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.

• not_specified (47 variants)
• not_provided (9 variants)

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. These statistics are base on transcript: NM_000024578.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	3	4
missense			41	7	2	50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)					2	2
Total	0	0	41	8	7

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