ANTXR1

ANTXR cell adhesion molecule 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 2:69013175-69249327

Links

ENSG00000169604 ∙ NCBI:84168 ∙ OMIM:606410 ∙ HGNC:21014 ∙ Uniprot:Q9H6X2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• GAPO syndrome (Definitive), mode of inheritance: AR
• GAPO syndrome (Strong), mode of inheritance: AR
• capillary infantile hemangioma (Limited), mode of inheritance: AD
• GAPO syndrome (Supportive), mode of inheritance: AR
• GAPO syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hemangioma, capillary infantile, susceptibility to; Growth retardation, alopecia, pseudoanodontia, and optic atrophy (GAPO syndrome)	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dental; Dermatologic; Musculoskeletal; Ophthalmologic	9180938; 9298746; 18931684; 19367160; 23602711

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANTXR1 gene.

• not provided (92 variants)
• Inborn genetic diseases (28 variants)
• GAPO syndrome (26 variants)
• Capillary infantile hemangioma (2 variants)
• not specified (1 variants)
• ANTXR1-related condition (1 variants)
• Bladder exstrophy-epispadias-cloacal extrophy complex (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANTXR1 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				10	6	16
missense		2	37	2	2	43
nonsense		1				1
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region		1	2		1	4
non coding			1	3	55	59
Total	0	6	38	15	63

Variants in ANTXR1

This is a list of pathogenic ClinVar variants found in the ANTXR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-69013206-G-A			Benign (May 20, 2021)
2-69013211-G-T			Benign (May 20, 2021)
2-69013458-G-A			Benign (May 20, 2021)
2-69013517-G-A			Benign/Likely benign (Jan 20, 2024)
2-69013519-G-A		ANTXR1-related disorder	Benign (Jan 02, 2024)
2-69013554-G-A		Inborn genetic diseases	Uncertain significance (May 17, 2023)
2-69013576-C-T		Inborn genetic diseases	Uncertain significance (Aug 17, 2023)
2-69013579-G-T		GAPO syndrome	Uncertain significance (Dec 13, 2018)
2-69013599-G-A		Inborn genetic diseases	Uncertain significance (Apr 13, 2022)
2-69013600-A-T		Inborn genetic diseases	Uncertain significance (Apr 13, 2022)
2-69013632-C-G		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
2-69013668-G-T			Likely benign (Nov 25, 2022)
2-69013669-T-TC			Benign (Jan 15, 2024)
2-69013740-G-C		GAPO syndrome	Benign (Dec 05, 2021)
2-69039896-A-T			Benign (May 10, 2021)
2-69040002-G-A		GAPO syndrome	Benign (Dec 05, 2021)
2-69040036-T-C			Likely benign (Dec 31, 2022)
2-69040135-T-G			Likely benign (Feb 01, 2023)
2-69040172-T-C			Benign (May 20, 2021)
2-69040196-A-G		GAPO syndrome	Benign (Dec 05, 2021)
2-69044779-C-T		GAPO syndrome	Pathogenic (May 02, 2013)
2-69044780-G-A		Inborn genetic diseases	Uncertain significance (Feb 17, 2024)
2-69044961-G-A			Benign (May 11, 2021)
2-69044974-G-A			Benign (May 10, 2021)
2-69044984-C-T			Benign (May 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANTXR1	protein_coding	protein_coding	ENST00000303714	18	236150

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.986	0.0137	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	240	316	0.759	0.0000187	3638
Missense in Polyphen		78	132.44	0.58893		1543
Synonymous	-1.74	142	118	1.20	0.00000745	1103
Loss of Function	4.70	5	35.0	0.143	0.00000186	406

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in cell attachment and migration. Interacts with extracellular matrix proteins and with the actin cytoskeleton. Mediates adhesion of cells to type 1 collagen and gelatin, reorganization of the actin cytoskeleton and promotes cell spreading. Plays a role in the angiogenic response of cultured umbilical vein endothelial cells. {ECO:0000269|PubMed:15777794, ECO:0000269|PubMed:16762926}.
• Disease: DISEASE: Hemangioma, capillary infantile (HCI) [MIM:602089]: A condition characterized by dull red, firm, dome-shaped hemangiomas, sharply demarcated from surrounding skin, usually presenting at birth or occurring within the first two or three months of life. They result from highly proliferative, localized growth of capillary endothelium and generally undergo regression and involution without scarring. {ECO:0000269|PubMed:18931684}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: GAPO syndrome (GAPO) [MIM:230740]: A disease characterized by growth retardation, alopecia, failure of tooth eruption, and progressive optic atrophy in some patients. {ECO:0000269|PubMed:23602711}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Disease;Uptake and actions of bacterial toxins;Uptake and function of anthrax toxins;Infectious disease;EGFR1;Cellular roles of Anthrax toxin (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.156
• rvis_EVS: -0.91
• rvis_percentile_EVS: 10.03

Haploinsufficiency Scores

• pHI: 0.520
• hipred: Y
• hipred_score: 0.851
• ghis: 0.661

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.545

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Antxr1
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; craniofacial phenotype; neoplasm; reproductive system 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); skeleton phenotype

Gene ontology

• Biological process: blood vessel development;reproductive process;actin cytoskeleton reorganization;substrate adhesion-dependent cell spreading;negative regulation of extracellular matrix assembly;toxin transport;positive regulation of metallopeptidase activity
• Cellular component: plasma membrane;external side of plasma membrane;cell surface;endosome membrane;integral component of membrane;lamellipodium membrane;filopodium membrane
• Molecular function: transmembrane signaling receptor activity;protein binding;collagen binding;metal ion binding;actin filament binding