SYNJ2

synaptojanin 2, the group of Phosphoinositide phosphatases

Basic information

Region (hg38): 6:157981862-158099176

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.

• Inborn genetic diseases (73 variants)
• not provided (10 variants)
• not specified (1 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.

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				6		6
missense			71	3	1	75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	71	9	2

Variants in SYNJ2

This is a list of pathogenic ClinVar variants found in the SYNJ2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-157981971-A-G		not specified	Uncertain significance (Apr 29, 2022)
6-157982083-C-T		not specified	Uncertain significance (Dec 28, 2022)
6-158017257-T-A		not specified	Uncertain significance (Jul 20, 2022)
6-158017263-T-A		not specified	Uncertain significance (Jan 29, 2024)
6-158028809-A-G		not specified	Uncertain significance (Jun 18, 2021)
6-158028975-G-A		not specified	Uncertain significance (Oct 05, 2023)
6-158033471-G-T		not specified	Uncertain significance (Dec 12, 2023)
6-158033499-G-C		not specified	Uncertain significance (Jun 28, 2022)
6-158033501-T-C		not specified	Uncertain significance (Mar 07, 2023)
6-158033504-G-A		not specified	Uncertain significance (May 17, 2023)
6-158033592-G-A		not specified	Uncertain significance (Dec 17, 2023)
6-158033607-G-A		not specified	Uncertain significance (Aug 22, 2023)
6-158043367-G-A		not specified	Uncertain significance (Jul 09, 2021)
6-158059282-T-C		not specified	Uncertain significance (Apr 13, 2022)
6-158059290-G-T		not specified	Uncertain significance (Mar 02, 2023)
6-158059294-G-A		not specified	Uncertain significance (Nov 30, 2021)
6-158059304-A-G		not specified	Uncertain significance (Feb 16, 2023)
6-158059324-G-A		not specified	Uncertain significance (Mar 01, 2023)
6-158059348-T-G		not specified	Uncertain significance (May 05, 2023)
6-158062016-G-A		not specified	Uncertain significance (Jan 31, 2024)
6-158062031-A-G		not specified	Uncertain significance (Sep 16, 2021)
6-158062127-T-G		not specified	Uncertain significance (Feb 14, 2024)
6-158062145-G-T		not specified	Uncertain significance (Jul 20, 2021)
6-158062163-C-T		not specified	Uncertain significance (May 24, 2023)
6-158062174-G-A			Benign (Nov 15, 2017)

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-<i>myo</i>-inositol (1,3,4)-trisphosphate biosynthesis;superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism;Vesicle-mediated transport;endocytotic role of ndk phosphins and dynamin;Membrane Trafficking;Metabolism of lipids;1D-<i>myo</i>-inositol hexakisphosphate biosynthesis II (mammalian);Inositol phosphate metabolism;3-phosphoinositide degradation;D-<i>myo</i>-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