SYNGR4

synaptogyrin 4, the group of Synaptogyrins

Basic information

Region (hg38): 19:48364367-48376377

Links

ENSG00000105467 ∙ NCBI:23546 ∙ OMIM:608373 ∙ HGNC:11502 ∙ Uniprot:O95473 ∙ 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 SYNGR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNGR4 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			23	3		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	3	0

Variants in SYNGR4

This is a list of pathogenic ClinVar variants found in the SYNGR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48365882-G-A		not specified	Uncertain significance (Aug 03, 2022)
19-48365930-G-A		not specified	Uncertain significance (Aug 02, 2022)
19-48373553-G-A		not specified	Uncertain significance (Jul 02, 2024)
19-48373595-A-G		not specified	Likely benign (Jul 02, 2024)
19-48373603-C-A		not specified	Uncertain significance (Feb 10, 2022)
19-48373607-A-G		not specified	Uncertain significance (Jan 24, 2024)
19-48373641-G-T		not specified	Uncertain significance (May 31, 2023)
19-48373647-T-C		not specified	Uncertain significance (Mar 30, 2024)
19-48373670-T-C		not specified	Uncertain significance (Nov 29, 2023)
19-48373676-G-A		not specified	Uncertain significance (May 24, 2024)
19-48373693-G-T		not specified	Uncertain significance (Jun 29, 2023)
19-48373700-A-G		not specified	Uncertain significance (Dec 07, 2024)
19-48373710-C-T		not specified	Uncertain significance (Jan 03, 2024)
19-48375624-G-A		not specified	Uncertain significance (Jul 25, 2024)
19-48375676-C-T			Likely benign (Feb 01, 2023)
19-48375697-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-48375706-G-A		not specified	Uncertain significance (Jan 01, 2025)
19-48375738-T-C		not specified	Uncertain significance (Jun 29, 2022)
19-48375744-C-T		not specified	Uncertain significance (Oct 03, 2022)
19-48376110-A-G		not specified	Uncertain significance (Jul 10, 2024)
19-48376143-A-C		not specified	Uncertain significance (Jul 12, 2023)
19-48376157-G-A		not specified	Uncertain significance (Feb 26, 2024)
19-48376163-G-A		not specified	Uncertain significance (May 02, 2024)
19-48376187-T-G		not specified	Uncertain significance (Jun 12, 2023)
19-48376227-G-A		not specified	Uncertain significance (Mar 07, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNGR4	protein_coding	protein_coding	ENST00000344846	4	11982

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.11e-9	0.0269	125689	0	58	125747	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.100	143	140	1.02	0.00000815	1536
Missense in Polyphen		36	37.241	0.96668		458
Synonymous	0.146	61	62.5	0.977	0.00000416	479
Loss of Function	-0.929	12	8.99	1.33	4.73e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000565	0.000564
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000321	0.000299
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.828
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.36

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.408

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Syngr4
• Phenotype: normal phenotype

Gene ontology

• Cellular component: integral component of membrane;synaptic vesicle membrane;neuromuscular junction