LRRC4C

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

Basic information

Region (hg38): 11:40114202-41459773

Links

ENSG00000148948 ∙ NCBI:57689 ∙ OMIM:608817 ∙ HGNC:29317 ∙ Uniprot:Q9HCJ2 ∙ 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 LRRC4C gene.

• Inborn genetic diseases (14 variants)
• not provided (1 variants)
• LRRC4C-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC4C 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in LRRC4C

This is a list of pathogenic ClinVar variants found in the LRRC4C region.

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

Position	Type	Phenotype	Significance	ClinVar
11-40114483-G-A		not specified	Uncertain significance (Jan 31, 2024)
11-40114522-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-40114561-C-T		Inborn genetic diseases	Uncertain significance (Jan 26, 2022)
11-40114566-G-A		not specified	Uncertain significance (Jun 09, 2022)
11-40114613-G-A			Likely benign (Jan 01, 2023)
11-40114846-C-T		not specified	Uncertain significance (Jan 30, 2024)
11-40114855-G-A		not specified	Uncertain significance (Jan 18, 2023)
11-40114875-T-A		not specified	Uncertain significance (Nov 15, 2023)
11-40114956-G-A		not specified	Uncertain significance (Apr 18, 2023)
11-40115064-G-A		not specified	Uncertain significance (Jan 10, 2023)
11-40115088-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-40115100-G-A		not specified	Uncertain significance (Jul 20, 2021)
11-40115202-T-C		not specified	Uncertain significance (Jan 20, 2023)
11-40115328-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-40115420-A-T		LRRC4C-related disorder	Uncertain significance (May 31, 2023)
11-40115430-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-40115470-C-T		not specified	Uncertain significance (Jan 30, 2024)
11-40115514-C-T		not specified	Uncertain significance (Jan 06, 2023)
11-40115527-G-T		not specified	Uncertain significance (Jan 04, 2022)
11-40115563-G-A		not specified	Uncertain significance (Mar 14, 2023)
11-40115595-G-A		Inborn genetic diseases	Uncertain significance (Feb 17, 2022)
11-40115595-G-T		not specified	Uncertain significance (Oct 03, 2022)
11-40115617-G-T		not specified	Uncertain significance (Jan 06, 2023)
11-40115799-G-A		not specified	Uncertain significance (Mar 01, 2024)
11-40115819-G-T		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC4C	protein_coding	protein_coding	ENST00000278198	1	1345571

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.972	0.0277	125725	0	5	125730	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.52	224	358	0.625	0.0000197	4220
Missense in Polyphen		50	119.97	0.41678		1450
Synonymous	-0.302	143	138	1.03	0.00000752	1320
Loss of Function	3.41	1	15.5	0.0646	9.17e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00000893	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May promote neurite outgrowth of developing thalamic neurons. {ECO:0000269|PubMed:14595443}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.0242
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.46

Haploinsufficiency Scores

• pHI: 0.855
• hipred: Y
• hipred_score: 0.809
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc4c
• Phenotype: immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: regulation of axonogenesis;modulation of chemical synaptic transmission;synaptic membrane adhesion
• Cellular component: extracellular space;membrane;integral component of membrane;cell junction;Schaffer collateral - CA1 synapse;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: protein binding;cell adhesion molecule binding;cell-cell adhesion mediator activity