ABI3BP

protein-coding

ABI family member 3 binding protein, the group of Fibronectin type III domain containing

Gene summary

Predicted to enable actin filament binding activity; collagen binding activity; and heparin binding activity. Predicted to be involved in actin cytoskeleton organization; regulation of dendritic spine morphogenesis; and regulation of postsynaptic density assembly. Predicted to act upstream of or within extracellular matrix organization and positive regulation of cell-substrate adhesion. Located in extracellular matrix and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001375547.2

Inheritance

—

ClinVar variants

U:166B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr3:100,749,156-100,993,515

External References & Databases

Ensembl (ENSG00000154175)

Transcript & Mutation Effects

hg38 • Region Span ~244.4 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 ABI3BP variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 150

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001375547.2. 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			6 clinvar	1 clinvar		7
missense			154 clinvar	6 clinvar		160
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	166	7	0	173

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 197 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001375547.2	RefSeq	NP_001362476.1	68	MANE Select
ENST00000471714.6	Ensembl	ENSP00000420524.2	68	MANE Select
NM_001349329.2	RefSeq	NP_001336258.2	65	Standard
NM_001349330.2	RefSeq	NP_001336259.2	62	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of cell-substrate adhesion
extracellular matrix organization

Molecular Function

extracellular matrix structural constituent
collagen binding
heparin binding

Cellular Component

extracellular region
interstitial matrix
extracellular space
collagen-containing extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000284322
Coding exons: 35
Length: 244360
Individuals with no LoFs: 124523
Homozygous LoFs: 1
Heterozygous LoFs: 114
Defined: 124638
p: 0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.829	489	543	0.900	0.0000276	6826
Missense (PolyPhen)		128	155.71	0.82202		1863
Synonymous	1.32	161	184	0.876	0.00000900	2096
Loss of Function	4.40	25	62.6	0.400	0.00000332	783

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.0037	0.0037	notable
East Asian	0.00041	0.00039	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00050	0.00045	rare
South Asian	0.00036	0.00033	rare
Other	0.00087	0.00083	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.100

Intolerance Scores

LoFtool: 0.868
RVIS EVS: 0.45
RVIS percentile EVS: 78.05

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.571

Gene Damage Prediction

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