SYNJ2BP-COX16

SYNJ2BP-COX16 readthrough

Basic information

Region (hg38): 14:70326063-70417074

Links

ENSG00000258644 ∙ NCBI:100529257 ∙ ∙ HGNC:48350 ∙ ∙ ∙ 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 SYNJ2BP-COX16 gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)
• Mitochondrial complex IV deficiency, nuclear type 22 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNJ2BP-COX16 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			3			3
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			3			3
Total	1	0	7	0	0

Highest pathogenic variant AF is 0.0000329

Variants in SYNJ2BP-COX16

This is a list of pathogenic ClinVar variants found in the SYNJ2BP-COX16 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-70326403-G-A		not specified	Uncertain significance (Apr 12, 2022)
14-70326410-G-A		Mitochondrial complex IV deficiency, nuclear type 22	Pathogenic (Jun 04, 2022)
14-70326416-T-C		not specified	Uncertain significance (May 23, 2023)
14-70326444-G-A			Likely benign (Apr 01, 2024)
14-70326444-G-C		not specified	Uncertain significance (Jun 24, 2022)
14-70326449-T-C		not specified	Uncertain significance (Dec 05, 2022)
14-70329183-C-T		not specified	Likely benign (Jan 03, 2024)
14-70329184-G-A		not specified	Uncertain significance (Aug 16, 2021)
14-70329194-A-G		not specified	Uncertain significance (Aug 01, 2023)
14-70329212-G-T		not specified	Uncertain significance (Oct 27, 2021)
14-70342698-C-T		not specified	Uncertain significance (Apr 04, 2023)
14-70359530-C-T		not specified	Uncertain significance (Jun 06, 2023)
14-70359539-C-T		not specified	Uncertain significance (Jan 24, 2024)
14-70359547-T-G		not specified	Uncertain significance (Dec 03, 2021)
14-70373005-G-A		not specified	Uncertain significance (Dec 27, 2022)
14-70373031-A-G		not specified	Uncertain significance (Aug 21, 2023)
14-70375717-G-A		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Gene ontology

• Biological process: chemical synaptic transmission;receptor clustering;establishment or maintenance of epithelial cell apical/basal polarity;receptor localization to synapse;cell-cell adhesion
• Cellular component: ionotropic glutamate receptor complex;basolateral plasma membrane;cell junction;neuromuscular junction;mitochondrial membrane;neuron projection;postsynaptic density membrane
• Molecular function: ionotropic glutamate receptor binding