ABI3 ABI family member 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ABI3provided by HGNC
Official Full Name: ABI family member 3provided by HGNC
Primary source: HGNC:HGNC:29859
See related: Ensembl:ENSG00000108798 MIM:606363; AllianceGenome:HGNC:29859
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NESH; SSH3BP3
Summary: This gene encodes a member of an adaptor protein family. Members of this family encode proteins containing a homeobox homology domain, proline rich region and Src-homology 3 (SH3) domain, and are components of the Abi/WAVE complex which regulates actin polymerization. The encoded protein inhibits ectopic metastasis of tumor cells as well as cell migration. This may be accomplished through interaction with p21-activated kinase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
Expression: Broad expression in spleen (RPKM 23.3), lymph node (RPKM 10.1) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q21.32

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (49210707..49223225)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (50073790..50086309)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (47288069..47300587)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification and Quantitation of Novel ABI3 Isoforms Relative to Alzheimer's Disease Genetics and Neuropathology.
Title: Identification and Quantitation of Novel ABI3 Isoforms Relative to Alzheimer's Disease Genetics and Neuropathology.
ABI3 Is a Novel Early Biomarker of Alzheimer's Disease.
Title: ABI3 Is a Novel Early Biomarker of Alzheimer's Disease.
Association of ABI3 and PLCG2 missense variants with disease risk and neuropathology in Lewy body disease and progressive supranuclear palsy.
Title: Association of ABI3 and PLCG2 missense variants with disease risk and neuropathology in Lewy body disease and progressive supranuclear palsy.
Examination of the Effect of Rare Variants in TREM2, ABI3, and PLCG2 in LOAD Through Multiple Phenotypes.
Title: Examination of the Effect of Rare Variants in TREM2, ABI3, and PLCG2 in LOAD Through Multiple Phenotypes.
Common Variants in ABI3 Influence Cerebrospinal Fluid Total Tau Levels and Cognitive Decline in Progressive Mild Cognitive Impairment Patients.
Title: Common Variants in ABI3 Influence Cerebrospinal Fluid Total Tau Levels and Cognitive Decline in Progressive Mild Cognitive Impairment Patients.
Study shows that rare coding variants in TREM2, PLCG2, and ABI3 modulate susceptibility to Alzheimer disease in populations from Argentina, and they may have a European heritage.
Title: Transethnic meta-analysis of rare coding variants in PLCG2, ABI3, and TREM2 supports their general contribution to Alzheimer's disease.
suggest distinct effects of the microglial genes, ABI3 and PLCG2 in neurodegenerative diseases that harbor significant vs. low/no amyloid ss pathology
Title: ABI3 and PLCG2 missense variants as risk factors for neurodegenerative diseases in Caucasians and African Americans.
Low ABI3 expression is associated with thyroid carcinomas.
Title: Transcriptional regulation of the potential tumor suppressor ABI3 gene in thyroid carcinomas: interplay between methylation and NKX2-1 availability.
Data show that protein-altering changes are in PLCG2, ABI3, and TREM2 genes highly expressed in microglia and highlight an immune-related protein-protein interaction network in Alzheimer's disease.
Title: Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease.
Result links ABI3 to the pathogenesis and progression of some cancers and suggests that ABI3 or its pathway might have interest as therapeutic target.
Title: ABI3 ectopic expression reduces in vitro and in vivo cell growth properties while inducing senescence.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin filament binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling adaptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell projection morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in defense response to tumor cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in modification of postsynaptic actin cytoskeleton	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of lamellipodium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of protein localization to plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of ruffle assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in neuron migration	IBA Inferred from Biological aspect of Ancestor more info
NOT acts_upstream_of_or_within peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cellular senescence	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of dendritic spine morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of postsynaptic density assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of SCAR complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SCAR complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in actin-based cell projection	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info
located_in cytoplasm	NAS Non-traceable Author Statement more info	PubMed
located_in dendritic shaft	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	ISS Inferred from Sequence or Structural Similarity more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in lamellipodium	IBA Inferred from Biological aspect of Ancestor more info
located_in lamellipodium	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
located_in postsynaptic density	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: ABI gene family member 3

Names: new molecule including SH3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001135186.2 → NP_001128658.2 ABI gene family member 3 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 2).

Source sequence(s)

AC004797, AC069454

Consensus CDS

CCDS45725.1

Related

ENSP00000406651.2, ENST00000419580.6

Conserved Domains (2) summary

cd11826
Location:306 → 357

SH3_Abi; Src homology 3 domain of Abl Interactor proteins

pfam07815
Location:88 → 150

Abi_HHR; Abl-interactor HHR
NM_016428.3 → NP_057512.2 ABI gene family member 3 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC004797, AC069454

Consensus CDS

CCDS11546.1

UniProtKB/Swiss-Prot

C9IZN8, Q9H0P6, Q9P2A4

Related

ENSP00000225941.1, ENST00000225941.6

Conserved Domains (2) summary

cd11826
Location:312 → 363

SH3_Abi; Src homology 3 domain of Abl Interactor proteins

pfam07815
Location:93 → 164

Abi_HHR; Abl-interactor HHR

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

49210707..49223225

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005257429.3 → XP_005257486.1 ABI gene family member 3 isoform X1

Conserved Domains (2) summary

cd11826
Location:319 → 370

SH3_Abi; Src homology 3 domain of Abl Interactor proteins

pfam07815
Location:93 → 164

Abi_HHR; Abl-interactor HHR
XM_011524873.2 → XP_011523175.1 ABI gene family member 3 isoform X2

Conserved Domains (2) summary

cd11826
Location:318 → 369

SH3_Abi; Src homology 3 domain of Abl Interactor proteins

pfam07815
Location:93 → 164

Abi_HHR; Abl-interactor HHR
XM_017024721.2 → XP_016880210.1 ABI gene family member 3 isoform X3