LRRC10

leucine rich repeat containing 10

Basic information

Region (hg38): 12:69608564-69610907

Links

ENSG00000198812 ∙ NCBI:376132 ∙ OMIM:610846 ∙ HGNC:20264 ∙ Uniprot:Q5BKY1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• dilated cardiomyopathy (No Known Disease Relationship), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LRRC10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC10 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			3	48	1	52
missense			87	7	1	95
nonsense			1			1
start loss						0
frameshift			4			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	96	55	4

Variants in LRRC10

This is a list of pathogenic ClinVar variants found in the LRRC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-69609715-G-A			Benign (Sep 11, 2018)
12-69609852-T-G			Benign (Sep 11, 2018)
12-69610007-A-G		Dilated Cardiomyopathy, Dominant	Uncertain significance (Jun 14, 2022)
12-69610012-T-A		Dilated Cardiomyopathy, Dominant	Uncertain significance (Oct 04, 2023)
12-69610021-G-C		Dilated Cardiomyopathy, Dominant	Uncertain significance (Jun 04, 2020)
12-69610026-T-G		Dilated Cardiomyopathy, Dominant	Likely benign (Aug 05, 2021)
12-69610026-TAGAG-T		Dilated Cardiomyopathy, Dominant	Uncertain significance (Aug 10, 2022)
12-69610034-C-T		Dilated Cardiomyopathy, Dominant	Uncertain significance (May 09, 2023)
12-69610036-G-A		Dilated Cardiomyopathy, Dominant	Uncertain significance (Oct 23, 2023)
12-69610039-G-T		not specified	Uncertain significance (Apr 01, 2024)
12-69610041-C-G		Dilated Cardiomyopathy, Dominant	Uncertain significance (Dec 14, 2022)
12-69610065-G-A		Dilated Cardiomyopathy, Dominant	Likely benign (Jul 13, 2018)
12-69610071-C-T		Dilated Cardiomyopathy, Dominant	Benign/Likely benign (Jan 18, 2024)
12-69610074-A-G		Dilated Cardiomyopathy, Dominant	Likely benign (Jan 14, 2022)
12-69610077-G-A		Dilated Cardiomyopathy, Dominant	Likely benign (Mar 09, 2022)
12-69610078-C-T		Dilated Cardiomyopathy, Dominant	Uncertain significance (Aug 16, 2022)
12-69610079-G-A		Dilated Cardiomyopathy, Dominant • not specified	Uncertain significance (Jan 29, 2023)
12-69610092-A-G		Dilated Cardiomyopathy, Dominant	Likely benign (Oct 17, 2022)
12-69610093-G-C		Dilated Cardiomyopathy, Dominant	Uncertain significance (May 20, 2021)
12-69610097-C-T		Dilated Cardiomyopathy, Dominant	Uncertain significance (Mar 18, 2023)
12-69610098-G-A		Dilated Cardiomyopathy, Dominant	Likely benign (Aug 10, 2022)
12-69610103-CT-C		Dilated Cardiomyopathy, Dominant	Uncertain significance (Oct 04, 2023)
12-69610106-G-A		Dilated Cardiomyopathy, Dominant • not specified	Uncertain significance (Nov 14, 2023)
12-69610107-C-T		Dilated Cardiomyopathy, Dominant	Likely benign (Oct 07, 2023)
12-69610108-G-A		Dilated Cardiomyopathy, Dominant	Uncertain significance (Dec 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC10	protein_coding	protein_coding	ENST00000361484	1	2592

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.435	0.537	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.390	155	169	0.916	0.0000105	1796
Missense in Polyphen		52	63.331	0.82108		773
Synonymous	-0.214	78	75.6	1.03	0.00000457	598
Loss of Function	1.75	1	5.39	0.185	2.30e-7	60

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play important roles in cardiac development and/or cardiac function. {ECO:0000250}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.305
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.231
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.364

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc10
• 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); muscle phenotype

Zebrafish Information Network

• Gene name: lrrc10
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased fluid flow

Gene ontology

• Biological process: cardiac muscle cell development
• Cellular component: nucleus;mitochondrion;cytoskeleton;sarcomere
• Molecular function: actin binding;alpha-actinin binding