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.

• Dilated_Cardiomyopathy,_Dominant (166 variants)
• not_specified (41 variants)
• not_provided (14 variants)
• LRRC10-related_disorder (1 variants)

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. These statistics are base on transcript: NM_000201550.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	47	2	53
missense			104	10	1	115
nonsense			2			2
start loss						0
frameshift			6			6
splice donor/acceptor (+/-2bp)						0
Total	0	0	116	57	3

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