ANTXR2

ANTXR cell adhesion molecule 2

Basic information

Region (hg38): 4:79901145-80125454

Links

ENSG00000163297 ∙ NCBI:118429 ∙ OMIM:608041 ∙ HGNC:21732 ∙ Uniprot:P58335 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hyaline fibromatosis syndrome (Strong), mode of inheritance: AR
• juvenile hyaline fibromatosis (Supportive), mode of inheritance: AR
• infantile systemic hyalinosis (Supportive), mode of inheritance: AR
• hyaline fibromatosis syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hyaline fibromatosis syndrome	AR	Allergy/Immunology/Infectious; Dermatologic; Musculoskeletal	The condition may be clinically recognizable, but involves manifestations that require clinical care, such as fracture susceptibility, intractable diarrhea, and infection susceptibility, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious; Dental; Dermatologic; Gastrointestinal; Musculoskeletal	20896407; 20896998; 55105; 2434938; 2433666; 3544844; 487969; 11206353; 12214284; 11298373; 12973667; 14508707

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ANTXR2 gene.

• Hyaline fibromatosis syndrome (168 variants)
• not provided (72 variants)
• Inborn genetic diseases (18 variants)
• not specified (8 variants)
• ANTXR2-related condition (1 variants)
• Central core myopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANTXR2 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	3	4	8
missense	2	3	35	4	2	46
nonsense	1	1	1			3
start loss			1			1
frameshift	7	4				11
inframe indel						0
splice donor/acceptor (+/-2bp)		5				5
splice region			4	3	2	9
non coding			85	22	46	153
Total	10	13	123	29	52

Highest pathogenic variant AF is 0.000132

Variants in ANTXR2

This is a list of pathogenic ClinVar variants found in the ANTXR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-79901668-T-C		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79901827-G-C		Hyaline fibromatosis syndrome	Benign (Jan 13, 2018)
4-79901882-A-G		Hyaline fibromatosis syndrome	Benign (Jan 13, 2018)
4-79901902-T-C		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79901904-C-T		Hyaline fibromatosis syndrome	Uncertain significance (Jan 12, 2018)
4-79901905-G-A		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79902004-C-T		Hyaline fibromatosis syndrome	Likely benign (Jan 13, 2018)
4-79902016-T-C		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79902071-T-C		Hyaline fibromatosis syndrome	Uncertain significance (Mar 30, 2018)
4-79902119-A-C		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79902163-T-G		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79902206-C-A		Hyaline fibromatosis syndrome	Likely benign (Jan 13, 2018)
4-79902512-C-T		Hyaline fibromatosis syndrome	Uncertain significance (Jan 12, 2018)
4-79902573-G-A		Hyaline fibromatosis syndrome	Likely benign (Jan 12, 2018)
4-79902582-G-A		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79902717-G-A		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79902726-A-T		Hyaline fibromatosis syndrome	Uncertain significance (Jan 12, 2018)
4-79902761-A-G		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79902799-T-A		Hyaline fibromatosis syndrome	Likely benign (Jan 13, 2018)
4-79902853-T-C		Hyaline fibromatosis syndrome	Uncertain significance (Jan 13, 2018)
4-79902925-G-A		Hyaline fibromatosis syndrome	Uncertain significance (Jan 12, 2018)
4-79902967-T-C		Hyaline fibromatosis syndrome	Uncertain significance (Jan 12, 2018)
4-79903097-C-T		Hyaline fibromatosis syndrome	Uncertain significance (Mar 30, 2018)
4-79903157-G-A		Hyaline fibromatosis syndrome	Benign (Jan 13, 2018)
4-79903165-A-T		Hyaline fibromatosis syndrome	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANTXR2	protein_coding	protein_coding	ENST00000307333	16	224306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0869	0.913	124607	0	29	124636	0.000116

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	191	235	0.812	0.0000118	3083
Missense in Polyphen		64	93.821	0.68215		1254
Synonymous	0.606	75	82.0	0.915	0.00000407	946
Loss of Function	3.47	7	26.1	0.268	0.00000124	362

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000359	0.000351
Ashkenazi Jewish	0.000101	0.0000994
East Asian	0.000114	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000165	0.000159
Middle Eastern	0.000114	0.000111
South Asian	0.0000341	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for cellular interactions with laminin and the extracellular matrix. {ECO:0000269|PubMed:11683410, ECO:0000269|PubMed:12973667}.
• Disease: DISEASE: Hyaline fibromatosis syndrome (HFS) [MIM:228600]: An autosomal recessive syndrome characterized by abnormal growth of hyalinized fibrous tissue usually affecting subcutaneous regions on the scalp, ears, neck, face, hands, and feet. The lesions appear as pearly papules or fleshy nodules. Additional features include gingival hypertrophy, progressive joint contractures resulting in severe limitation of mobility, osteopenia, and osteoporosis. Disease severity is variable. Some individuals manifest symptoms in infancy and have additional visceral or systemic involvement. Hyaline deposits in multiple organs, recurrent infections and intractable diarrhea often lead to early death. Surviving children may suffer from severely reduced mobility due to joint contractures. Other patients have later onset of a milder disorder affecting only the face and digits. {ECO:0000269|PubMed:12973667, ECO:0000269|PubMed:14508707, ECO:0000269|PubMed:15725249}. 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;Cellular roles of Anthrax toxin (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.540
• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• pHI: 0.297
• hipred: N
• hipred_score: 0.465
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.669

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Antxr2
• 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); reproductive system phenotype; 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); immune system phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: antxr2a
• Affected structure: anterior neural plate
• Phenotype tag: abnormal
• Phenotype quality: increased width

Gene ontology

• Biological process: reproductive process;toxin transport
• Cellular component: extracellular region;endoplasmic reticulum membrane;plasma membrane;external side of plasma membrane;cell surface;endosome membrane;integral component of membrane
• Molecular function: transmembrane signaling receptor activity;protein binding;metal ion binding