SNAP47

synaptosome associated protein 47

Basic information

Region (hg38): 1:227728199-227781826

Previous symbols: [ "C1orf142" ]

Links

ENSG00000143740 ∙ NCBI:116841 ∙ OMIM:619659 ∙ HGNC:30669 ∙ Uniprot:Q5SQN1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNAP47 gene.

• Inborn genetic diseases (48 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNAP47 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			15	3		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			29	1	1	31
Total	0	0	44	4	1

Variants in SNAP47

This is a list of pathogenic ClinVar variants found in the SNAP47 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-227732428-C-A		not specified	Uncertain significance (Feb 13, 2024)
1-227732435-A-T		not specified	Uncertain significance (Oct 27, 2022)
1-227732463-C-T		not specified	Uncertain significance (Oct 25, 2022)
1-227732487-C-T		not specified	Uncertain significance (Mar 04, 2024)
1-227732495-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-227732499-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-227732514-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-227732516-T-C		not specified	Uncertain significance (Sep 14, 2023)
1-227732525-C-T		not specified	Uncertain significance (Nov 29, 2023)
1-227732625-G-A		not specified	Uncertain significance (Apr 12, 2022)
1-227732660-C-G		not specified	Uncertain significance (Mar 11, 2022)
1-227732903-G-T		not specified	Uncertain significance (Apr 22, 2022)
1-227732967-G-A		Inborn genetic diseases	Uncertain significance (Dec 07, 2021)
1-227733027-C-A		not specified	Uncertain significance (Mar 07, 2024)
1-227733508-C-T		not specified	Uncertain significance (Jan 29, 2024)
1-227733552-G-A			Benign (Feb 13, 2018)
1-227733561-G-T		not specified	Uncertain significance (Jan 23, 2023)
1-227733565-C-T		not specified	Uncertain significance (Oct 31, 2023)
1-227733920-G-T		not specified	Uncertain significance (Jan 19, 2022)
1-227733925-G-A		not specified	Uncertain significance (Apr 13, 2022)
1-227733926-C-A		not specified	Uncertain significance (Jan 23, 2024)
1-227733982-T-C		not specified	Uncertain significance (Dec 02, 2022)
1-227734024-G-A		not specified	Uncertain significance (Dec 18, 2023)
1-227734693-G-A		not specified	Uncertain significance (Jun 13, 2022)
1-227734718-C-T		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNAP47	protein_coding	protein_coding	ENST00000366759	5	52688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000207	0.908	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.130	274	268	1.02	0.0000149	3001
Missense in Polyphen		64	81.239	0.7878		1017
Synonymous	0.691	103	112	0.917	0.00000690	954
Loss of Function	1.58	10	17.1	0.586	8.77e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000424	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000598	0.000598
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in intracellular membrane fusion. {ECO:0000250}.

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.604
• rvis_EVS: 0.76
• rvis_percentile_EVS: 86.75

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.170
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.190

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Snap47
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: exocytosis;vesicle fusion;synaptic vesicle priming;synaptic vesicle fusion to presynaptic active zone membrane;long-term synaptic potentiation;exocytic insertion of neurotransmitter receptor to postsynaptic membrane
• Cellular component: plasma membrane;dendrite;synaptic vesicle membrane;BLOC-1 complex;SNARE complex;neuronal cell body;perinuclear region of cytoplasm;glutamatergic synapse
• Molecular function: SNAP receptor activity;protein binding;syntaxin binding