ANTXR2
Basic information
Region (hg38): 4:79901146-80125454
Links
Phenotypes
GenCC
Source:
- 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:
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
- Hyaline fibromatosis syndrome (8 variants)
- not provided (3 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 | 9 | |||||
missense | 44 | 55 | ||||
nonsense | 3 | |||||
start loss | 1 | |||||
frameshift | 11 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
splice region | 4 | 4 | 2 | 10 | ||
non coding | 87 | 25 | 45 | 157 | ||
Total | 9 | 14 | 134 | 33 | 51 |
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:
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:
- 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