SYNGR1

synaptogyrin 1, the group of Synaptogyrins

Basic information

Region (hg38): 22:39349924-39385575

Links

ENSG00000100321 ∙ NCBI:9145 ∙ OMIM:603925 ∙ HGNC:11498 ∙ Uniprot:O43759 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
• bipolar disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYNGR1 gene.

• Inborn genetic diseases (15 variants)
• not provided (1 variants)
• Schizophrenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNGR1 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		1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	1

Variants in SYNGR1

This is a list of pathogenic ClinVar variants found in the SYNGR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39350017-G-C		not specified	Uncertain significance (May 27, 2022)
22-39350070-G-A			Likely benign (Sep 01, 2022)
22-39374323-C-T		not specified	Uncertain significance (May 05, 2023)
22-39374335-T-C		not specified	Uncertain significance (Mar 21, 2023)
22-39374345-C-G		not specified	Uncertain significance (Aug 12, 2021)
22-39374349-A-G		not specified	Uncertain significance (Jan 30, 2024)
22-39374410-C-G		not specified	Uncertain significance (May 27, 2022)
22-39374430-G-A		not specified	Uncertain significance (May 25, 2023)
22-39374436-G-A		not specified	Uncertain significance (Dec 21, 2022)
22-39374448-G-A		not specified	Uncertain significance (Jul 14, 2023)
22-39374517-C-T		not specified	Uncertain significance (Jan 30, 2024)
22-39374547-G-T		not specified	Uncertain significance (Jun 06, 2023)
22-39376138-G-A		not specified	Uncertain significance (Nov 17, 2022)
22-39376147-G-T		not specified	Uncertain significance (May 13, 2022)
22-39376150-G-A		not specified	Uncertain significance (Aug 16, 2022)
22-39377595-C-T		Malignant tumor of prostate	Uncertain significance (-)
22-39381773-C-A		not specified	Uncertain significance (Nov 09, 2023)
22-39381779-C-G		not specified	Uncertain significance (Nov 29, 2023)
22-39381783-G-C		not specified	Uncertain significance (Dec 06, 2021)
22-39381817-C-CCAA		Schizophrenia	Benign (-)
22-39381829-A-T		not specified	Uncertain significance (Oct 03, 2023)
22-39381844-G-C		not specified	Uncertain significance (Mar 16, 2023)
22-39381876-G-A		not specified	Uncertain significance (Feb 28, 2024)
22-39381889-A-G		not specified	Uncertain significance (May 03, 2023)
22-39381901-C-T		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNGR1	protein_coding	protein_coding	ENST00000328933	4	35664

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.451	0.543	125744	0	2	125746	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.419	137	152	0.904	0.0000107	1503
Missense in Polyphen		58	64.124	0.9045		646
Synonymous	-0.0603	72	71.4	1.01	0.00000620	460
Loss of Function	2.32	2	9.87	0.203	4.32e-7	103

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	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in regulated exocytosis. Modulates the localization of synaptophysin/SYP into synaptic-like microvesicles and may therefore play a role in synaptic-like microvesicle formation and/or maturation (By similarity). Involved in the regulation of short-term and long-term synaptic plasticity (By similarity). {ECO:0000250|UniProtKB:O55100, ECO:0000250|UniProtKB:Q62876}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.130
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.392
• hipred: N
• hipred_score: 0.285
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0833

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syngr1
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein targeting;neutrophil degranulation;regulated exocytosis;regulation of long-term neuronal synaptic plasticity;regulation of short-term neuronal synaptic plasticity;synaptic vesicle membrane organization;cellular response to leukemia inhibitory factor
• Cellular component: plasma membrane;cell junction;integral component of synaptic vesicle membrane;synaptic vesicle membrane;neuromuscular junction;azurophil granule membrane;melanosome
• Molecular function: protein binding