NM_001159773.2(CANT1):c.902_906dup (p.Ser303fs) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Dec 26, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000726652.11

Allele description [Variation Report for NM_001159773.2(CANT1):c.902_906dup (p.Ser303fs)]

NM_001159773.2(CANT1):c.902_906dup (p.Ser303fs)

Gene:

CANT1:calcium activated nucleotidase 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_001159773.2(CANT1):c.902_906dup (p.Ser303fs)

HGVS:

NC_000017.10:g.76989931_76989932insGGCGC
NC_000017.11:g.78993853GCGGC[3]
NG_016645.1:g.20959GCGCC[3]
NM_001159772.2:c.902_906dup
NM_001159773.2:c.902_906dupMANE SELECT
NM_138793.3:c.902_906dup5
NM_138793.4:c.902_906dup
NP_001153244.1:p.Ser303fs
NP_001153245.1:p.Ser303fs
NP_620148.1:p.Ser303fs
NC_000017.10:g.76989931_76989932insGGCGC
NC_000017.10:g.76989932_76989936dup
NC_000017.10:g.76989935GCGGC[3]
NM_001159772.1:c.893_894insGCCGC
NM_001159772.1:c.902_906dup
NM_001159773.2:c.902_906dup
NM_001159773.2:c.906_907insGCGCCMANE SELECT
NM_138793.3:c.902_906dup
NM_138793.3:c.902_906dup5
NM_138793.3:c.902_906dupGCGCC

Protein change:

S303fs

Links:

OMIM: 613165.0008; dbSNP: rs587776895

NCBI 1000 Genomes Browser:

rs587776895

Molecular consequence:

NM_001159772.2:c.902_906dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001159773.2:c.902_906dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_138793.4:c.902_906dup - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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MULTISPECIES: YmjA family protein [Bacteria]
MULTISPECIES: YmjA family protein [Bacteria]
gi|490284235|ref|WP_004180069.1|

Protein
Fistularia commersonii voucher EIL060506 D-loop, partial sequence; mitochondrial
Fistularia commersonii voucher EIL060506 D-loop, partial sequence; mitochondrial
gi|756766354|gb|KP053057.1|

Nucleotide
phosphatidylinositol 4-kinase beta isoform X1 [Homo sapiens]
phosphatidylinositol 4-kinase beta isoform X1 [Homo sapiens]
gi|767909543|ref|XP_011507936.1|

Protein
U5 small nuclear ribonucleoprotein TSSC4 isoform X1 [Danio rerio]
U5 small nuclear ribonucleoprotein TSSC4 isoform X1 [Danio rerio]
gi|528485143|ref|XP_005168945.1|

Protein
RecName: Full=Conotoxin LeD51; Flags: Precursor
RecName: Full=Conotoxin LeD51; Flags: Precursor
gi|122011887|sp|Q3YEF7.1|O2651_CONL

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000701968	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Pathogenic (May 21, 2018)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19853239, 20425819, 28229453 Citation Link,
SCV001790795	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jun 13, 2023)	germline	clinical testing	Citation Link,
SCV001832321	Blueprint Genetics	criteria provided, single submitter (Blueprint Genetics Variant Classification Scheme)	Pathogenic (Nov 30, 2019)	germline	clinical testing	Citation Link,
SCV004297572	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 26, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 19853239, 28229453, 29620724, 28492532

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	8	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutation of CANT1 causes Desbuquois dysplasia.

Faden M, Al-Zahrani F, Arafah D, Alkuraya FS.

Am J Med Genet A. 2010 May;152A(5):1157-60. doi: 10.1002/ajmg.a.33404.

PubMed [citation]

PMID:: 20425819

Identification of CANT1 mutations in Desbuquois dysplasia.

Huber C, Oulès B, Bertoli M, Chami M, Fradin M, Alanay Y, Al-Gazali LI, Ausems MG, Bitoun P, Cavalcanti DP, Krebs A, Le Merrer M, Mortier G, Shafeghati Y, Superti-Furga A, Robertson SP, Le Goff C, Muda AO, Paterlini-Bréchot P, Munnich A, Cormier-Daire V.

Am J Hum Genet. 2009 Nov;85(5):706-10. doi: 10.1016/j.ajhg.2009.10.001. Epub 2009 Oct 22.

PubMed [citation]

PMID:: 19853239
PMCID:: PMC2775828

See all PubMed Citations (5)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000701968.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	8	not provided	not provided	clinical testing	PubMed (3)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		8	not provided	not provided	not provided

From GeneDx, SCV001790795.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Frameshift variant predicted to result in protein truncation, as the last 99 amino acids are replaced with 20 different amino acids, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 34853893, 34645488, 19853239, 31585110, 28229453, 20425819, 31130284, 32860008, 29620724, 34406647, 36331722)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Blueprint Genetics, SCV001832321.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004297572.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Ser303Alafs*21) in the CANT1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 99 amino acid(s) of the CANT1 protein. This variant is present in population databases (no rsID available, gnomAD 0.003%). This premature translational stop signal has been observed in individuals with Desbuquois dysplasia (PMID: 19853239, 28229453, 29620724). ClinVar contains an entry for this variant (Variation ID: 31013). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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