LRRC4B

leucine rich repeat containing 4B, the group of I-set domain containing|Ig-like cell adhesion molecule family|Receptor ligands

Basic information

Region (hg38): 19:50516892-50568435

Previous symbols: [ "LRIG4" ]

Links

ENSG00000131409 ∙ NCBI:94030 ∙ ∙ HGNC:25042 ∙ Uniprot:Q9NT99 ∙ 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 LRRC4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC4B 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			28	1		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	28	3	0

Variants in LRRC4B

This is a list of pathogenic ClinVar variants found in the LRRC4B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50517678-T-G		not specified	Uncertain significance (Jan 08, 2024)
19-50517728-T-C		not specified	Uncertain significance (Feb 10, 2022)
19-50517753-C-T		not specified	Uncertain significance (Sep 28, 2022)
19-50517786-C-A		not specified	Uncertain significance (Mar 28, 2024)
19-50517791-C-G		not specified	Uncertain significance (Apr 07, 2023)
19-50517795-T-C		not specified	Likely benign (Apr 07, 2023)
19-50517801-C-T		not specified	Uncertain significance (Jul 06, 2021)
19-50517818-A-G		not specified	Uncertain significance (Nov 21, 2023)
19-50517976-G-A			Likely benign (Jul 01, 2022)
19-50518095-C-T		not specified	Uncertain significance (Feb 24, 2023)
19-50518175-G-T		not specified	Uncertain significance (Dec 09, 2023)
19-50518190-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-50518194-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-50518274-C-T		not specified	Uncertain significance (Feb 05, 2024)
19-50518315-G-T		not specified	Uncertain significance (Feb 28, 2023)
19-50518325-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-50518345-C-A			Likely benign (Nov 01, 2022)
19-50518422-T-C		not specified	Uncertain significance (Jul 20, 2022)
19-50518439-T-C		not specified	Uncertain significance (Sep 29, 2023)
19-50518509-T-A		not specified	Uncertain significance (Mar 24, 2023)
19-50518520-G-A		not specified	Uncertain significance (Apr 12, 2023)
19-50518538-G-A		not specified	Uncertain significance (Aug 17, 2022)
19-50518602-T-C		not specified	Uncertain significance (Jul 12, 2022)
19-50518727-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-50518947-G-A		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC4B	protein_coding	protein_coding	ENST00000599957	2	51154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.884	0.116	117707	0	2	117709	0.00000850

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.36	222	495	0.448	0.0000374	4517
Missense in Polyphen		20	137.81	0.14512		1337
Synonymous	1.50	221	251	0.880	0.0000220	1578
Loss of Function	3.22	2	15.8	0.127	7.45e-7	167

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)	0.0000210	0.0000192
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Synaptic adhesion protein. Regulates the formation of excitatory synapses. The trans-synaptic adhesion between LRRC4B and PTPRF regulates the formation of excitatory synapses in a bidirectional manner (By similarity). {ECO:0000250}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Neuronal System;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.0528
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.209
• hipred: Y
• hipred_score: 0.559
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc4b

Gene ontology

• Biological process: positive regulation of synapse assembly;regulation of postsynaptic density assembly;synaptic membrane adhesion;regulation of presynapse assembly
• Cellular component: plasma membrane;cell junction;presynaptic membrane;cerebellar mossy fiber;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: signaling receptor binding