OPALIN

oligodendrocytic myelin paranodal and inner loop protein

Basic information

Region (hg38): 10:96343221-96359365

Previous symbols: [ "TMEM10" ]

Links

ENSG00000197430 ∙ NCBI:93377 ∙ OMIM:617200 ∙ HGNC:20707 ∙ Uniprot:Q96PE5 ∙ 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 OPALIN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OPALIN 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			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	2

Variants in OPALIN

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

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

Position	Type	Phenotype	Significance	ClinVar
10-96346034-G-A			Benign (Jul 17, 2018)
10-96346071-T-C		not specified	Uncertain significance (Mar 14, 2023)
10-96346081-T-A		not specified	Uncertain significance (May 27, 2022)
10-96346089-T-C		not specified	Uncertain significance (Dec 27, 2023)
10-96346101-G-A		not specified	Uncertain significance (Mar 02, 2023)
10-96348293-G-T		not specified	Uncertain significance (Apr 25, 2023)
10-96348345-C-T		not specified	Uncertain significance (Jun 24, 2022)
10-96349728-T-G		not specified	Uncertain significance (Jun 06, 2023)
10-96349766-G-C		not specified	Uncertain significance (Jul 29, 2023)
10-96349778-C-A			Benign (Jul 17, 2018)
10-96349813-G-C		not specified	Uncertain significance (Jan 10, 2022)
10-96349816-G-A		not specified	Uncertain significance (Sep 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OPALIN	protein_coding	protein_coding	ENST00000371172	6	16120

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00149	0.694	125719	0	16	125735	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.603	66	81.3	0.812	0.00000440	899
Missense in Polyphen		22	23.653	0.9301		236
Synonymous	0.185	29	30.3	0.957	0.00000177	281
Loss of Function	0.752	5	7.17	0.697	3.88e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0668

Intolerance Scores

• loftool: 0.196
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.0644
• hipred: N
• hipred_score: 0.170
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Opalin

Gene ontology

• Cellular component: Golgi apparatus;plasma membrane;integral component of membrane;cell-cell contact zone