		not specified	Likely benign (Jun 05, 2024)
19-17226281-G-A		not specified	Uncertain significance (Oct 03, 2024)
19-17226294-C-G		not specified	Uncertain significance (Nov 14, 2024)
19-17226294-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-17226300-T-G		not specified	Uncertain significance (Jul 05, 2023)
19-17226696-G-T		not specified	Uncertain significance (May 25, 2022)
19-17226768-C-A		not specified	Uncertain significance (Dec 21, 2022)
19-17226768-C-G		not specified	Uncertain significance (Jan 19, 2024)
19-17226784-G-A		not specified	Likely benign (Jun 13, 2024)
19-17226819-C-T		not specified	Uncertain significance (Sep 26, 2022)
19-17226825-T-G		not specified	Uncertain significance (Apr 07, 2023)
19-17226850-C-G			Benign (Dec 31, 2019)
19-17226854-T-A			Benign (Feb 20, 2018)
19-17226993-G-A			Benign (Dec 31, 2019)
19-17226993-G-C			Benign (Dec 31, 2019)
19-17227000-G-A		not specified	Likely benign (Jul 21, 2021)
19-17227037-G-T		not specified	Uncertain significance (Jan 24, 2023)
19-17227072-G-A		not specified	Uncertain significance (Nov 09, 2024)
19-17227117-G-A		not specified	Uncertain significance (Aug 26, 2024)
19-17227129-G-A		not specified	Likely benign (Jan 03, 2024)
19-17227141-A-G		not specified	Uncertain significance (Feb 05, 2024)
19-17227174-C-A		not specified	Uncertain significance (Jun 03, 2024)
19-17227196-A-C		not specified	Uncertain significance (Nov 15, 2024)
19-17227196-A-G		not specified	Uncertain significance (Jun 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OCEL1	protein_coding	protein_coding	ENST00000215061	6	3016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000306	0.819	125227	10	510	125747	0.00207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.336	158	147	1.08	0.00000774	1668
Missense in Polyphen		44	45.898	0.95865		523
Synonymous	-0.685	70	63.1	1.11	0.00000344	542
Loss of Function	1.19	7	11.3	0.619	5.64e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0347	0.0285
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000437	0.000416
European (Non-Finnish)	0.000202	0.000185
Middle Eastern	0.00	0.00
South Asian	0.000244	0.000229
Other	0.00242	0.00196

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0802

Intolerance Scores

• loftool: 0.806
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.68

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.146
• ghis: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0417

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ocel1