SNAP29

synaptosome associated protein 29, the group of SNAREs

Basic information

Region (hg38): 22:20859006-20891214

Links

ENSG00000099940 ∙ NCBI:9342 ∙ OMIM:604202 ∙ HGNC:11133 ∙ Uniprot:O95721 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• CEDNIK syndrome (Strong), mode of inheritance: AR
• CEDNIK syndrome (Strong), mode of inheritance: AR
• CEDNIK syndrome (Strong), mode of inheritance: AR
• CEDNIK syndrome (Supportive), mode of inheritance: AR
• CEDNIK syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome (CEDNIK syndrome)	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic; Neurologic	15968592

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNAP29 gene.

• CEDNIK syndrome (149 variants)
• not provided (114 variants)
• Inborn genetic diseases (18 variants)
• not specified (10 variants)
• Hypomyelinating leukodystrophy 2 (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNAP29 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			1	22	2	25
missense		1	52	4		57
nonsense	5	1	2			8
start loss	1					1
frameshift	3	1				4
inframe indel						0
splice donor/acceptor (+/-2bp)		2				2
splice region			5	5		10
non coding			85	25	31	141
Total	9	5	140	51	33

Highest pathogenic variant AF is 0.0000131

Variants in SNAP29

This is a list of pathogenic ClinVar variants found in the SNAP29 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-20859018-G-T		CEDNIK syndrome	Uncertain significance (Jan 13, 2018)
22-20859035-G-A		CEDNIK syndrome	Uncertain significance (Jan 13, 2018)
22-20859039-GGC-G		CEDNIK syndrome	Uncertain significance (Jun 14, 2016)
22-20859043-A-T		CEDNIK syndrome	Benign (Jan 13, 2018)
22-20859051-G-A		CEDNIK syndrome	Uncertain significance (Jan 13, 2018)
22-20859053-C-A		CEDNIK syndrome	Uncertain significance (Jan 13, 2018)
22-20859057-G-T			Likely benign (Feb 04, 2019)
22-20859071-T-G		CEDNIK syndrome	Uncertain significance (Jan 12, 2018)
22-20859079-C-G		CEDNIK syndrome	Benign/Likely benign (Jul 08, 2018)
22-20859092-C-T		CEDNIK syndrome • not specified	Benign (Jul 15, 2021)
22-20859103-C-G		CEDNIK syndrome • not specified	Benign/Likely benign (Aug 07, 2018)
22-20859106-G-A		CEDNIK syndrome • not specified	Benign/Likely benign (Mar 09, 2022)
22-20859108-A-G		SNAP29-related disorder	Likely benign (Feb 22, 2021)
22-20859112-T-C		Hypomyelinating leukodystrophy 2 • CEDNIK syndrome	Pathogenic (Apr 11, 2016)
22-20859116-A-G		CEDNIK syndrome	Conflicting classifications of pathogenicity (May 09, 2023)
22-20859121-A-G		Inborn genetic diseases	Uncertain significance (Aug 26, 2022)
22-20859122-C-T			Likely benign (Mar 08, 2023)
22-20859124-C-G		Inborn genetic diseases	Uncertain significance (Aug 22, 2023)
22-20859125-T-G			Likely benign (Apr 05, 2021)
22-20859126-A-G			Uncertain significance (Mar 23, 2020)
22-20859128-A-G		CEDNIK syndrome • not specified	Benign (Feb 01, 2024)
22-20859130-G-A			Uncertain significance (Jul 15, 2022)
22-20859132-T-C			Uncertain significance (Jul 22, 2019)
22-20859136-A-G		Inborn genetic diseases	Uncertain significance (May 27, 2022)
22-20859146-C-T			Likely benign (Sep 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNAP29	protein_coding	protein_coding	ENST00000215730	5	32236

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0136	0.958	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.872	178	148	1.20	0.00000780	1692
Missense in Polyphen		54	44.887	1.203		592
Synonymous	1.52	41	55.4	0.739	0.00000282	489
Loss of Function	1.91	5	12.2	0.409	6.81e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000231
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000284	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.000296	0.000294
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: SNAREs, soluble N-ethylmaleimide-sensitive factor- attachment protein receptors, are essential proteins for fusion of cellular membranes. SNAREs localized on opposing membranes assemble to form a trans-SNARE complex, an extended, parallel four alpha-helical bundle that drives membrane fusion. SNAP29 is a SNARE involved in autophagy through the direct control of autophagosome membrane fusion with the lysososome membrane. Plays also a role in ciliogenesis by regulating membrane fusions. {ECO:0000269|PubMed:23217709, ECO:0000269|PubMed:25686250, ECO:0000269|PubMed:25686604}.
• Pathway: Autophagy - animal - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Neutrophil degranulation;Vesicle-mediated transport;Membrane Trafficking;Innate Immune System;Immune System;Intra-Golgi traffic;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.247
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.0363
• hipred: Y
• hipred_score: 0.582
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snap29
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: snap29
• Affected structure: keratinocyte
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: exocytosis;vesicle targeting;vesicle fusion;protein transport;synaptic vesicle priming;autophagosome membrane docking;synaptic vesicle fusion to presynaptic active zone membrane;neutrophil degranulation;cilium assembly;membrane fusion;autophagosome maturation
• Cellular component: Golgi membrane;autophagosome membrane;nucleoplasm;cytoplasm;autophagosome;centrosome;cytosol;plasma membrane;ciliary pocket membrane;SNARE complex;azurophil granule membrane;presynapse
• Molecular function: SNAP receptor activity;protein binding;syntaxin binding