SYT14

synaptotagmin 14, the group of Synaptotagmins

Basic information

Region (hg38): 1:209900922-210171389

Links

ENSG00000143469 ∙ NCBI:255928 ∙ OMIM:610949 ∙ HGNC:23143 ∙ Uniprot:Q8NB59 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive spinocerebellar ataxia 11 (Supportive), mode of inheritance: AR
• autosomal recessive spinocerebellar ataxia 11 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia, autosomal recessive 11	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	Neurologic	21835308

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYT14 gene.

• not provided (60 variants)
• Inborn genetic diseases (15 variants)
• not specified (7 variants)
• Autosomal recessive spinocerebellar ataxia 11 (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYT14 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			2	11	4	17
missense			26	3		29
nonsense						0
start loss						0
frameshift						0
inframe indel			2			2
splice donor/acceptor (+/-2bp)		1				1
splice region					1	1
non coding			4	6	14	24
Total	0	1	34	20	18

Variants in SYT14

This is a list of pathogenic ClinVar variants found in the SYT14 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-209937897-A-T			Benign (Jun 22, 2021)
1-209938148-C-T			Benign (May 16, 2021)
1-209938201-C-T			Likely benign (Feb 21, 2022)
1-209938252-T-C			Uncertain significance (Mar 11, 2019)
1-209938260-G-A		not specified	Likely benign (Jan 04, 2022)
1-209938262-A-G			Likely benign (Apr 06, 2018)
1-209938272-T-C		SYT14-related disorder • not specified	Likely benign (Jul 12, 2023)
1-209938278-G-A			Likely pathogenic (Feb 23, 2016)
1-209938388-G-A			Benign (Apr 13, 2021)
1-209952535-T-C			Benign (May 17, 2021)
1-209952737-A-G			Uncertain significance (Dec 07, 2021)
1-209952919-CTTA-C			Benign (Jul 26, 2021)
1-209965724-G-A			Benign (Apr 13, 2021)
1-209965877-C-CTT		SYT14-related disorder	Likely benign (Jan 31, 2020)
1-209965898-G-T			Uncertain significance (Jan 06, 2020)
1-209965932-A-G			Uncertain significance (Jan 08, 2021)
1-209965957-G-A			Uncertain significance (Sep 16, 2020)
1-209966161-C-T			Benign (Jun 22, 2021)
1-210013689-C-A			Uncertain significance (Mar 31, 2021)
1-210013692-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-210013763-A-G			Likely benign (Sep 06, 2018)
1-210013766-CAGTACA-C			Uncertain significance (May 24, 2021)
1-210013773-A-G		not specified	Uncertain significance (Jun 28, 2023)
1-210020855-A-ATG			Benign (May 25, 2021)
1-210020857-A-G			Benign (May 25, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYT14	protein_coding	protein_coding	ENST00000422431	10	226099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.945	0.0554	125716	0	9	125725	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	249	316	0.789	0.0000152	4037
Missense in Polyphen		42	77.205	0.54401		984
Synonymous	1.23	100	117	0.855	0.00000590	1170
Loss of Function	4.08	4	26.8	0.149	0.00000121	379

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues. Is Ca(2+)-independent.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.294
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.148
• hipred: Y
• hipred_score: 0.748
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.659

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syt14

Gene ontology

• Cellular component: integral component of membrane