AEBP1

AE binding protein 1, the group of MicroRNA protein coding host genes|M14 carboxypeptidases

Basic information

Region (hg38): 7:44104345-44114562

Links

ENSG00000106624 ∙ NCBI:165 ∙ OMIM:602981 ∙ HGNC:303 ∙ Uniprot:Q8IUX7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Ehlers-Danlos syndrome, classic-like, 2 (Moderate), mode of inheritance: AR
• Ehlers-Danlos syndrome, classic-like, 2 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, classic-like, 2 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, classic-like, 2 (Supportive), mode of inheritance: AR
• Ehlers-Danlos syndrome, classic-like, 2 (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ehlers-Danlos syndrome, classic-like, 2	AR	Cardiovascular; Gastrointestinal	The condition can include manifestations such as bowel rupture and cardiovascular complications including aortic root dilatation, and awareness may allow surveillance, preventative measures, and early management	Cardiovascular; Gastrointestinal; Genitourinary; Musculoskeletal	27023906; 29606302

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AEBP1 gene.

• not_provided (663 variants)
• not_specified (138 variants)
• AEBP1-related_disorder (36 variants)
• Ehlers-Danlos_syndrome,_classic-like,_2 (27 variants)
• Inborn_genetic_diseases (6 variants)
• High_myopia (1 variants)
• Autism_spectrum_disorder (1 variants)
• Ehlers-Danlos_syndrome,_classic_type,_2 (1 variants)
• Ehlers-Danlos_syndrome,_classic_type,_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AEBP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001129.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	223	4	228
missense		1	253	13	4	271
nonsense	7	5	1			13
start loss		1				1
frameshift	20	4	5			29
splice donor/acceptor (+/-2bp)	2	8	3			13
Total	29	19	263	236	8

Highest pathogenic variant AF is 0.000012440596

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AEBP1	protein_coding	protein_coding	ENST00000223357	21	10202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124409	5	1332	125746	0.00533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	654	730	0.896	0.0000467	7495
Missense in Polyphen		222	268.07	0.82815		2638
Synonymous	1.23	279	306	0.911	0.0000212	2287
Loss of Function	3.79	27	58.2	0.464	0.00000329	624

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00487	0.00477
Ashkenazi Jewish	0.00494	0.00477
East Asian	0.000440	0.000435
Finnish	0.00526	0.00486
European (Non-Finnish)	0.00842	0.00769
Middle Eastern	0.000440	0.000435
South Asian	0.00458	0.00435
Other	0.00628	0.00588

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: As a positive regulator of collagen fibrillogenesis, it is probably involved in the organization and remodeling of the extracellualr matrix. {ECO:0000269|PubMed:29606302}.
• Disease: DISEASE: Ehlers-Danlos syndrome, classic-like, 2 (EDSCLL2) [MIM:618000]: A variant form of Ehlers-Danlos syndrome, a connective tissue disorder. EDSCLL2 patients show severe joint and skin laxity, osteoporosis affecting the hips and spine, osteoarthritis, soft redundant skin that can be acrogeria-like, delayed wound healing with abnormal atrophic scarring, and shoulder, hip, knee, and ankle dislocations. Additional variable features include gastrointestinal and genitourinary manifestations (bowel rupture, gut dysmotility, cryptorchidism, and hernias), vascular complications (mitral valve prolapse and aortic root dilation), and skeletal anomalies. EDSCLL2 inheritance is autosomal recessive. {ECO:0000269|PubMed:27023906, ECO:0000269|PubMed:29606302}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.140
• rvis_EVS: 0.12
• rvis_percentile_EVS: 62.21

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.108

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;skeletal system development;peptide metabolic process;muscle organ development;protein processing;regulation of collagen fibril organization
• Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;carboxypeptidase activity;metallocarboxypeptidase activity;extracellular matrix structural constituent;calmodulin binding;collagen binding;zinc ion binding