SYNGR3

synaptogyrin 3, the group of Synaptogyrins

Basic information

Region (hg38): 16:1989660-1994275

Links

ENSG00000127561 ∙ NCBI:9143 ∙ OMIM:603927 ∙ HGNC:11501 ∙ Uniprot:O43761 ∙ 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 SYNGR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNGR3 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	1		23
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	1	0

Variants in SYNGR3

This is a list of pathogenic ClinVar variants found in the SYNGR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1990120-C-A		not specified	Uncertain significance (Jun 22, 2021)
16-1990158-G-A		not specified	Uncertain significance (Jun 06, 2023)
16-1990166-C-T		not specified	Uncertain significance (Nov 08, 2022)
16-1991975-T-C		not specified	Uncertain significance (Mar 01, 2024)
16-1991999-C-T		not specified	Uncertain significance (Dec 30, 2023)
16-1992004-G-C		not specified	Uncertain significance (Oct 27, 2023)
16-1992038-C-G		not specified	Uncertain significance (Dec 07, 2023)
16-1992040-G-A		not specified	Uncertain significance (May 03, 2023)
16-1992092-C-T		not specified	Likely benign (Mar 11, 2022)
16-1992121-G-T		not specified	Uncertain significance (Oct 13, 2023)
16-1992124-G-A		not specified	Uncertain significance (Jan 21, 2025)
16-1992134-T-C		not specified	Uncertain significance (Jan 19, 2025)
16-1992146-G-T		not specified	Uncertain significance (Jan 23, 2023)
16-1992154-C-A		not specified	Uncertain significance (May 03, 2023)
16-1992156-A-T		not specified	Uncertain significance (Dec 03, 2024)
16-1992740-G-A		not specified	Uncertain significance (Aug 17, 2021)
16-1992743-G-A		not specified	Uncertain significance (Jun 17, 2024)
16-1992765-C-T		not specified	Uncertain significance (Nov 25, 2024)
16-1992881-G-A		not specified	Uncertain significance (May 05, 2023)
16-1992909-A-T		not specified	Uncertain significance (Jan 28, 2025)
16-1992952-C-G		not specified	Uncertain significance (Sep 22, 2023)
16-1992965-G-T		not specified	Uncertain significance (Oct 29, 2024)
16-1992983-G-A		not specified	Uncertain significance (Feb 23, 2023)
16-1992989-G-A		not specified	Uncertain significance (Oct 03, 2024)
16-1993034-G-C		not specified	Uncertain significance (Feb 27, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNGR3	protein_coding	protein_coding	ENST00000248121	4	4616

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.529	0.456	118495	0	3	118498	0.0000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	84	116	0.726	0.00000677	1425
Missense in Polyphen		22	38.951	0.56481		532
Synonymous	0.0532	57	57.5	0.991	0.00000395	488
Loss of Function	1.97	1	6.36	0.157	2.74e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000516	0.0000475
European (Non-Finnish)	0.0000212	0.0000194
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in regulated exocytosis. May indirectly regulate the activity of the plasma membrane dopamine transporter SLC6A3 and thereby regulate dopamine transport back from the synaptic cleft into the presynaptic terminal. {ECO:0000250|UniProtKB:Q8R191}.

Haploinsufficiency Scores

• pHI: 0.489
• hipred: N
• hipred_score: 0.459
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.181

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syngr3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: substantia nigra development;positive regulation of transporter activity;regulated exocytosis
• Cellular component: synaptic vesicle;integral component of membrane;cell junction;synaptic vesicle membrane;neuromuscular junction
• Molecular function: SH2 domain binding;protein N-terminus binding