ANKH

ANKH inorganic pyrophosphate transport regulator, the group of MicroRNA protein coding host genes|Solute carrier family 62

Basic information

Region (hg38): 5:14704800-14871778

Previous symbols: [ "CCAL2", "CMDJ" ]

Links

ENSG00000154122NCBI:56172OMIM:605145HGNC:15492Uniprot:Q9HCJ1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Craniometaphyseal dysplasia, autosomal dominant; Chondrocalcinosis 2ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal8528213; 9915952; 11326272; 11326338; 12297987; 12297989; 20301634; 20358596; 22150416; 22647861

ClinVar

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

  • 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
4
clinvar
54
clinvar
7
clinvar
65
missense
1
clinvar
72
clinvar
3
clinvar
76
nonsense
1
clinvar
1
start loss
0
frameshift
2
clinvar
2
inframe indel
1
clinvar
1
clinvar
2
clinvar
4
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
2
splice region
1
9
1
1
12
non coding
102
clinvar
68
clinvar
99
clinvar
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)351387
5-14704829-C-T Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Uncertain significance (Jan 13, 2018)906739
5-14704962-C-T Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Uncertain significance (Jan 13, 2018)906740
5-14704971-C-T Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Benign (Jan 12, 2018)906741
5-14704992-C-T Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Uncertain significance (Jan 13, 2018)351388
5-14705034-T-C Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Benign (Jan 13, 2018)351389
5-14705068-C-T Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 Uncertain significance (Jan 13, 2018)351390
5-14705156-A-G Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Uncertain significance (Jan 12, 2018)351391
5-14705163-T-G Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Uncertain significance (Jan 13, 2018)351392
5-14705185-A-G Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Conflicting classifications of pathogenicity (Sep 01, 2022)351393
5-14705191-T-A Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 Uncertain significance (Jan 12, 2018)904414
5-14705217-G-T Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 Uncertain significance (Jan 12, 2018)904415
5-14705267-G-A Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Uncertain significance (Jan 12, 2018)905213
5-14705284-TA-T Chondrocalcinosis • Craniometadiaphyseal dysplasia wormian bone type Uncertain significance (Jun 14, 2016)351395
5-14705284-T-TA Craniometadiaphyseal dysplasia wormian bone type • Chondrocalcinosis Uncertain significance (Jun 14, 2016)351394
5-14705285-A-T Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Uncertain significance (Jan 13, 2018)351396
5-14705291-A-G Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 Uncertain significance (Jan 13, 2018)905214
5-14705297-A-G Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 Uncertain significance (Jan 13, 2018)905215
5-14705298-T-C Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 Uncertain significance (Jan 12, 2018)906804
5-14705299-C-T Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 Uncertain significance (Jan 13, 2018)351397
5-14705302-G-C Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 Uncertain significance (Jan 12, 2018)351398
5-14705302-G-T Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Benign (Jan 13, 2018)351399
5-14705310-C-G Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Uncertain significance (Jan 13, 2018)907799
5-14705429-A-G Chondrocalcinosis 2 • Craniometaphyseal dysplasia, autosomal dominant Benign (Jan 13, 2018)351400
5-14705438-C-G Craniometaphyseal dysplasia, autosomal dominant • Chondrocalcinosis 2 Benign (Jan 13, 2018)907800

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ANKHprotein_codingprotein_codingENST00000284268 12166978
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.2790.7211257320161257480.0000636
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.351842980.6170.00001883220
Missense in Polyphen38124.850.304351349
Synonymous-1.211411241.140.00000902995
Loss of Function3.24521.10.2379.11e-7263

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002460.000239
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004760.0000462
European (Non-Finnish)0.00007040.0000703
Middle Eastern0.000.00
South Asian0.00003280.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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