CANT1

Chr 17AR

calcium activated nucleotidase 1

Also known as: DBQD, DBQD1, EDM7, SCAN-1, SCAN1, SHAPY

NCBI Gene: 124583ENSG00000171302UniProt: Q8WVQ1

This protein encoded by this gene belongs to the apyrase family. It functions as a calcium-dependent nucleotidase with a preference for UDP. Mutations in this gene are associated with Desbuquois dysplasia with hand anomalies. Alternatively spliced transcript variants have been noted for this gene.[provided by RefSeq, Mar 2010]

Primary Disease Associations & Inheritance

Desbuquois dysplasia 1MIM #251450
AR
Epiphyseal dysplasia, multiple, 7MIM #617719
AR
0
Active trials
66
Pathogenic / LP
485
ClinVar variants
6
Pubs (1 yr)
0.5
Missense Z
1.31
LOEUF
Clinical Summary— CANT1
🧬
Gene-Disease Validity (ClinGen)
Desbuquois dysplasia 1 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
66 Pathogenic / Likely Pathogenic· 172 VUS of 485 total submissions
📖
GeneReview available — CANT1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.31LOEUF
pLI 0.000
Z-score 0.76
OE 0.77 (0.47–1.31)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.49Z-score
OE missense 0.92 (0.82–1.02)
243 obs / 265.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.77 (0.47–1.31)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.92 (0.82–1.02)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.89
0≤1.21.6
LoF obs/exp: 10 / 13.0Missense obs/exp: 243 / 265.4Syn Z: 0.94

ClinVar Variant Classifications

485 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic45
Likely Pathogenic21
VUS172
Likely Benign193
Benign27
Conflicting27
45
Pathogenic
21
Likely Pathogenic
172
VUS
193
Likely Benign
27
Benign
27
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
14
4
27
0
45
Likely Pathogenic
6
10
5
0
21
VUS
2
108
60
2
172
Likely Benign
0
7
40
146
193
Benign
0
0
21
6
27
Conflicting
—27
Total22129153154485

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CANT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Gene2Phenotype Curations

CANT1-related Desbuquois dysplasia

definitive
ARLoss Of FunctionAbsent Gene Product
Dev. DisordersEyeSkeletal
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
First Thai Case of Lethal Desbuquois Dysplasia Type I Caused by Novel Compound Heterozygous CANT1 Mutations: Expanding the Molecular Spectrum.
Thamissarakul S et al.·Case Rep Genet
2026Open Access
Immunohistochemical expression of CANT1 and B3GNT3 in invasive ductal carcinoma of the breast: diagnostic and prognostic significance in lymph node metastasis.
Thabet DM et al.·Diagn Pathol
2026Open Access
Genetic Association of CANT1 Gene with Scoliosis: An Integrative Study Involving Methylation, Immune Factors, and Metabolites.
Zhang X et al.·J Mol Neurosci
2025
Prenatal diagnosis and management of desbuquois dysplasia type 1 due to CANT1 mutation: A case report.
Özalp M et al.·Taiwan J Obstet Gynecol
2025Case report
CANT1 Is Involved in Collagen Fibrogenesis in Tendons by Regulating the Synthesis of Dermatan/Chondroitin Sulfate Attached to the Decorin Core Protein.
Yamashita R et al.·Int J Mol Sci
2025Open Access
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients