LLPH
protein-codingLLP homolog, long-term synaptic facilitation factor
Gene summary
Enables RNA binding activity. Predicted to be involved in dendrite extension and positive regulation of dendritic spine development. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Jul 2025]
- C12orf31
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.2 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 LLPH variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032338.4. 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 | 0 | |||||
| missense | 22 | 1 | 23 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 22 | 1 | 0 | 23 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_115714.1 | 2 | MANE Select | |
| Ensembl | ENSP00000266604.2 | 2 | MANE Select | |
| Ensembl | ENSP00000437372.1 | 2 | Standard | |
| Ensembl | ENSP00000591957.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of dendritic spine development
- dendrite extension
Molecular Function
- basal RNA polymerase II transcription machinery binding
- RNA binding
Cellular Component
- chromosome
- nucleolus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000266604
- Coding exons
- 2
- Length
- 7707
- Individuals with no LoFs
- 125385
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 312
- Defined
- 125699
- p
- 0.00125
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.262 | 75 | 68.9 | 1.09 | 0.00000342 | 867 |
| Missense (PolyPhen) | 23 | 23.971 | 0.95949 | 337 | ||
| Synonymous | 0.669 | 16 | 19.8 | 0.809 | 8.47e-7 | 212 |
| Loss of Function | 1.53 | 1 | 4.51 | 0.222 | 1.89e-7 | 63 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00063 | 0.00062 | rare |
| Latino/Admixed American | 0.0013 | 0.0012 | notable |
| Ashkenazi Jewish | 0.00086 | 0.00079 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0023 | 0.0022 | notable |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00087 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: In hippocampal neurons, regulates dendritic and spine growth and synaptic transmission. {ECO:0000250|UniProtKB:Q9D945}.;
Intolerance Scores
- LoFtool
- 0.594
- RVIS EVS
- 0.24
- RVIS percentile EVS
- 68.72
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |