LINGO4

leucine rich repeat and Ig domain containing 4, the group of I-set domain containing

Basic information

Region (hg38): 1:151800263-151805419

Previous symbols: [ "LRRN6D" ]

Links

ENSG00000213171 ∙ NCBI:339398 ∙ OMIM:609794 ∙ HGNC:31814 ∙ Uniprot:Q6UY18 ∙ 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 LINGO4 gene.

• Inborn genetic diseases (31 variants)
• Polymicrogyria (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LINGO4 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			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in LINGO4

This is a list of pathogenic ClinVar variants found in the LINGO4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151800945-C-T		not specified	Uncertain significance (Jan 24, 2023)
1-151800967-C-T		not specified	Uncertain significance (Oct 25, 2023)
1-151801020-C-A		not specified	Uncertain significance (Sep 16, 2021)
1-151801072-T-G		not specified	Uncertain significance (May 24, 2023)
1-151801119-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-151801127-A-C		not specified	Uncertain significance (Jul 31, 2023)
1-151801160-G-C		not specified	Uncertain significance (Dec 27, 2022)
1-151801353-T-C		not specified	Uncertain significance (Mar 24, 2023)
1-151801413-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-151801443-C-T		Polymicrogyria	Uncertain significance (Sep 01, 2017)
1-151801452-G-A		not specified	Uncertain significance (Feb 11, 2022)
1-151801453-A-G		not specified	Uncertain significance (Apr 12, 2023)
1-151801537-G-T		not specified	Uncertain significance (Dec 21, 2023)
1-151801588-G-A		not specified	Uncertain significance (Oct 06, 2021)
1-151801612-G-A		not specified	Uncertain significance (May 16, 2022)
1-151801615-A-C		not specified	Uncertain significance (Feb 14, 2023)
1-151801687-C-G		not specified	Uncertain significance (Sep 14, 2022)
1-151801842-A-T		not specified	Uncertain significance (Aug 17, 2021)
1-151801854-G-A		Polymicrogyria	Uncertain significance (Sep 01, 2017)
1-151801918-T-G		not specified	Uncertain significance (Feb 07, 2023)
1-151801923-C-T		not specified	Uncertain significance (Oct 26, 2022)
1-151801924-G-A		not specified	Uncertain significance (Dec 14, 2023)
1-151801968-G-C		not specified	Uncertain significance (Jan 16, 2024)
1-151802002-T-G		not specified	Uncertain significance (Dec 19, 2022)
1-151802036-G-A			Likely benign (Jun 01, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LINGO4	protein_coding	protein_coding	ENST00000368820	1	5891

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000824	0.783	125585	0	163	125748	0.000648

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.678	296	331	0.895	0.0000190	3763
Missense in Polyphen		109	120.98	0.90099		1492
Synonymous	1.04	128	144	0.890	0.00000737	1401
Loss of Function	1.14	8	12.3	0.649	7.05e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00105	0.00105
Ashkenazi Jewish	0.00	0.00
East Asian	0.00343	0.00343
Finnish	0.000463	0.000462
European (Non-Finnish)	0.000373	0.000369
Middle Eastern	0.00343	0.00343
South Asian	0.000621	0.000621
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.268

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.42

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.248
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.299

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lingo4

Gene ontology

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