AMMECR1
Basic information
Region (hg38): X:110194185-110440318
Links
Phenotypes
GenCC
Source:
- midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (Strong), mode of inheritance: XL
- midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (Moderate), mode of inheritance: XL
- Alport syndrome-intellectual disability-midface hypoplasia-elliptocytosis syndrome (Supportive), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis | XL | Hematologic | Ellipsocytosis requiring red blood cell transfusion has been described, and awareness may allow early diagnosis and management | Audiologic/Otolaryngologic; Craniofacial; Hematologic; Musculoskeletal; Renal | 27811305; 28089922 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (25 variants)
- Inborn genetic diseases (9 variants)
- Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (5 variants)
- AMMECR1-related condition (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMMECR1 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 | 8 | |||||
| missense | 17 | 19 | ||||
| nonsense | 4 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region ? | 0 | |||||
| non coding ? | 4 | |||||
| Total | 1 | 3 | 21 | 8 | 5 |
Variants in AMMECR1
This is a list of pathogenic ClinVar variants found in the AMMECR1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AMMECR1 | protein_coding | protein_coding | ENST00000262844 | 6 | 246048 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.821 | 0.178 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.08 | 90 | 124 | 0.727 | 0.00000918 | 2095 |
| Missense in Polyphen | 19 | 45.226 | 0.42011 | 736 | ||
| Synonymous | 0.273 | 47 | 49.4 | 0.951 | 0.00000353 | 710 |
| Loss of Function | 2.64 | 1 | 10.0 | 0.0995 | 6.96e-7 | 187 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Disease
- DISEASE: Midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis (MFHIEN) [MIM:300990]: An X-linked recessive disorder with onset in early childhood, characterized by midface hypoplasia, hearing impairment, elliptocytosis, and nephrocalcinosis. Variable clinical features include anemia, and mild early motor or speech delay. {ECO:0000269|PubMed:27811305, ECO:0000269|PubMed:28089922}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Alport syndrome with mental retardation, midface hypoplasia and elliptocytosis (ATS-MR) [MIM:300194]: A X-linked contiguous gene deletion syndrome characterized by glomerulonephritis, sensorineural hearing loss, mental retardation, midface hypoplasia and elliptocytosis. {ECO:0000269|PubMed:10049589}. Note=The gene represented in this entry may be involved in disease pathogenesis.;
Recessive Scores
- pRec
- 0.338
Intolerance Scores
- loftool
- 0.0853
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.896
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.652
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ammecr1
- Phenotype
Zebrafish Information Network
- Gene name
- ammecr1
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- kinked
Gene ontology
- Biological process
- biological_process
- Cellular component
- nucleus
- Molecular function
- protein binding