OPCML

opioid binding protein/cell adhesion molecule like, the group of I-set domain containing|IgLON cell adhesion molecules

Basic information

Region (hg38): 11:132414976-133532501

Links

ENSG00000183715 ∙ NCBI:4978 ∙ OMIM:600632 ∙ HGNC:8143 ∙ Uniprot:Q14982 ∙ 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 OPCML gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPCML 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in OPCML

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

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

Position	Type	Phenotype	Significance	ClinVar
11-132420213-G-A		not specified	Uncertain significance (Mar 22, 2023)
11-132420217-T-A		not specified	Likely benign (Dec 13, 2023)
11-132435149-C-T		OPCML-related disorder	Benign (Feb 19, 2019)
11-132436127-G-T		not specified	Uncertain significance (Feb 27, 2024)
11-132436130-G-A		not specified	Uncertain significance (Apr 25, 2022)
11-132436213-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-132436692-A-G		not specified	Uncertain significance (Dec 21, 2023)
11-132436788-AACAC-A		OPCML-related disorder	Likely benign (Jun 27, 2019)
11-132436788-A-AAC		OPCML-related disorder	Likely benign (Jun 06, 2019)
11-132437305-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-132437306-G-C		not specified	Uncertain significance (Dec 20, 2023)
11-132529107-A-G		OPCML-related disorder	Likely benign (May 24, 2019)
11-132529168-T-G		not specified	Uncertain significance (Apr 10, 2023)
11-132657112-C-T			Likely benign (Mar 01, 2023)
11-132657203-G-C		Neoplasm of ovary	Pathogenic (Jul 01, 2003)
11-132657249-C-T		not specified	Uncertain significance (Jun 29, 2023)
11-132657302-C-T		not specified	Uncertain significance (May 05, 2023)
11-132943017-G-A		not specified	Uncertain significance (Oct 02, 2023)
11-133125672-TAGTATATGTATATAGTATATATAGTATATATATAGTG-T		Schizophrenia	Uncertain significance (Nov 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPCML	protein_coding	protein_coding	ENST00000331898	7	1117544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.228	0.771	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	133	207	0.644	0.0000113	2231
Missense in Polyphen		39	88.164	0.44236		902
Synonymous	-0.891	96	85.5	1.12	0.00000500	714
Loss of Function	2.77	4	15.9	0.251	7.60e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds opioids in the presence of acidic lipids; probably involved in cell contact.
• Disease: DISEASE: Ovarian cancer (OC) [MIM:167000]: The term ovarian cancer defines malignancies originating from ovarian tissue. Although many histologic types of ovarian tumors have been described, epithelial ovarian carcinoma is the most common form. Ovarian cancers are often asymptomatic and the recognized signs and symptoms, even of late-stage disease, are vague. Consequently, most patients are diagnosed with advanced disease. {ECO:0000269|PubMed:12819783}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.184

Intolerance Scores

• loftool: 0.278
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.584
• hipred: Y
• hipred_score: 0.701
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0664

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Opcml

Gene ontology

• Biological process: cell adhesion;neuron recognition
• Cellular component: extracellular region;plasma membrane;anchored component of membrane