AGGF1

angiogenic factor with G-patch and FHA domains 1, the group of G-patch domain containing

Basic information

Region (hg38): 5:77029250-77065234

Links

ENSG00000164252 ∙ NCBI:55109 ∙ OMIM:608464 ∙ HGNC:24684 ∙ Uniprot:Q8N302 ∙ 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 AGGF1 gene.

• Inborn genetic diseases (23 variants)
• not provided (9 variants)
• not specified (1 variants)
• Non-syndromic syndactyly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGGF1 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			22	4	2	28
nonsense						0
start loss						0
frameshift						0
inframe indel		1				1
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	1	22	5	2

Highest pathogenic variant AF is 0.00000656

Variants in AGGF1

This is a list of pathogenic ClinVar variants found in the AGGF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-77030872-C-CTGCGGAGCTGCAAGCGGCAGG		Non-syndromic syndactyly	Likely pathogenic (Oct 20, 2022)
5-77034463-A-G		not specified	Uncertain significance (Sep 07, 2022)
5-77034526-T-C			Benign (Dec 31, 2019)
5-77035556-C-T		not specified	Uncertain significance (Feb 27, 2023)
5-77035562-A-G			Likely benign (Apr 26, 2018)
5-77035570-G-A		not specified	Uncertain significance (Dec 11, 2023)
5-77035594-G-A			Benign (Mar 30, 2018)
5-77035624-G-A		not specified	Benign/Likely benign (Dec 06, 2018)
5-77035645-A-G		not specified	Likely benign (Feb 27, 2023)
5-77035709-A-G		not specified	Likely benign (Oct 28, 2023)
5-77035736-A-G		not specified	Uncertain significance (May 23, 2023)
5-77036593-T-C		not specified	Uncertain significance (Jun 29, 2023)
5-77039594-C-T		not specified	Uncertain significance (Sep 22, 2023)
5-77039662-T-A		not specified	Uncertain significance (Sep 22, 2023)
5-77039697-C-T		not specified	Uncertain significance (Mar 24, 2023)
5-77046354-A-G		not specified	Uncertain significance (Oct 12, 2022)
5-77046377-A-G		not specified	Uncertain significance (Feb 06, 2024)
5-77046461-A-G		not specified	Uncertain significance (Oct 12, 2022)
5-77046524-A-G		not specified	Uncertain significance (Mar 29, 2022)
5-77046622-T-C			Benign/Likely benign (Apr 01, 2022)
5-77046632-A-G		not specified	Uncertain significance (Sep 14, 2022)
5-77048161-A-G		not specified	Uncertain significance (Sep 27, 2021)
5-77048268-G-C		not specified	Uncertain significance (Sep 14, 2023)
5-77052729-C-G		not specified	Uncertain significance (Jan 18, 2023)
5-77053967-G-A			Likely benign (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGGF1	protein_coding	protein_coding	ENST00000312916	14	35984

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000273	1.00	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.166	367	376	0.976	0.0000190	4713
Missense in Polyphen		87	117.41	0.74102		1486
Synonymous	-0.592	145	136	1.06	0.00000695	1297
Loss of Function	3.62	15	39.6	0.379	0.00000221	478

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000306	0.000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000310	0.000308
Middle Eastern	0.000217	0.000217
South Asian	0.000556	0.000555
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes angiogenesis and the proliferation of endothelial cells. Able to bind to endothelial cells and promote cell proliferation, suggesting that it may act in an autocrine fashion. {ECO:0000269|PubMed:14961121}.
• Pathway: Disease;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.0950

Intolerance Scores

• loftool: 0.447
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.06

Haploinsufficiency Scores

• pHI: 0.496
• hipred: Y
• hipred_score: 0.652
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.827

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aggf1
• Phenotype: cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); neoplasm; 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype

Zebrafish Information Network

• Gene name: aggf1
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: angiogenesis;vasculogenesis;positive regulation of endothelial cell proliferation;cell adhesion;positive regulation of angiogenesis
• Cellular component: extracellular region;cytoplasm;perinuclear region of cytoplasm
• Molecular function: nucleic acid binding;protein binding