ABI3BP

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

Basic information

Region (hg38): 3:100749156-100993515

Links

ENSG00000154175 ∙ NCBI:25890 ∙ OMIM:606279 ∙ HGNC:17265 ∙ Uniprot:Q7Z7G0 ∙ 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 ABI3BP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ABI3BP 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				1		1
missense			57	4		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	5	0

Variants in ABI3BP

This is a list of pathogenic ClinVar variants found in the ABI3BP region.

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

Position	Type	Phenotype	Significance	ClinVar
3-100751557-T-A		not specified	Uncertain significance (Mar 07, 2023)
3-100751665-T-C		not specified	Uncertain significance (May 18, 2023)
3-100752829-T-G		not specified	Uncertain significance (Dec 18, 2023)
3-100752907-C-T		not specified	Uncertain significance (Dec 12, 2023)
3-100753840-T-C		not specified	Uncertain significance (Aug 28, 2023)
3-100770860-C-A		not specified	Uncertain significance (Dec 18, 2023)
3-100770893-C-T		not specified	Uncertain significance (Jul 31, 2023)
3-100774609-G-T		not specified	Uncertain significance (Sep 07, 2022)
3-100774616-G-A		not specified	Uncertain significance (Nov 18, 2022)
3-100775295-C-A		not specified	Uncertain significance (Dec 02, 2022)
3-100778367-C-T		not specified	Uncertain significance (May 23, 2023)
3-100780143-G-A		not specified	Uncertain significance (Jun 22, 2024)
3-100780183-C-G		not specified	Uncertain significance (Jan 24, 2024)
3-100780206-A-T		not specified	Uncertain significance (Jan 26, 2022)
3-100789501-T-C		not specified	Uncertain significance (Apr 26, 2023)
3-100789507-C-A		not specified	Uncertain significance (Jun 29, 2023)
3-100789516-G-A		not specified	Uncertain significance (Aug 12, 2021)
3-100792738-A-G		not specified	Uncertain significance (Jun 24, 2022)
3-100792744-T-C		not specified	Uncertain significance (Nov 30, 2021)
3-100794965-T-G		not specified	Uncertain significance (Apr 08, 2024)
3-100794995-C-T		not specified	Uncertain significance (Dec 20, 2023)
3-100796429-T-C		not specified	Uncertain significance (Apr 28, 2022)
3-100796457-C-G		not specified	Uncertain significance (Nov 10, 2022)
3-100808163-G-T		not specified	Uncertain significance (Jan 09, 2024)
3-100808187-C-T		not specified	Likely benign (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ABI3BP	protein_coding	protein_coding	ENST00000284322	35	244360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-8	1.00	124523	1	114	124638	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.829	489	543	0.900	0.0000276	6826
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00369	0.00368
East Asian	0.000408	0.000389
Finnish	0.00	0.00
European (Non-Finnish)	0.000504	0.000451
Middle Eastern	0.000408	0.000389
South Asian	0.000365	0.000327
Other	0.000869	0.000826

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.868
• rvis_EVS: 0.45
• rvis_percentile_EVS: 78.05

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.331
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.571

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Abi3bp
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: positive regulation of cell-substrate adhesion;extracellular matrix organization
• Cellular component: extracellular region;interstitial matrix;extracellular space;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent;collagen binding;heparin binding