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 (Strong), mode of inheritance: AR
• Ehlers-Danlos syndrome, classic-like, 2 (Strong), mode of inheritance: AR
• 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 (Supportive), 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 (16 variants)
• Ehlers-Danlos syndrome, classic-like, 2 (5 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.

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	133	5	139
missense	1		160	10	7	178
nonsense	8	2				10
start loss		1				1
frameshift	10	1	3			14
inframe indel			14			14
splice donor/acceptor (+/-2bp)	2	6				8
splice region			4	20	1	25
non coding			4	83	25	112
Total	21	10	182	226	37

Highest pathogenic variant AF is 0.0000198

Variants in AEBP1

This is a list of pathogenic ClinVar variants found in the AEBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-44104602-C-G			Benign (Jul 09, 2018)
7-44104662-G-T		AEBP1-related disorder	Likely benign (Jul 31, 2024)
7-44104667-T-A			Likely pathogenic (Nov 01, 2020)
7-44104680-C-T			Likely benign (Apr 06, 2023)
7-44104685-C-A			Benign/Likely benign (Jan 31, 2024)
7-44104686-G-A		AEBP1-related disorder	Benign/Likely benign (Jan 29, 2024)
7-44104692-G-A			Likely benign (Mar 01, 2023)
7-44104695-C-T			Likely benign (May 22, 2023)
7-44104702-C-T			Uncertain significance (Sep 24, 2021)
7-44104704-C-T			Likely benign (Jul 31, 2022)
7-44104708-G-A			Uncertain significance (Apr 09, 2022)
7-44104713-G-A			Likely benign (Jun 04, 2023)
7-44104719-C-T			Likely benign (May 03, 2023)
7-44104737-C-T			Likely benign (Feb 10, 2023)
7-44104744-A-T			Uncertain significance (Aug 16, 2022)
7-44104752-G-C			Likely benign (Nov 11, 2022)
7-44104764-G-A			Likely benign (May 23, 2023)
7-44104800-A-G			Likely benign (May 04, 2022)
7-44104808-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 30, 2023)
7-44104810-C-T			Uncertain significance (Aug 05, 2021)
7-44104859-G-A		Ehlers-Danlos syndrome, classic-like, 2	Uncertain significance (Apr 20, 2021)
7-44104862-T-G			Uncertain significance (Jun 26, 2022)
7-44104866-A-G			Likely benign (Nov 27, 2023)
7-44104877-CG-C			Pathogenic (Nov 12, 2023)
7-44104878-G-T			Likely benign (Jan 16, 2024)

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
7.35e-11	1.00	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

Haploinsufficiency Scores

• pHI: 0.888
• hipred: N
• hipred_score: 0.482
• ghis: 0.537

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

Mouse Genome Informatics

• Gene name: Aebp1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); digestive/alimentary phenotype; limbs/digits/tail phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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: 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