rs587776509

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5

The NM_001159773.2(CANT1):​c.734delC​(p.Pro245ArgfsTer4) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 33)

Consequence

CANT1
NM_001159773.2 frameshift

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 9.34
Variant links:
Genes affected
CANT1 (HGNC:19721): (calcium activated nucleotidase 1) 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]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 5 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-78995118-CG-C is Pathogenic according to our data. Variant chr17-78995118-CG-C is described in ClinVar as [Pathogenic]. Clinvar id is 278.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CANT1NM_001159773.2 linkc.734delC p.Pro245ArgfsTer4 frameshift_variant Exon 4 of 5 ENST00000392446.10 NP_001153245.1 Q8WVQ1-1A0A024R8U8
CANT1NM_001159772.2 linkc.734delC p.Pro245ArgfsTer4 frameshift_variant Exon 5 of 6 NP_001153244.1 Q8WVQ1-1A0A024R8U8
CANT1NM_138793.4 linkc.734delC p.Pro245ArgfsTer4 frameshift_variant Exon 3 of 4 NP_620148.1 Q8WVQ1-1A0A024R8U8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CANT1ENST00000392446.10 linkc.734delC p.Pro245ArgfsTer4 frameshift_variant Exon 4 of 5 1 NM_001159773.2 ENSP00000376241.4 Q8WVQ1-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Desbuquois dysplasia 1 Pathogenic:1
Nov 01, 2009
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs587776509; hg19: chr17-76991200; API