ABI3

ABI family member 3

Basic information

Region (hg38): 17:49210411-49223225

Links

ENSG00000108798 ∙ NCBI:51225 ∙ OMIM:606363 ∙ HGNC:29859 ∙ Uniprot:Q9P2A4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ABI3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABI3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	20	2	3

Variants in ABI3

This is a list of pathogenic ClinVar variants found in the ABI3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-49210771-G-A		not specified	Uncertain significance (Aug 10, 2021)
17-49210776-G-A		not specified	Uncertain significance (Sep 23, 2023)
17-49216654-G-C		not specified	Uncertain significance (May 15, 2024)
17-49216674-A-G			Benign (Dec 31, 2019)
17-49216678-C-T		not specified	Uncertain significance (Aug 01, 2022)
17-49216679-G-A		not specified	Uncertain significance (Apr 20, 2024)
17-49216688-C-T		not specified	Uncertain significance (Oct 24, 2023)
17-49216707-C-T			Benign (Dec 31, 2019)
17-49217742-G-A		not specified	Uncertain significance (Feb 23, 2023)
17-49217743-T-A		Early-onset dementia of unclear type	Uncertain significance (Oct 28, 2019)
17-49217749-T-C		not specified	Uncertain significance (Jan 23, 2024)
17-49217752-A-G		not specified	Uncertain significance (Apr 25, 2023)
17-49217773-G-T		not specified	Uncertain significance (Feb 06, 2024)
17-49217781-G-A		not specified	Uncertain significance (Feb 17, 2022)
17-49217837-G-T		not specified	Uncertain significance (Apr 18, 2023)
17-49217844-C-T		not specified	Uncertain significance (Aug 12, 2021)
17-49219599-T-C			Benign (Dec 31, 2019)
17-49219609-G-A		not specified	Uncertain significance (Sep 14, 2023)
17-49219881-C-T		not specified	Uncertain significance (Jul 31, 2023)
17-49219898-G-T		not specified	Uncertain significance (Apr 23, 2024)
17-49219931-G-C		not specified	Uncertain significance (May 14, 2024)
17-49219932-C-A		not specified	Uncertain significance (May 30, 2023)
17-49220257-C-G		not specified	Uncertain significance (Sep 17, 2021)
17-49222153-G-A		not specified	Uncertain significance (Apr 05, 2023)
17-49222207-G-T		not specified	Uncertain significance (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABI3	protein_coding	protein_coding	ENST00000225941	8	12999

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000501	0.881	125720	0	27	125747	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.396	204	221	0.925	0.0000133	2276
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000299	0.000299
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000990	0.0000879
Middle Eastern	0.0000546	0.0000544
South Asian	0.000233	0.000229
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.295
• hipred: N
• hipred_score: 0.338
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.799

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abi3

Gene ontology

• Biological process: peptidyl-tyrosine phosphorylation;regulation of cell migration
• Cellular component: cytoplasm;membrane;lamellipodium
• Molecular function: protein binding;SH3 domain binding;identical protein binding