LRRC4

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

Basic information

Region (hg38): 7:128027071-128032107

Links

ENSG00000128594 ∙ NCBI:64101 ∙ OMIM:610486 ∙ HGNC:15586 ∙ Uniprot:Q9HBW1 ∙ 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 LRRC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC4 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					4	4
missense			24	1		25
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	4

Variants in LRRC4

This is a list of pathogenic ClinVar variants found in the LRRC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-128028716-G-A		not specified	Uncertain significance (Apr 13, 2022)
7-128028741-T-C		not specified	Uncertain significance (Jan 23, 2024)
7-128028810-T-G		not specified	Uncertain significance (Nov 18, 2022)
7-128028846-G-A		not specified	Uncertain significance (Jun 09, 2022)
7-128028857-G-A		not specified	Uncertain significance (Apr 20, 2024)
7-128028925-G-C		not specified	Uncertain significance (Mar 01, 2023)
7-128028948-T-C		not specified	Uncertain significance (May 14, 2024)
7-128028951-G-A		not specified	Uncertain significance (Sep 22, 2023)
7-128028955-G-A			Benign (May 31, 2018)
7-128029006-A-G			Benign (Dec 31, 2019)
7-128029095-G-A			Uncertain significance (Oct 26, 2021)
7-128029190-T-C		not specified	Uncertain significance (Jan 23, 2023)
7-128029232-G-A		not specified	Uncertain significance (Dec 06, 2021)
7-128029233-T-G		not specified	Uncertain significance (Apr 07, 2023)
7-128029244-G-A		not specified	Uncertain significance (Aug 15, 2023)
7-128029322-T-C		not specified	Uncertain significance (Aug 08, 2023)
7-128029328-T-A		not specified	Uncertain significance (Mar 16, 2024)
7-128029334-G-C		not specified	Uncertain significance (Jan 16, 2024)
7-128029418-G-A		not specified	Uncertain significance (Jan 08, 2024)
7-128029451-C-T		not specified	Uncertain significance (Dec 19, 2022)
7-128029502-G-T		not specified	Uncertain significance (Dec 19, 2023)
7-128029527-G-A			Likely benign (Dec 31, 2019)
7-128029531-T-C			Benign (Nov 12, 2018)
7-128029568-G-A		not specified	Uncertain significance (Sep 22, 2023)
7-128029608-G-C		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC4	protein_coding	protein_coding	ENST00000249363	1	5037

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00213	125738	0	4	125742	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	287	397	0.723	0.0000245	4252
Missense in Polyphen		55	118.79	0.463		1365
Synonymous	-2.09	204	169	1.20	0.0000110	1392
Loss of Function	3.93	0	18.0	0.00	0.00000108	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
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 exitatory synapses through the recruitment of pre-and-postsynaptic proteins. Organize the lamina/pathway-specific differentiation of dendrites. Plays a important role for auditory synaptic responses. Involved in the suppression of glioma (By similarity). {ECO:0000250}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.0214
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.17

Haploinsufficiency Scores

• pHI: 0.430
• hipred: Y
• hipred_score: 0.715
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.245

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc4
• Phenotype: hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: modulation of chemical synaptic transmission;regulation of synapse organization;postsynaptic density protein 95 clustering;synaptic membrane adhesion
• Cellular component: cell junction;dendritic spine;excitatory synapse;Schaffer collateral - CA1 synapse;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: protein binding