LGI2

leucine rich repeat LGI family member 2, the group of LGI family

Basic information

Region (hg38): 4:24998847-25030946

Links

ENSG00000153012 ∙ NCBI:55203 ∙ OMIM:608301 ∙ HGNC:18710 ∙ Uniprot:Q8N0V4 ∙ 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 LGI2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGI2 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				2		2
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	0

Variants in LGI2

This is a list of pathogenic ClinVar variants found in the LGI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-25003474-T-C		not specified	Uncertain significance (Apr 01, 2024)
4-25003534-C-T		not specified	Uncertain significance (Nov 30, 2022)
4-25003537-T-C		not specified	Uncertain significance (Nov 15, 2023)
4-25003705-G-A		not specified	Uncertain significance (Mar 16, 2022)
4-25003809-C-T		not specified	Uncertain significance (Dec 20, 2021)
4-25003831-C-T		not specified	Uncertain significance (Aug 08, 2023)
4-25003870-T-G		not specified	Uncertain significance (Oct 10, 2023)
4-25003882-T-C		not specified	Uncertain significance (Aug 11, 2022)
4-25003957-A-T		not specified	Uncertain significance (May 08, 2023)
4-25004124-C-T		not specified	Uncertain significance (Jun 07, 2024)
4-25004140-C-G		not specified	Uncertain significance (Mar 31, 2024)
4-25004165-A-C		not specified	Uncertain significance (Apr 13, 2022)
4-25004173-C-T		not specified	Uncertain significance (Feb 28, 2023)
4-25012345-G-T		not specified	Uncertain significance (Jul 19, 2023)
4-25012376-T-A		not specified	Uncertain significance (Jun 28, 2022)
4-25012426-G-A			Likely benign (Jun 01, 2022)
4-25012435-G-T		not specified	Uncertain significance (Nov 07, 2023)
4-25012463-A-C		not specified	Uncertain significance (Jun 26, 2023)
4-25018010-C-G		not specified	Uncertain significance (Dec 06, 2022)
4-25018022-C-T		not specified	Uncertain significance (Jun 07, 2023)
4-25018040-C-T		not specified	Uncertain significance (Aug 10, 2021)
4-25018079-C-T		not specified	Uncertain significance (Dec 30, 2023)
4-25024835-C-T		not specified	Uncertain significance (Jan 17, 2024)
4-25024844-C-T		not specified	Uncertain significance (Aug 12, 2021)
4-25024845-G-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGI2	protein_coding	protein_coding	ENST00000382114	8	32033

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000149	0.962	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	230	311	0.739	0.0000178	3606
Missense in Polyphen		76	124.2	0.61193		1484
Synonymous	0.246	124	128	0.972	0.00000782	1027
Loss of Function	1.95	13	23.1	0.563	0.00000116	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000486	0.000484
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000972	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.0000986	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Developmental Biology;LGI-ADAM interactions (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.357
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.06

Haploinsufficiency Scores

• pHI: 0.270
• hipred: Y
• hipred_score: 0.557
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lgi2

Gene ontology

• Cellular component: extracellular region