CANT1

calcium activated nucleotidase 1

Basic information

Region (hg38): 17:78991716-79009867

Links

ENSG00000171302

∙ NCBI:124583 ∙ OMIM:613165 ∙ HGNC:19721 ∙ Uniprot:Q8WVQ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Desbuquois dysplasia 1 (Definitive), mode of inheritance: AR
Desbuquois dysplasia (Supportive), mode of inheritance: AR
Desbuquois dysplasia 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Desbuquois dysplasia 1	AR	Ophthalmologic	As the condition can include glaucoma, appropriate surveillance may allow early detection and management	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	1080993; 1959544; 7977470; 14679586; 14679587; 15211652; 19853239; 20358610; 20425819; 20358597; 21037275; 21412251; 21654728; 22539336

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CANT1 gene.

not_provided (304 variants)
Desbuquois_dysplasia_1 (73 variants)
Inborn_genetic_diseases (61 variants)
Epiphyseal_dysplasia,_multiple,_7 (16 variants)
CANT1-related_disorder (8 variants)
not_specified (6 variants)
Short_stature (1 variants)
Multiple_epiphyseal_dysplasia (1 variants)
Joint_dislocation (1 variants)
Abnormality_of_the_skeletal_system (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CANT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001159773.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	155 clinvar	3 clinvar	160
missense	4 clinvar	13 clinvar	102 clinvar	17 clinvar		136
nonsense	8 clinvar	4 clinvar				12
start loss						0
frameshift	13 clinvar	6 clinvar	2 clinvar			21
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	26	23	106	172	3

Highest pathogenic variant AF is 0.000047206

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CANT1	protein_coding	protein_coding	ENST00000302345	3	18151

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000254	0.520	125671	0	77	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.488	243	265	0.916	0.0000192	2594
Missense in Polyphen		72	87.406	0.82374		909
Synonymous	0.943	115	129	0.894	0.0000113	812
Loss of Function	0.760	10	13.0	0.772	6.33e-7	132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000833	0.000824
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000151	0.000139
European (Non-Finnish)	0.000365	0.000360
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Calcium-dependent nucleotidase with a preference for UDP. The order of activity with different substrates is UDP > GDP > UTP > GTP. Has very low activity towards ADP and even lower activity towards ATP. Does not hydrolyze AMP and GMP (PubMed:12234496, PubMed:15248776, PubMed:15006348, PubMed:16835225). Involved in proteoglycan synthesis (PubMed:22539336). {ECO:0000269|PubMed:12234496, ECO:0000269|PubMed:15006348, ECO:0000269|PubMed:15248776, ECO:0000269|PubMed:16835225, ECO:0000269|PubMed:22539336}.;
Disease: DISEASE: Desbuquois dysplasia 1 (DBQD1) [MIM:251450]: A chondrodysplasia characterized by severe prenatal and postnatal growth retardation (less than -5 SD), joint laxity, short extremities, progressive scoliosis, round face, midface hypoplasia, prominent bulging eyes. The main radiologic features are short long bones with metaphyseal splay, a 'Swedish key' appearance of the proximal femur (exaggerated trochanter), and advance carpal and tarsal bone age. Two forms of Desbuquois dysplasia are distinguished on the basis of the presence or absence of characteristic hand anomalies: an extra ossification center distal to the second metacarpal, delta phalanx, bifid distal thumb phalanx, and phalangeal dislocations. {ECO:0000269|PubMed:19853239, ECO:0000269|PubMed:20425819, ECO:0000269|PubMed:21037275, ECO:0000269|PubMed:21412251, ECO:0000269|PubMed:21654728, ECO:0000269|PubMed:22539336}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Epiphyseal dysplasia, multiple, 7 (EDM7) [MIM:617719]: A form of multiple epiphyseal dysplasia, a generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal. EDM7 inheritance is autosomal recessive. {ECO:0000269|PubMed:28742282}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Pyrimidine metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Pyrimidine Metabolism;GLUT-1 deficiency syndrome;UMP Synthase Deiciency (Orotic Aciduria);Congenital disorder of glycosylation CDG-IId;Lactose Synthesis;MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Neutrophil degranulation;UTP and CTP dephosphorylation II;Purine metabolism;Innate Immune System;Immune System;Pyrimidine metabolism;Purine nucleotides nucleosides metabolism;Pyrimidine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

pRec: 0.142

Intolerance Scores

loftool: 0.0660
rvis_EVS: 0.02
rvis_percentile_EVS: 55.69

Haploinsufficiency Scores

pHI: 0.152
hipred: N
hipred_score: 0.301
ghis: 0.509

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.108

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cant1
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); 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); vision/eye phenotype; immune system phenotype;

Gene ontology

Biological process: proteoglycan biosynthetic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;neutrophil degranulation
Cellular component: extracellular region;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane;Golgi cisterna membrane;specific granule lumen;extracellular exosome;tertiary granule lumen;ficolin-1-rich granule lumen
Molecular function: guanosine-diphosphatase activity;calcium ion binding;protein homodimerization activity;adenosine-diphosphatase activity;uridine-diphosphatase activity