SYNJ2

synaptojanin 2, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 6:157981863-158099176

Links

ENSG00000078269

∙ NCBI:8871 ∙ OMIM:609410 ∙ HGNC:11504 ∙ Uniprot:O15056 ∙ 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 SYNJ2 gene.

not_specified (218 variants)
not_provided (10 variants)
Meniere_disease (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNJ2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003898.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				6 clinvar		6
missense			212 clinvar	10 clinvar	1 clinvar	223
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	212	16	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SYNJ2	protein_coding	protein_coding	ENST00000355585	27	117321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.50e-14	1.00	125527	0	221	125748	0.000879

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.715	824	884	0.932	0.0000540	9723
Missense in Polyphen		248	280.42	0.8844		2933
Synonymous	-0.110	377	374	1.01	0.0000265	3030
Loss of Function	3.55	32	62.2	0.515	0.00000299	729

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00169	0.00169
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000859	0.000853
Middle Eastern	0.000219	0.000217
South Asian	0.00213	0.00213
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

Function: FUNCTION: Inositol 5-phosphatase which may be involved in distinct membrane trafficking and signal transduction pathways. May mediate the inhibitory effect of Rac1 on endocytosis.;
Pathway: Inositol phosphate metabolism - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);D-myo-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-myo-inositol (1,4,5)-trisphosphate metabolism;Vesicle-mediated transport;endocytotic role of ndk phosphins and dynamin;Membrane Trafficking;Metabolism of lipids;1D-myo-inositol hexakisphosphate biosynthesis II (mammalian);Inositol phosphate metabolism;3-phosphoinositide degradation;D-myo-inositol (1,4,5)-trisphosphate degradation;Metabolism;superpathway of inositol phosphate compounds;Clathrin-mediated endocytosis;Synthesis of PIPs at the plasma membrane;PI Metabolism;Phospholipid metabolism (Consensus)

Intolerance Scores

loftool: 0.108
rvis_EVS: -1.9
rvis_percentile_EVS: 1.95

Haploinsufficiency Scores

pHI: 0.235
hipred: Y
hipred_score: 0.668
ghis: 0.517

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Synj2
Phenotype: growth/size/body region phenotype; hearing/vestibular/ear 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);

Gene ontology

Biological process: phosphatidylinositol biosynthetic process;brain development;phosphatidylinositol-3-phosphate biosynthetic process;inositol phosphate dephosphorylation;phosphatidylinositol dephosphorylation;membrane organization
Cellular component: cytosol;membrane raft;perinuclear region of cytoplasm;presynapse
Molecular function: RNA binding;phosphatidylinositol-3-phosphatase activity;phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity;protein binding;SH3 domain binding;PDZ domain binding;phosphatidylinositol phosphate 4-phosphatase activity;phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity;phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity