GeneBe

SNAPIN

protein-coding

SNAP associated protein, the group of BLOC-1 related complex subunits|Biogenesis of lysosomal organelles complex 1 subunits

Gene summary

The protein encoded by this gene is a coiled-coil-forming protein that associates with the SNARE (soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor) complex of proteins and the BLOC-1 (biogenesis of lysosome-related organelles) complex. Biochemical studies have identified additional binding partners. As part of the SNARE complex, it is required for vesicle docking and fusion and regulates neurotransmitter release. The BLOC-1 complex is required for the biogenesis of specialized organelles such as melanosomes and platelet dense granules. Mutations in gene products that form the BLOC-1 complex have been identified in mouse strains that are models of Hermansky-Pudlak syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012]

Previous symbols:
  • SNAPAP

MANE transcript

NM_012437.6

Inheritance

—

ClinVar variants

P:5U:17

Top phenotype

Neurodevelopmental disorder with structural brain abnormalities and craniofacial abnormalities

gnomAD constraint

pLI —, LoF o/e 0.69

Max pathogenic AF

—

Genomic locus

chr1:153,658,703-153,661,852

External References & Databases

Ensembl (ENSG00000143553)NCBI Gene (23557)OMIM (607007)HGNC:17145GenCCUniProt (O95295)AlphaFoldClinVar (SNAPIN)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~3.1 kb
Loading mutation effect viewer...

GenCC 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 SNAPIN variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 14
Neurodevelopmental disorder with structural brain abnormalities and craniofacial abnormalitiesTotal: 6
See casesTotal: 5
Abnormal brain morphologyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012437.6. 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
0
missense
2
clinvar
15
clinvar
 17
nonsense
2
clinvar
1
clinvar
 3
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
 2
Total32170022

Highest pathogenic variant AF is 0.00010470166

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_012437.6RefSeqNP_036569.14MANE Select
ENST00000368685.6EnsemblENSP00000357674.54MANE Select
ENST00000911963.1EnsemblENSP00000582022.14Standard
ENST00000911964.1EnsemblENSP00000582023.14Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Golgi Associated Vesicle Biogenesis
  • Clathrin derived vesicle budding
  • trans-Golgi Network Vesicle Budding
  • Vesicle-mediated transport
  • Membrane Trafficking

Biological Process

  • intracellular protein transport
  • lysosomal lumen acidification
  • neurotransmitter secretion
  • anterograde axonal transport
  • retrograde axonal transport

Molecular Function

  • SNARE binding
  • protein binding

Cellular Component

  • Golgi membrane
  • lysosomal membrane
  • synaptic vesicle
  • cell junction
  • secretory granule

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000368685
Coding exons
4
Length
3177
Individuals with no LoFs
125724
Homozygous LoFs
0
Heterozygous LoFs
24
Defined
125748
p
0.0000954
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.8785981.30.7260.00000443850
Missense (PolyPhen)1023.2070.43091249
Synonymous-0.6913933.91.150.00000167304
Loss of Function0.76757.220.6924.64e-764

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000140.00012rare
Latino/Admixed American00.0absent
Ashkenazi Jewish0.000690.00069rare
East Asian0.0000540.000054rare
Finnish0.0000920.000092rare
European (Non-Finnish)0.0000530.000053rare
South Asian0.000160.00016rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Component of the BLOC-1 complex, a complex that is required for normal biogenesis of lysosome-related organelles (LRO), such as platelet dense granules and melanosomes. In concert with the AP-3 complex, the BLOC-1 complex is required to target membrane protein cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals. The BLOC-1 complex, in association with SNARE proteins, is also proposed to be involved in neurite extension. Plays a role in intracellular vesicle trafficking and synaptic vesicle recycling. May modulate a step between vesicle priming, fusion and calcium-dependent neurotransmitter release through its ability to potentiate the interaction of synaptotagmin with the SNAREs and the plasma- membrane-associated protein SNAP25. Its phosphorylation state influences exocytotic protein interactions and may regulate synaptic vesicle exocytosis. May also have a role in the mechanisms of SNARE-mediated membrane fusion in non-neuronal cells (PubMed:17182842, PubMed:18167355). As part of the BORC complex may play a role in lysosomes movement and localization at the cell periphery. Associated with the cytosolic face of lysosomes, the BORC complex may recruit ARL8B and couple lysosomes to microtubule plus-end-directed kinesin motor (PubMed:25898167). {ECO:0000269|PubMed:17182842, ECO:0000269|PubMed:18167355, ECO:0000269|PubMed:25898167}.;

Recessive Scores

pRec
0.155

Intolerance Scores

LoFtool
0.672
RVIS EVS
0.01
RVIS percentile EVS
54.63

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.860

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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