NM_001159773.2(CANT1):c.675C>G (p.Tyr225Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 31, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001953459.4

Allele description [Variation Report for NM_001159773.2(CANT1):c.675C>G (p.Tyr225Ter)]

NM_001159773.2(CANT1):c.675C>G (p.Tyr225Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

17q25.3

Genomic location:

Preferred name:

NM_001159773.2(CANT1):c.675C>G (p.Tyr225Ter)

HGVS:

NC_000017.11:g.78995178G>C
NG_016645.1:g.19640C>G
NM_001159772.2:c.675C>G
NM_001159773.2:c.675C>GMANE SELECT
NM_138793.4:c.675C>G
NP_001153244.1:p.Tyr225Ter
NP_001153245.1:p.Tyr225Ter
NP_620148.1:p.Tyr225Ter
NC_000017.10:g.76991260G>C

Protein change:

Y225*

Links:

dbSNP: rs780527463

NCBI 1000 Genomes Browser:

rs780527463

Molecular consequence:

NM_001159772.2:c.675C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_001159773.2:c.675C>G - nonsense - [Sequence Ontology: SO:0001587]
NM_138793.4:c.675C>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: zinc finger and BTB domain-containing protein 6 [Bison bison bison]
PREDICTED: zinc finger and BTB domain-containing protein 6 [Bison bison bison]
gi|742140282|ref|XP_010842324.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002242766	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 31, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 19853239, 21037275, 22539336, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002242766

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 31, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

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

CANT1 mutation is also responsible for Desbuquois dysplasia, type 2 and Kim variant.

Furuichi T, Dai J, Cho TJ, Sakazume S, Ikema M, Matsui Y, Baynam G, Nagai T, Miyake N, Matsumoto N, Ohashi H, Unger S, Superti-Furga A, Kim OH, Nishimura G, Ikegawa S.

J Med Genet. 2011 Jan;48(1):32-7. doi: 10.1136/jmg.2010.080226. Epub 2010 Oct 30.

PubMed [citation]

PMID:: 21037275

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV002242766.4

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1456837). This variant has not been reported in the literature in individuals affected with CANT1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Tyr225*) in the CANT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CANT1 are known to be pathogenic (PMID: 19853239, 21037275, 22539336).

#	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: Feb 28, 2024

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