LRRC15

leucine rich repeat containing 15

Basic information

Region (hg38): 3:194355248-194369743

Links

ENSG00000172061 ∙ NCBI:131578 ∙ OMIM:619327 ∙ HGNC:20818 ∙ Uniprot:Q8TF66 ∙ 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 LRRC15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC15 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	2
missense			45	1	1	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	2	2

Variants in LRRC15

This is a list of pathogenic ClinVar variants found in the LRRC15 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-194359312-G-T		not specified	Uncertain significance (Dec 19, 2022)
3-194359353-C-G		not specified	Uncertain significance (Jun 22, 2023)
3-194359369-C-T		not specified	Likely benign (May 24, 2023)
3-194359377-G-A		not specified	Uncertain significance (Apr 23, 2024)
3-194359432-C-T		not specified	Uncertain significance (Jun 06, 2023)
3-194359449-A-T		not specified	Uncertain significance (Nov 06, 2023)
3-194359450-T-A		not specified	Uncertain significance (Aug 08, 2022)
3-194359460-G-A			Benign (Mar 29, 2018)
3-194359465-G-A		not specified	Uncertain significance (Apr 01, 2024)
3-194359492-G-C		not specified	Uncertain significance (Mar 30, 2024)
3-194359595-A-T			Benign (Jan 25, 2018)
3-194359596-C-T		not specified	Uncertain significance (Nov 28, 2023)
3-194359642-T-G		not specified	Uncertain significance (Apr 25, 2022)
3-194359675-C-T		not specified	Uncertain significance (May 18, 2023)
3-194359708-C-G		not specified	Uncertain significance (Nov 22, 2021)
3-194359741-G-A		not specified	Uncertain significance (Dec 14, 2022)
3-194359788-C-G		not specified	Uncertain significance (Apr 26, 2023)
3-194359803-T-C		not specified	Uncertain significance (Dec 21, 2022)
3-194359825-C-T		not specified	Uncertain significance (Oct 25, 2023)
3-194359882-C-T		not specified	Uncertain significance (Jul 26, 2022)
3-194359883-G-T		not specified	Uncertain significance (Oct 27, 2022)
3-194359959-C-T		not specified	Uncertain significance (Oct 20, 2021)
3-194359961-G-A			Likely benign (Jul 01, 2022)
3-194359972-C-T		not specified	Uncertain significance (Jun 09, 2022)
3-194359990-C-T		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC15	protein_coding	protein_coding	ENST00000439944	2	14497

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.73e-9	0.160	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.462	375	351	1.07	0.0000212	3827
Missense in Polyphen		96	93.596	1.0257		1221
Synonymous	-1.51	182	158	1.15	0.0000101	1245
Loss of Function	0.344	14	15.5	0.906	8.39e-7	152

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000673	0.000673
Ashkenazi Jewish	0.00	0.00
East Asian	0.00109	0.00109
Finnish	0.00	0.00
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.00109	0.00109
South Asian	0.000229	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.939
• rvis_EVS: -0.9
• rvis_percentile_EVS: 10.14

Haploinsufficiency Scores

• pHI: 0.619
• hipred: N
• hipred_score: 0.241
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.545

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc15
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: positive regulation of cell migration;receptor-mediated virion attachment to host cell;negative regulation of protein localization to plasma membrane
• Cellular component: extracellular space;integral component of membrane;extracellular matrix;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: fibronectin binding;collagen binding;laminin binding