OPTC

opticin

Basic information

Region (hg38): 1:203494121-203508949

Links

ENSG00000188770 ∙ NCBI:26254 ∙ OMIM:605127 ∙ HGNC:8158 ∙ Uniprot:Q9UBM4 ∙ 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 OPTC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPTC 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				4	1	5
missense			23	2	3	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				17	12	29
Total	0	0	23	23	16

Variants in OPTC

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

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

Position	Type	Phenotype	Significance	ClinVar
1-203495639-C-T			Benign (Jul 31, 2018)
1-203495640-A-G			Benign (Jun 26, 2018)
1-203495745-G-A			Likely benign (Nov 12, 2018)
1-203495804-C-T			Likely benign (May 20, 2019)
1-203495872-G-A			Likely benign (Jul 26, 2019)
1-203495890-T-C			Likely benign (May 18, 2019)
1-203496013-T-C		not specified	Uncertain significance (Feb 03, 2022)
1-203496025-T-G		not specified	Uncertain significance (Dec 19, 2022)
1-203496108-C-T		not specified	Uncertain significance (Mar 11, 2024)
1-203496114-G-C		not specified	Uncertain significance (Sep 25, 2023)
1-203496118-G-T		not specified	Uncertain significance (Apr 05, 2023)
1-203496174-G-A		not specified	Uncertain significance (Dec 26, 2023)
1-203496184-T-C		not specified	Uncertain significance (Feb 03, 2022)
1-203496228-C-A		not specified	Uncertain significance (Dec 19, 2022)
1-203496264-T-G			Benign (Jun 26, 2018)
1-203496268-T-C			Benign (Jun 26, 2018)
1-203496342-T-C			Benign (Jun 26, 2018)
1-203496442-C-G			Benign (Jun 26, 2018)
1-203496712-G-A			Likely benign (Apr 12, 2019)
1-203497062-C-T		OPTC-related disorder	Benign (Oct 28, 2017)
1-203497095-T-G		not specified	Uncertain significance (Oct 12, 2021)
1-203497138-G-A			Likely benign (Dec 05, 2020)
1-203497221-G-A			Benign (Jun 26, 2018)
1-203498532-G-A			Benign (Jul 31, 2018)
1-203498663-G-A			Likely benign (May 18, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPTC	protein_coding	protein_coding	ENST00000367222	6	14722

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.82e-10	0.0317	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.529	206	186	1.11	0.0000123	2155
Missense in Polyphen		46	44.578	1.0319		546
Synonymous	-0.874	91	81.0	1.12	0.00000533	708
Loss of Function	-0.639	13	10.7	1.21	4.78e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000969	0.0000879
Middle Eastern	0.000217	0.000217
South Asian	0.000523	0.000523
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds collagen fibrils. {ECO:0000250}.
• Pathway: Extracellular matrix organization;Degradation of the extracellular matrix (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.799
• rvis_EVS: 0.64
• rvis_percentile_EVS: 84.05

Haploinsufficiency Scores

• pHI: 0.0788
• hipred: N
• hipred_score: 0.146
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.288

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Optc
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Cellular component: extracellular region;extracellular matrix
• Molecular function: extracellular matrix structural constituent