SYNGR2

synaptogyrin 2, the group of Synaptogyrins

Basic information

Region (hg38): 17:78168581-78173527

Links

ENSG00000108639 ∙ NCBI:9144 ∙ OMIM:603926 ∙ HGNC:11499 ∙ Uniprot:O43760 ∙ 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 SYNGR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNGR2 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in SYNGR2

This is a list of pathogenic ClinVar variants found in the SYNGR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-78168629-G-C		not specified	Uncertain significance (Oct 04, 2024)
17-78168630-C-T		not specified	Uncertain significance (Feb 24, 2025)
17-78168641-G-A		not specified	Uncertain significance (Mar 31, 2024)
17-78168642-C-G		not specified	Uncertain significance (Apr 18, 2023)
17-78168669-G-T		not specified	Uncertain significance (Sep 27, 2024)
17-78168704-G-A		not specified	Uncertain significance (Mar 17, 2023)
17-78168704-G-T		not specified	Uncertain significance (Oct 26, 2021)
17-78170823-G-A		not specified	Uncertain significance (Dec 13, 2023)
17-78170848-A-G		not specified	Uncertain significance (Jan 29, 2025)
17-78170895-G-A		not specified	Uncertain significance (Jan 18, 2022)
17-78170908-A-G		not specified	Uncertain significance (Feb 13, 2024)
17-78170982-G-A		not specified	Uncertain significance (Feb 27, 2023)
17-78170985-G-A		not specified	Uncertain significance (Aug 28, 2024)
17-78170991-T-C		not specified	Uncertain significance (Sep 29, 2023)
17-78171009-G-A		not specified	Uncertain significance (Jun 18, 2021)
17-78171048-T-C		not specified	Uncertain significance (Feb 08, 2025)
17-78171581-G-A		not specified	Uncertain significance (Apr 27, 2024)
17-78171584-G-A		not specified	Uncertain significance (May 08, 2023)
17-78171594-G-A		not specified	Uncertain significance (Feb 07, 2023)
17-78171788-A-G		not specified	Uncertain significance (Sep 03, 2024)
17-78171839-C-A		not specified	Uncertain significance (Aug 12, 2024)
17-78171896-C-T		not specified	Uncertain significance (May 05, 2022)
17-78171902-C-A		not specified	Uncertain significance (Nov 25, 2024)
17-78171920-C-T		not specified	Uncertain significance (Nov 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNGR2	protein_coding	protein_coding	ENST00000225777	4	4970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000519	0.453	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.296	109	118	0.923	0.00000761	1440
Missense in Polyphen		32	42.165	0.75892		569
Synonymous	-1.28	66	54.0	1.22	0.00000431	443
Loss of Function	0.374	7	8.15	0.859	3.52e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000657	0.0000653
Other	0.000188	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in regulated exocytosis. In neuronal cells, modulates the localization of synaptophysin/SYP into synaptic-like microvesicles and may therefore play a role in the formation and/or the maturation of this vesicles. May also play a role in GLUT4 storage and transport to the plasma membrane. {ECO:0000250|UniProtKB:O54980}.

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.596
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.197
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syngr2

Gene ontology

• Biological process: regulated exocytosis;synaptic vesicle membrane organization
• Cellular component: lipid droplet;integral component of membrane;cell junction;synaptic vesicle membrane;neuromuscular junction;extracellular exosome
• Molecular function: protein binding