ANKH
Basic information
Region (hg38): 5:14704800-14871778
Previous symbols: [ "CCAL2", "CMDJ" ]
Links
Phenotypes
GenCC
Source:
- craniometaphyseal dysplasia, autosomal dominant (Definitive), mode of inheritance: AD
- chondrocalcinosis 2 (Definitive), mode of inheritance: AD
- chondrocalcinosis 2 (Strong), mode of inheritance: AD
- craniometaphyseal dysplasia, autosomal dominant (Strong), mode of inheritance: AD
- chondrocalcinosis 2 (Supportive), mode of inheritance: AD
- craniometaphyseal dysplasia (Supportive), mode of inheritance: AD
- chondrocalcinosis 2 (Strong), mode of inheritance: AD
- craniometaphyseal dysplasia, autosomal dominant (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Craniometaphyseal dysplasia, autosomal dominant; Chondrocalcinosis 2 | AD | 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; Musculoskeletal | 8528213; 9915952; 11326272; 11326338; 12297987; 12297989; 20301634; 20358596; 22150416; 22647861 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (1 variants)
- Chondrocalcinosis 2 (1 variants)
- Craniometaphyseal dysplasia, autosomal dominant (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKH 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 | 54 | 65 | ||||
missense | 72 | 76 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 4 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 1 | 9 | 1 | 1 | 12 | |
non coding | 102 | 68 | 99 | 269 | ||
Total | 1 | 3 | 184 | 125 | 106 |
Variants in ANKH
This is a list of pathogenic ClinVar variants found in the ANKH region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
5-14704811-C-G | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Benign (Jan 12, 2018) | ||
5-14704829-C-T | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Uncertain significance (Jan 13, 2018) | ||
5-14704962-C-T | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Uncertain significance (Jan 13, 2018) | ||
5-14704971-C-T | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Benign (Jan 12, 2018) | ||
5-14704992-C-T | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Uncertain significance (Jan 13, 2018) | ||
5-14705034-T-C | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Benign (Jan 13, 2018) | ||
5-14705068-C-T | Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 | Uncertain significance (Jan 13, 2018) | ||
5-14705156-A-G | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Uncertain significance (Jan 12, 2018) | ||
5-14705163-T-G | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Uncertain significance (Jan 13, 2018) | ||
5-14705185-A-G | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Conflicting classifications of pathogenicity (Sep 01, 2022) | ||
5-14705191-T-A | Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 | Uncertain significance (Jan 12, 2018) | ||
5-14705217-G-T | Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 | Uncertain significance (Jan 12, 2018) | ||
5-14705267-G-A | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Uncertain significance (Jan 12, 2018) | ||
5-14705284-TA-T | Chondrocalcinosis • Craniometadiaphyseal dysplasia wormian bone type | Uncertain significance (Jun 14, 2016) | ||
5-14705284-T-TA | Craniometadiaphyseal dysplasia wormian bone type • Chondrocalcinosis | Uncertain significance (Jun 14, 2016) | ||
5-14705285-A-T | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Uncertain significance (Jan 13, 2018) | ||
5-14705291-A-G | Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 | Uncertain significance (Jan 13, 2018) | ||
5-14705297-A-G | Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 | Uncertain significance (Jan 13, 2018) | ||
5-14705298-T-C | Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 | Uncertain significance (Jan 12, 2018) | ||
5-14705299-C-T | Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 | Uncertain significance (Jan 13, 2018) | ||
5-14705302-G-C | Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 | Uncertain significance (Jan 12, 2018) | ||
5-14705302-G-T | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Benign (Jan 13, 2018) | ||
5-14705310-C-G | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Uncertain significance (Jan 13, 2018) | ||
5-14705429-A-G | Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant | Benign (Jan 13, 2018) | ||
5-14705438-C-G | Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 | Benign (Jan 13, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ANKH | protein_coding | protein_coding | ENST00000284268 | 12 | 166978 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.279 | 0.721 | 125732 | 0 | 16 | 125748 | 0.0000636 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.35 | 184 | 298 | 0.617 | 0.0000188 | 3220 |
Missense in Polyphen | 38 | 124.85 | 0.30435 | 1349 | ||
Synonymous | -1.21 | 141 | 124 | 1.14 | 0.00000902 | 995 |
Loss of Function | 3.24 | 5 | 21.1 | 0.237 | 9.11e-7 | 263 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000246 | 0.000239 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000476 | 0.0000462 |
European (Non-Finnish) | 0.0000704 | 0.0000703 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000328 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulates intra- and extracellular levels of inorganic pyrophosphate (PPi), probably functioning as PPi transporter.;
- Disease
- DISEASE: Craniometaphyseal dysplasia, autosomal dominant (CMDD) [MIM:123000]: An osteochondrodysplasia characterized by hyperostosis and sclerosis of the craniofacial bones associated with abnormal modeling of the metaphyses. Sclerosis of the skull may lead to asymmetry of the mandible, as well as to cranial nerve compression, that may finally result in hearing loss and facial palsy. {ECO:0000269|PubMed:11326272, ECO:0000269|PubMed:11326338}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- regulators of bone mineralization;Transport of small molecules;Miscellaneous transport and binding events
(Consensus)
Intolerance Scores
- loftool
- 0.115
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 28.01
Haploinsufficiency Scores
- pHI
- 0.122
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.534
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.405
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ank
- Phenotype
- growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; craniofacial 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); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; skeleton phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype;
Gene ontology
- Biological process
- skeletal system development;locomotory behavior;regulation of bone mineralization;inorganic diphosphate transport;phosphate ion transmembrane transport;transmembrane transport
- Cellular component
- plasma membrane;integral component of plasma membrane;integral component of membrane;outer membrane
- Molecular function
- inorganic phosphate transmembrane transporter activity;phosphate ion transmembrane transporter activity;inorganic diphosphate transmembrane transporter activity