SPAAR
protein-codingsmall regulatory polypeptide of amino acid response
Gene summary
Involved in cellular response to amino acid stimulus and negative regulation of TORC1 signaling. Located in late endosome membrane and lysosomal proton-transporting V-type ATPase complex. [provided by Alliance of Genome Resources, Jul 2025]
- LINC00961
MANE transcript
Inheritance
ClinVar variants
Top phenotype
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.7 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 SPAAR variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001348107.3. 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 1 | 0 | 0 | 1 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001335036.2 | 1 | MANE Select | |
| Ensembl | ENSP00000490187.1 | 1 | MANE Select | |
| Ensembl | ENSP00000490606.1 | 1 | Standard | |
| Ensembl | ENSP00000489755.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of skeletal muscle tissue regeneration
- cellular response to amino acid stimulus
- negative regulation of TORC1 signaling
Cellular Component
- late endosome membrane
- lysosomal proton-transporting V-type ATPase complex
- integral component of lysosomal membrane
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Isoform 2: Negative regulator of amino acid sensing and mTORC1, a signaling complex promoting cell growth in response to growth factors, energy levels and amino acids (PubMed:28024296). Negatively regulates mTORC1 activation by inhibiting recruitment of mTORC1 to lysosomes upon stimulation with amino acids: acts by promoting the formation of a tightly bound supercomplex composed of the lysosomal V-ATPase, Ragulator and Rag GTPases, preventing recruitment of mTORC1 (PubMed:28024296). Acts as a regulator of muscle regeneration following injury by regulating mTORC1 activation (By similarity). {ECO:0000250|UniProtKB:A0A1B0GSZ0, ECO:0000269|PubMed:28024296}.;