LINGO3

leucine rich repeat and Ig domain containing 3, the group of I-set domain containing

Basic information

Region (hg38): 19:2287164-2308154

Previous symbols: [ "LRRN6B" ]

Links

ENSG00000220008 ∙ NCBI:645191 ∙ OMIM:609792 ∙ HGNC:21206 ∙ Uniprot:P0C6S8 ∙ 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 LINGO3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINGO3 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						0
missense			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	0

Variants in LINGO3

This is a list of pathogenic ClinVar variants found in the LINGO3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2290050-G-A		not specified	Uncertain significance (May 10, 2024)
19-2290101-T-G		not specified	Uncertain significance (Jul 15, 2021)
19-2290137-A-G		not specified	Uncertain significance (Dec 20, 2021)
19-2290221-C-T		not specified	Uncertain significance (Nov 07, 2022)
19-2290258-G-A		not specified	Uncertain significance (Mar 12, 2024)
19-2290263-C-A		not specified	Uncertain significance (Jun 24, 2022)
19-2290284-C-A		not specified	Uncertain significance (Aug 17, 2022)
19-2290317-C-A		not specified	Uncertain significance (Sep 27, 2022)
19-2290323-G-C		not specified	Uncertain significance (Dec 28, 2022)
19-2290332-G-A		not specified	Uncertain significance (Jun 04, 2024)
19-2290402-C-T		not specified	Uncertain significance (May 28, 2024)
19-2290411-G-C		not specified	Uncertain significance (Jan 26, 2023)
19-2290579-C-T		not specified	Uncertain significance (Apr 25, 2023)
19-2290601-G-C		not specified	Uncertain significance (Feb 16, 2023)
19-2290612-C-A		not specified	Uncertain significance (Feb 27, 2024)
19-2290677-C-A		not specified	Uncertain significance (Jan 16, 2024)
19-2290789-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-2290968-G-A		not specified	Uncertain significance (Jun 13, 2024)
19-2290978-G-A		not specified	Uncertain significance (Jul 26, 2022)
19-2291132-G-T		not specified	Uncertain significance (Apr 18, 2024)
19-2291160-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-2291172-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-2291182-T-G		not specified	Uncertain significance (Jan 31, 2024)
19-2291206-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-2291209-A-G		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINGO3	protein_coding	protein_coding	ENST00000585527	1	18383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0121	0.862	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	222	306	0.726	0.0000142	3657
Missense in Polyphen		74	103.19	0.71713		1311
Synonymous	1.09	140	157	0.889	0.00000756	1410
Loss of Function	1.26	4	7.78	0.514	3.35e-7	94

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.308

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lingo3

Gene ontology

• Cellular component: extracellular space;integral component of membrane;extracellular matrix