SYNJ2BP

protein-coding

synaptojanin 2 binding protein, the group of PDZ domain containing

Gene summary

Predicted to enable type II activin receptor binding activity. Involved in several processes, including negative regulation of endothelial cell migration; negative regulation of sprouting angiogenesis; and regulation of signal transduction. Located in mitochondrial outer membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018373.3

Inheritance

—

ClinVar variants

U:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr14:70,366,499-70,417,090

External References & Databases

Ensembl (ENSG00000213463)

Transcript & Mutation Effects

hg38 • Region Span ~50.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SYNJ2BP variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018373.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			4 clinvar			4
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	4	0	0	4

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018373.3	RefSeq	NP_060843.2	4	MANE Select
ENST00000256366.6	Ensembl	ENSP00000256366.4	4	MANE Select
ENST00000863002.1	Ensembl	ENSP00000533061.1	5	Standard
ENST00000863002.2	Ensembl	ENSP00000533061.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of endothelial cell proliferation
protein targeting
Rho protein signal transduction
chemical synaptic transmission
regulation of Notch signaling pathway

Molecular Function

protein binding
protein C-terminus binding
ionotropic glutamate receptor binding

Cellular Component

mitochondrion
ionotropic glutamate receptor complex
basolateral plasma membrane
cell junction
integral component of mitochondrial outer membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000256366
Coding exons: 4
Length: 45631
Individuals with no LoFs: 125600
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125608
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.745	65	84.2	0.772	0.00000465	939
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.00027	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.513

Gene Damage Prediction

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