LINGO2

leucine rich repeat and Ig domain containing 2, the group of I-set domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 9:27937616-29213601

Previous symbols: [ "LRRN6C" ]

Links

ENSG00000174482 ∙ NCBI:158038 ∙ OMIM:609793 ∙ HGNC:21207 ∙ Uniprot:Q7L985 ∙ 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 LINGO2 gene.

• Inborn genetic diseases (16 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINGO2 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			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	1

Variants in LINGO2

This is a list of pathogenic ClinVar variants found in the LINGO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-27948924-G-A		not specified	Uncertain significance (Feb 06, 2023)
9-27948942-A-G		not specified	Uncertain significance (Oct 26, 2022)
9-27948948-T-C		not specified	Uncertain significance (Jul 06, 2021)
9-27948977-C-T			Likely benign (Feb 01, 2023)
9-27949078-T-C		not specified	Uncertain significance (Oct 26, 2021)
9-27949139-C-T		not specified	Likely benign (Mar 07, 2024)
9-27949234-T-C		not specified	Uncertain significance (Jun 22, 2023)
9-27949323-C-G		not specified	Uncertain significance (Nov 04, 2023)
9-27949506-C-T		not specified	Uncertain significance (Dec 14, 2023)
9-27949575-A-G		not specified	Uncertain significance (Oct 26, 2021)
9-27949668-G-C		not specified	Uncertain significance (Jul 12, 2023)
9-27949699-C-G			Benign (Dec 13, 2017)
9-27949764-T-C		not specified	Uncertain significance (Jul 19, 2023)
9-27949791-G-C		not specified	Uncertain significance (Feb 13, 2024)
9-27950030-G-C		not specified	Uncertain significance (Aug 10, 2021)
9-27950186-G-T		not specified	Uncertain significance (Sep 14, 2022)
9-27950245-T-G		not specified	Uncertain significance (Jul 17, 2023)
9-27950295-G-A		not specified	Uncertain significance (Jun 24, 2022)
9-27950314-C-G		not specified	Uncertain significance (Nov 07, 2022)
9-27950340-C-T		not specified	Uncertain significance (Feb 28, 2023)
9-27950364-T-C		not specified	Uncertain significance (Dec 15, 2022)
9-27950388-T-C		not specified	Uncertain significance (Feb 13, 2024)
9-27950496-G-A		not specified	Uncertain significance (Nov 29, 2023)
9-27950619-A-C		not specified	Uncertain significance (Sep 26, 2023)
9-27950658-G-A		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINGO2	protein_coding	protein_coding	ENST00000379992	1	722208

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.857	0.143	125667	0	10	125677	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.674	311	346	0.898	0.0000190	3990
Missense in Polyphen		93	133.45	0.69688		1592
Synonymous	-2.12	166	135	1.23	0.00000705	1250
Loss of Function	3.13	2	15.2	0.132	9.78e-7	174

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000565	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000182	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.0589
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.67

Haploinsufficiency Scores

• pHI: 0.941
• hipred: Y
• hipred_score: 0.699
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.154

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lingo2

Zebrafish Information Network

• Gene name: lingo2a
• Affected structure: olfactory bulb glomerulus
• Phenotype tag: abnormal
• Phenotype quality: aplastic/hypoplastic

Gene ontology

• Biological process: positive regulation of synapse assembly
• Cellular component: extracellular space;integral component of membrane;extracellular matrix