ABI3

protein-coding

ABI family member 3

Gene 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]

MANE transcript

NM_016428.3

Inheritance

—

ClinVar variants

U:67B:6

Top phenotype

Early-onset dementia of unclear type

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr17:49,210,411-49,223,225

External References & Databases

Ensembl (ENSG00000108798)

Transcript & Mutation Effects

hg38 • Region Span ~12.8 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 ABI3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 4

Early-onset dementia of unclear typeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016428.3. 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			3 clinvar	1 clinvar	2 clinvar	6
missense			64 clinvar	3 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	4	2	73

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016428.3	RefSeq	NP_057512.2	8	MANE Select
ENST00000225941.6	Ensembl	ENSP00000225941.1	8	MANE Select
NM_001135186.2	RefSeq	NP_001128658.2	8	Standard
ENST00000419580.6	Ensembl	ENSP00000406651.2	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

peptidyl-tyrosine phosphorylation
regulation of cell migration

Molecular Function

protein binding
SH3 domain binding
identical protein binding

Cellular Component

cytoplasm
membrane
lamellipodium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000225941
Coding exons: 8
Length: 12999
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125747
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.396	204	221	0.925	0.0000133	2276
Missense (PolyPhen)		36	52.893	0.68062		575
Synonymous	1.16	84	98.6	0.852	0.00000617	809
Loss of Function	1.45	9	15.1	0.596	7.70e-7	173

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000099	0.000088	rare
South Asian	0.00023	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May inhibit tumor metastasis (By similarity). In vitro, reduces cell motility. {ECO:0000250, ECO:0000269|PubMed:11956071}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

RVIS EVS: -0.03
RVIS percentile EVS: 51.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.799

Gene Damage Prediction

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