LRRC18

leucine rich repeat containing 18

Basic information

Region (hg38): 10:48909480-48939840

Links

ENSG00000165383 ∙ NCBI:474354 ∙ OMIM:619002 ∙ HGNC:23199 ∙ Uniprot:Q8N456 ∙ 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 LRRC18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC18 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						0
missense			18	2		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	2	0

Variants in LRRC18

This is a list of pathogenic ClinVar variants found in the LRRC18 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-48910253-C-T		not specified	Uncertain significance (Mar 14, 2023)
10-48913412-C-A		not specified	Uncertain significance (Mar 11, 2022)
10-48913429-G-A		not specified	Uncertain significance (Aug 21, 2023)
10-48913521-C-T		not specified	Likely benign (Jul 20, 2021)
10-48913531-C-T		not specified	Uncertain significance (Jan 08, 2024)
10-48913567-T-G		not specified	Uncertain significance (Jul 12, 2023)
10-48913602-G-A		not specified	Uncertain significance (Aug 03, 2022)
10-48913632-T-C		not specified	Uncertain significance (Mar 27, 2023)
10-48913642-G-C		not specified	Uncertain significance (Jun 09, 2022)
10-48913666-A-G		not specified	Uncertain significance (Jul 09, 2021)
10-48913685-G-T		not specified	Uncertain significance (Apr 13, 2023)
10-48913714-C-T		not specified	Uncertain significance (Feb 10, 2022)
10-48913783-C-T		not specified	Likely benign (Jul 22, 2022)
10-48913813-C-T		not specified	Uncertain significance (Jun 10, 2024)
10-48913871-C-T		not specified	Uncertain significance (Feb 27, 2023)
10-48913881-A-G		not specified	Uncertain significance (Feb 08, 2023)
10-48913967-C-G		not specified	Uncertain significance (Mar 11, 2022)
10-48914014-G-A		not specified	Uncertain significance (Nov 07, 2023)
10-48914014-G-T		not specified	Uncertain significance (Aug 12, 2021)
10-48914077-C-T		not specified	Uncertain significance (Oct 04, 2022)
10-48914086-T-C		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC18	protein_coding	protein_coding	ENST00000374160	2	25715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000351	0.216	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.728	182	156	1.16	0.00000928	1727
Missense in Polyphen		40	35.774	1.1181		429
Synonymous	-1.29	76	63.0	1.21	0.00000368	519
Loss of Function	-0.568	6	4.68	1.28	1.94e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of spermatogenesis and sperm maturation. {ECO:0000250}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.642
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.46

Haploinsufficiency Scores

• pHI: 0.148
• hipred: N
• hipred_score: 0.251
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.501

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc18

Gene ontology

• Biological process: inorganic anion transport;anion transmembrane transport
• Cellular component: cytoplasm;ion channel complex
• Molecular function: volume-sensitive anion channel activity