SYNJ2BP

synaptojanin 2 binding protein, the group of PDZ domain containing

Basic information

Region (hg38): 14:70366499-70417090

Links

ENSG00000213463 ∙ NCBI:55333 ∙ OMIM:609411 ∙ HGNC:18955 ∙ Uniprot:P57105 ∙ 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 SYNJ2BP gene.

Variants pathogenicity by type

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

Variants in SYNJ2BP

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

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

Position	Type	Phenotype	Significance	ClinVar
14-70373005-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

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNJ2BP	protein_coding	protein_coding	ENST00000256366	4	45631

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.512	0.472	125600	0	8	125608	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.745	65	84.2	0.772	0.00000465	939
Missense in Polyphen		21	30.854	0.68062		333
Synonymous	0.674	26	30.8	0.845	0.00000170	286
Loss of Function	1.93	1	6.18	0.162	3.28e-7	68

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)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000273	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. {ECO:0000250|UniProtKB:Q9D6K5}.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.386
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.45

Haploinsufficiency Scores

• pHI: 0.127
• hipred: Y
• hipred_score: 0.582
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.513

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Synj2bp

Gene ontology

• Biological process: negative regulation of endothelial cell proliferation;protein targeting;Rho protein signal transduction;chemical synaptic transmission;regulation of Notch signaling pathway;negative regulation of endothelial cell migration;negative regulation of angiogenesis;regulation of endocytosis;receptor clustering;establishment or maintenance of epithelial cell apical/basal polarity;intracellular distribution of mitochondria;negative regulation of ERK1 and ERK2 cascade;receptor localization to synapse;cell-cell adhesion;negative regulation of sprouting angiogenesis
• Cellular component: mitochondrion;ionotropic glutamate receptor complex;basolateral plasma membrane;cell junction;integral component of mitochondrial outer membrane;neuromuscular junction;neuron projection;postsynaptic density membrane
• Molecular function: protein binding;protein C-terminus binding;ionotropic glutamate receptor binding