LARP6
protein-codingLa ribonucleoprotein 6, translational regulator, the group of La ribonucleoproteins
Gene summary
Enables RNA binding activity and myosin binding activity. Involved in positive regulation of collagen biosynthetic process. Located in cytoplasm and nucleus. [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 ~25.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LARP6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018357.4. 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 | 3 | 1 | 4 | |||
| missense | 77 | 77 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 77 | 3 | 1 | 81 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060827.2 | 3 | MANE Select | |
| Ensembl | ENSP00000299213.7 | 3 | MANE Select | |
| RefSeq | NP_001273608.1 | 1 | Standard | |
| RefSeq | NP_932062.1 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| larp6a | Danio rerio | Structure: slow muscle cell Quality: malformed abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- RNA processing
- positive regulation of collagen biosynthetic process
- positive regulation of translation
- positive regulation of mRNA binding
Molecular Function
- protein binding
- myosin binding
- RNA stem-loop binding
- mRNA 5'-UTR binding
- sequence-specific mRNA binding
Cellular Component
- nucleus
- cytoplasm
- polysome
- ribonucleoprotein complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000299213
- Coding exons
- 3
- Length
- 22636
- Individuals with no LoFs
- 125741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125748
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.51 | 197 | 266 | 0.740 | 0.0000159 | 3211 |
| Missense (PolyPhen) | 55 | 98.114 | 0.56057 | 1106 | ||
| Synonymous | -0.300 | 115 | 111 | 1.04 | 0.00000700 | 983 |
| Loss of Function | 2.71 | 2 | 12.3 | 0.163 | 5.99e-7 | 179 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000030 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulates the coordinated translation of type I collagen alpha-1 and alpha-2 mRNAs, CO1A1 and CO1A2. Stabilizes mRNAs through high-affinity binding of a stem-loop structure in their 5' UTR. This regulation requires VIM and MYH10 filaments, and the helicase DHX9. {ECO:0000269|PubMed:20603131, ECO:0000269|PubMed:21746880, ECO:0000269|PubMed:22190748}.;
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- LoFtool
- 0.181
- RVIS EVS
- -0.29
- RVIS percentile EVS
- 33.34
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.728
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |