LRRC10

protein-coding

leucine rich repeat containing 10

Gene summary

Predicted to enable actin binding activity. Predicted to be involved in cardiac muscle cell development. Predicted to be located in mitochondrion; myofibril; and nucleus. Predicted to be active in cytoskeleton and sarcomere. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_201550.4

Inheritance

AR

ClinVar variants

U:145B:68

Top phenotype

Dilated Cardiomyopathy, Dominant

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr12:69,608,564-69,610,907

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~2.3 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

dilated cardiomyopathyNO_KNOWN

Inheritance Pattern: AR

Disease ID:MONDO:0005021

Submitter: ClinGen

LRRC10 was evaluated for autosomal recessive dilated cardiomyopathy (DCM). LRRC10 was originally evaluated for DCM by the ClinGen DCM GCEP on March 20, 2020. Evidence of the association of this gene with DCM was re-evaluated using SOP v10 on August 9, 2024. As a result, the classification did not change. A summary of the information contributing to the classification of this gene at the time of re-evaluation is summarized herein. There is a lack of robust human genetic evidence demonstrating this gene-disease relationship in the literature at the time of curation. Two publications were reviewed in regards to human genetic evidence, but neither was felt to meet the threshold for scoring. The variant reported by Woon et al. 2018 (PMID: 29431102) has subsequently been found at a frequency higher than would be expected for a monogenic, pathogenic effect in population reference data sets. The second publication that presented genetic evidence was excluded due to DCM GCEP concerns of suspect data (Qu et al, 2015, PMID 26017719). This gene-disease assertion is supported by animal models, expression studies, and protein interaction studies. LRRC10 expression in the heart has been demonstrated in both mice and zebrafish (Kim et al, 2007, PMID: 17626279; Kim et al, 2007, PMID: 17601532; Brody et al, 2013, PMID: 23751912). Protein interaction studies demonstrate interaction with ACTC1, GATA4, and NKX2-5 (Brody et al 2012, PMID: 23236519; Brody et al, 2013, PMID: 23751912; Brody et al, 2016, PMID: 26608339). Knockout LRRC10 animal models have been shown to develop dilated cardiomyopathy and heart failure (Brody et al 2012, PMID: 23236519; Kim et al, 2007, PMID: 17601532; Brody et al, 2013, PMID: 23751912). However, the DCM GCEP elected to reduce the points awarded for animal models given the mode of inheritance has not been confirmed in any human genetic evidence data and a knockout model is a severe genetic manipulation. Overall, no convincing evidence for a causal role for LRRC10 and autosomal recessive DCM has been reported. Although this gene-disease assertion is supported by animal models, expression studies, and protein interaction studies, no reports have directly implicated the gene in humans. This classification was approved by the ClinGen Dilated Cardiomyopathy Working Group on August 9, 2024 (SOP Version 10).

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LRRC10 variants in ClinVar

4 Conditions Cataloged
not providedTotal: 195
not specifiedTotal: 67
Dilated Cardiomyopathy, DominantTotal: 2
LRRC10-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_201550.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
8
clinvar
52
clinvar
2
clinvar
62
missense
128
clinvar
13
clinvar
1
clinvar
142
nonsense
2
clinvar
2
start loss
0
frameshift
7
clinvar
7
splice donor/acceptor (+/-2bp)
0
Total00145653213
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_201550.4RefSeqNP_963844.21MANE Select
ENST00000361484.5EnsemblENSP00000355166.31MANE Select

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
lrrc10Danio rerio

Structure: nucleate erythrocyte

Quality: decreased fluid flow

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • cardiac muscle cell development

Molecular Function

  • actin binding
  • alpha-actinin binding

Cellular Component

  • nucleus
  • mitochondrion
  • cytoskeleton
  • sarcomere

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000361484
Coding exons
1
Length
2592
Individuals with no LoFs
0
Homozygous LoFs
0
Heterozygous LoFs
0
Defined
0
p
0.00
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3901551690.9160.00001051796
Missense (PolyPhen)5263.3310.82108773
Synonymous-0.2147875.61.030.00000457598
Loss of Function1.7515.390.1852.30e-760

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.364

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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