LRRC10
protein-codingleucine 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
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
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
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | 52 | 2 | 62 | ||
| missense | 128 | 13 | 1 | 142 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 7 | 7 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 145 | 65 | 3 | 213 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_963844.2 | 1 | MANE Select | |
| Ensembl | ENSP00000355166.3 | 1 | MANE Select |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lrrc10 | Danio 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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.390 | 155 | 169 | 0.916 | 0.0000105 | 1796 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |