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NM_001159773.2(CANT1):c.836G>A (p.Gly279Asp) AND Desbuquois dysplasia 1

Germline classification:
Likely pathogenic (1 submission)
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:
RCV003991994.1

Allele description [Variation Report for NM_001159773.2(CANT1):c.836G>A (p.Gly279Asp)]

NM_001159773.2(CANT1):c.836G>A (p.Gly279Asp)

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.836G>A (p.Gly279Asp)
HGVS:
  • NC_000017.11:g.78993920C>T
  • NG_016645.1:g.20898G>A
  • NM_001159772.2:c.836G>A
  • NM_001159773.2:c.836G>AMANE SELECT
  • NM_138793.4:c.836G>A
  • NP_001153244.1:p.Gly279Asp
  • NP_001153245.1:p.Gly279Asp
  • NP_620148.1:p.Gly279Asp
  • NC_000017.10:g.76990002C>T
Protein change:
G279D
Links:
dbSNP: rs1233347902
NCBI 1000 Genomes Browser:
rs1233347902
Molecular consequence:
  • NM_001159772.2:c.836G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001159773.2:c.836G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_138793.4:c.836G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Desbuquois dysplasia 1 (DBQD1)
Synonyms:
MICROMELIC DWARFISM WITH VERTEBRAL AND METAPHYSEAL ABNORMALITIES AND ADVANCED CARPOTARSAL OSSIFICATION; DESBUQUOIS DYSPLASIA 1, KIM VARIANT
Identifiers:
MONDO: MONDO:0009629; MedGen: C4012146; Orphanet: 1425; OMIM: 251450

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004809180Lifecell International Pvt. Ltd
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Asiangermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Lifecell International Pvt. Ltd, SCV004809180.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Asian1not providednot providedclinical testing PubMed (1)

Description

The missense variant NM_138793.4(CANT1):c.836G>A (p.Gly279Asp) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. Although the variant is present at 0.0000% in gnomAD All, it has the flag "AC0" and may not represent the true population frequency. The p.Gly279Asp variant is novel (not in any individuals) in 1kG All. There is a moderate physicochemical difference between glycine and aspartic acid. The gene CANT1 contains 8 pathogenic missense variants, indicating that missense variants are a common mechanism of disease in this gene. The p.Gly279Asp missense variant is predicted to be damaging by both SIFT and PolyPhen2. The glycine residue at codon 279 of CANT1 is conserved in all mammalian species. The nucleotide c.836 in CANT1 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. Since the allele depth is less for the sample, sanger sequencing was performed to confirm the variant identifed in CVS sample. Sanger sequencing confirmed the variant in homozygous state in Fetal sample and parents were also found to be carriers for the reported variant. Based on the above evidence this variant has been classified aslikely pathogenic according to the ACMG guidelines.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Apr 15, 2024