BIN3

protein-coding

bridging integrator 3, the group of N-BAR domain containing

Gene summary

The product of this gene is a member of the BAR domain protein family. The encoded protein is comprised solely of a BAR domain which is predicted to form coiled-coil structures and proposed to mediate dimerization, sense and induce membrane curvature, and bind small GTPases. BAR domain proteins have been implicated in endocytosis, intracellular transport, and a diverse set of other processes. [provided by RefSeq, Jul 2008]

MANE transcript

NM_018688.6

Inheritance

—

ClinVar variants

U:74B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.08

Max pathogenic AF

—

Genomic locus

chr8:22,620,418-22,669,148

External References & Databases

Ensembl (ENSG00000147439)

Transcript & Mutation Effects

hg38 • Region Span ~48.7 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 BIN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018688.6. 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				1 clinvar		1
missense			71 clinvar	1 clinvar		72
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	74	2	0	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018688.6	RefSeq	NP_061158.1	9	MANE Select
ENST00000276416.11	Ensembl	ENSP00000276416.6	9	MANE Select
NM_001363046.2	RefSeq	NP_001349975.1	6	Standard
ENST00000399977.8	Ensembl	ENSP00000382859.4	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

division septum assembly
endocytosis
actin filament organization
protein localization
unidimensional cell growth

Molecular Function

protein binding
cytoskeletal protein binding
cytoskeletal adaptor activity
lipid binding

Cellular Component

cytoplasm
actin filament
actin cortical patch

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000276416
Coding exons: 9
Length: 48731
Individuals with no LoFs: 124611
Homozygous LoFs: 1
Heterozygous LoFs: 31
Defined: 124643
p: 0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.298	166	156	1.07	0.00000974	1665
Missense (PolyPhen)		37	34.407	1.0754		426
Synonymous	-2.78	90	62.1	1.45	0.00000403	448
Loss of Function	-0.313	18	16.6	1.08	8.84e-7	188

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000089	0.000088	rare
South Asian	0.00030	0.00026	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in cytokinesis and septation where it has a role in the localization of F-actin.;

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.553
RVIS EVS: -0.45
RVIS percentile EVS: 24.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.675

Gene Damage Prediction

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