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NM_001159773.2(CANT1):c.902_906dup (p.Ser303fs) AND CANT1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 6, 2023
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003904861.2

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]

Condition(s)

Name:
CANT1-related disorder
Synonyms:
CANT1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004728274PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Nov 6, 2023) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004728274.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The CANT1 c.902_906dup5 variant is predicted to result in a frameshift and premature protein termination (p.Ser303Alafs*21). This variant was reported in multiple individuals with autosomal recessive Desbuquois dysplasia (Huber. 2009. PubMed ID: 19853239; Al-Hamed. 2021. PubMed ID: 34853893; Table S6, Maddirevula. 2018. PubMed ID: 29620724; Ranza. 2017. PubMed ID: 28229453). This variant is reported in 0.0029% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/17-76989931-T-TGGCGC). Frameshift variants in CANT1 are expected to be pathogenic. This variant is interpreted as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024