SYNGR2

synaptogyrin 2, the group of Synaptogyrins

Basic information

Region (hg38): 17:78168581-78173527

Links

ENSG00000108639NCBI:9144OMIM:603926HGNC:11499Uniprot:O43760AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
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)3451974
17-78168630-C-T not specified Uncertain significance (Feb 24, 2025)3803482
17-78168641-G-A not specified Uncertain significance (Mar 31, 2024)3323946
17-78168642-C-G not specified Uncertain significance (Apr 18, 2023)2514070
17-78168669-G-T not specified Uncertain significance (Sep 27, 2024)3451973
17-78168704-G-A not specified Uncertain significance (Mar 17, 2023)2549336
17-78168704-G-T not specified Uncertain significance (Oct 26, 2021)2222532
17-78170823-G-A not specified Uncertain significance (Dec 13, 2023)3172772
17-78170848-A-G not specified Uncertain significance (Jan 29, 2025)3803481
17-78170895-G-A not specified Uncertain significance (Jan 18, 2022)2310298
17-78170908-A-G not specified Uncertain significance (Feb 13, 2024)3172773
17-78170982-G-A not specified Uncertain significance (Feb 27, 2023)2489479
17-78170985-G-A not specified Uncertain significance (Aug 28, 2024)3451967
17-78170991-T-C not specified Uncertain significance (Sep 29, 2023)3172774
17-78171009-G-A not specified Uncertain significance (Jun 18, 2021)3172775
17-78171048-T-C not specified Uncertain significance (Feb 08, 2025)2455359
17-78171581-G-A not specified Uncertain significance (Apr 27, 2024)3323945
17-78171584-G-A not specified Uncertain significance (May 08, 2023)2545058
17-78171594-G-A not specified Uncertain significance (Feb 07, 2023)2482029
17-78171788-A-G not specified Uncertain significance (Sep 03, 2024)3451971
17-78171839-C-A not specified Uncertain significance (Aug 12, 2024)3451970
17-78171896-C-T not specified Uncertain significance (May 05, 2022)2406304
17-78171902-C-A not specified Uncertain significance (Nov 25, 2024)3451969
17-78171920-C-T not specified Uncertain significance (Nov 21, 2024)3451968

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SYNGR2protein_codingprotein_codingENST00000225777 44970
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00005190.4531257300171257470.0000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2961091180.9230.000007611440
Missense in Polyphen3242.1650.75892569
Synonymous-1.286654.01.220.00000431443
Loss of Function0.37478.150.8593.52e-799

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002070.000207
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004720.0000462
European (Non-Finnish)0.00005290.0000527
Middle Eastern0.000.00
South Asian0.00006570.0000653
Other0.0001880.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Syngr2
Phenotype

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